Updating vg
Table of Contents
Updating to vg version 1.22.0 - Rotella
I don’t know what the best way is to update software that was cloned and built from GitHub, so I’ll start with git pull to get the latest changes and go from there.
git pull
-> click here for cloning output <-
remote: Enumerating objects: 4363, done.
remote: Counting objects: 100% (4363/4363), done.
remote: Compressing objects: 100% (270/270), done.
remote: Total 6749 (delta 4215), reused 4219 (delta 4092), pack-reused 2386
Receiving objects: 100% (6749/6749), 5.45 MiB | 5.96 MiB/s, done.
Resolving deltas: 100% (5536/5536), completed with 680 local objects.
From https://github.com/vgteam/vg
1ac878e5d..9cd9ba375 master -> origin/master
* [new branch] a-bit-more-handles -> origin/a-bit-more-handles
* [new branch] cap-mapq -> origin/cap-mapq
* [new branch] ccache -> origin/ccache
* [new branch] ccache-2 -> origin/ccache-2
* [new branch] circularize-bug -> origin/circularize-bug
* [new branch] codenames -> origin/codenames
3b94f4206..86b37082a cyclic-call -> origin/cyclic-call
* [new branch] de-vg -> origin/de-vg
* [new branch] debug-splice-surject -> origin/debug-splice-surject
* [new branch] depth -> origin/depth
* [new branch] filter-default -> origin/filter-default
* [new branch] find-mark-ref-kmers -> origin/find-mark-ref-kmers
* [new branch] fix-construct -> origin/fix-construct
* [new branch] fix-homebrew -> origin/fix-homebrew
* [new branch] fix_makefile -> origin/fix_makefile
* [new branch] gam-ids -> origin/gam-ids
2c1f1ce0f..6208214c3 gbwt-hg -> origin/gbwt-hg
75f455c7d..f93626c35 gh-pages -> origin/gh-pages
+ 6d2dc8025...ce8490c95 giraffe -> origin/giraffe (forced update)
* [new branch] giraffe-man-page -> origin/giraffe-man-page
* [new branch] giraffe-paired -> origin/giraffe-paired
ea138e861..60b2554bd glenn -> origin/glenn
* [new branch] grafimo-fixes -> origin/grafimo-fixes
* [new branch] group-mapq -> origin/group-mapq
* [new branch] handle-compiler-change -> origin/handle-compiler-change
* [new branch] handle-stats -> origin/handle-stats
* [new branch] harden-libbdsg -> origin/harden-libbdsg
* [new branch] htslib_1.10 -> origin/htslib_1.10
* [new branch] jeizenga-remove-alt-paths -> origin/jeizenga-remove-alt-paths
16090efc3..794f083a9 jenkins -> origin/jenkins
* [new branch] kubernetize -> origin/kubernetize
* [new branch] low-memory-chunk -> origin/low-memory-chunk
* [new branch] manpages -> origin/manpages
* [new branch] minor-mapq-bug -> origin/minor-mapq-bug
* [new branch] more-surject-bugs -> origin/more-surject-bugs
* [new branch] mpmap-long-read-rna -> origin/mpmap-long-read-rna
* [new branch] mpmap-mapq-defaults -> origin/mpmap-mapq-defaults
* [new branch] mr-c-hardening -> origin/mr-c-hardening
* [new branch] mr-c-hardening-gbwt -> origin/mr-c-hardening-gbwt
* [new branch] mr-c-hardening-gssw -> origin/mr-c-hardening-gssw
* [new branch] mr-c-hardening-libbdsg -> origin/mr-c-hardening-libbdsg
* [new branch] mr-c-hardening-sonlib -> origin/mr-c-hardening-sonlib
* [new branch] mr-c-hardening-structures -> origin/mr-c-hardening-structures
* [new branch] mr-c-sha1 -> origin/mr-c-sha1
* [new branch] nehalem -> origin/nehalem
* [new branch] new-bindings -> origin/new-bindings
* [new branch] no-fun -> origin/no-fun
76f37c041..946302d9e overlay-algorithms -> origin/overlay-algorithms
865bb0b19..80f7b6249 packed-call -> origin/packed-call
* [new branch] paired-giraffe -> origin/paired-giraffe
* [new branch] permissive-distance-indexing -> origin/permissive-distance-indexing
* [new branch] pull-in-pg-fix -> origin/pull-in-pg-fix
* [new branch] refactor-indexing -> origin/refactor-indexing
* [new branch] region-kmers -> origin/region-kmers
* [new branch] reject-star -> origin/reject-star
* [new branch] remove-alt-paths -> origin/remove-alt-paths
* [new branch] remove-mpmap-opts-2 -> origin/remove-mpmap-opts-2
* [new branch] rename-variant -> origin/rename-variant
* [new branch] rna-bed-intron -> origin/rna-bed-intron
* [new branch] rna-bidirectional -> origin/rna-bidirectional
* [new branch] rna-gff -> origin/rna-gff
* [new branch] rna-handlify -> origin/rna-handlify
* [new branch] rna-hap-break-fix -> origin/rna-hap-break-fix
* [new branch] rna-path-mem-optim -> origin/rna-path-mem-optim
* [new branch] rna-ref-name -> origin/rna-ref-name
* [new branch] rna-sim-good -> origin/rna-sim-good
* [new branch] rna-surject -> origin/rna-surject
* [new branch] single-cap -> origin/single-cap
* [new branch] single-node-snarls -> origin/single-node-snarls
* [new branch] singularity -> origin/singularity
* [new branch] slow-rna-reads -> origin/slow-rna-reads
* [new branch] splice-surject-crash-2 -> origin/splice-surject-crash-2
* [new branch] spliced-surject-crash -> origin/spliced-surject-crash
* [new branch] surject-edge-case -> origin/surject-edge-case
* [new branch] surject-fast -> origin/surject-fast
* [new branch] surject-soft-clips -> origin/surject-soft-clips
bde6e0acf..d762a4954 susanna -> origin/susanna
* [new branch] susanna-crash -> origin/susanna-crash
* [new branch] tag-odgi -> origin/tag-odgi
* [new branch] test-canonicalized-indexing -> origin/test-canonicalized-indexing
* [new branch] track-no-hits -> origin/track-no-hits
* [new branch] update-before-bundle -> origin/update-before-bundle
* [new branch] vcflib-hardening -> origin/vcflib-hardening
* [new branch] vgontologyfix -> origin/vgontologyfix
* [new branch] vgontologyfix2 -> origin/vgontologyfix2
* [new branch] weibull-calibration -> origin/weibull-calibration
* [new branch] wrangle-hgsvc -> origin/wrangle-hgsvc
* [new branch] xian-giraffe -> origin/xian-giraffe
* [new branch] yeet -> origin/yeet
* [new branch] yens -> origin/yens
* [new tag] v1.20.0 -> v1.20.0
* [new tag] v1.21.0 -> v1.21.0
* [new tag] v1.22.0 -> v1.22.0
Fetching submodule deps/gbwt
From https://github.com/jltsiren/gbwt
a1d400f..90edad1 master -> origin/master
Fetching submodule deps/gbwtgraph
From https://github.com/jltsiren/gbwtgraph
acf690d..afc5097 master -> origin/master
* [new tag] v0.2 -> v0.2
Fetching submodule deps/gssw
From https://github.com/ekg/gssw
b0940ee..9f8efbc master -> origin/master
Fetching submodule deps/htslib
Fetching submodule deps/libbdsg
From https://github.com/vgteam/libbdsg
* [new branch] binding-build -> origin/binding-build
* [new branch] cmakeify -> origin/cmakeify
* [new branch] fix-cecilia-build -> origin/fix-cecilia-build
* [new branch] fix-mac-cmake -> origin/fix-mac-cmake
* [new branch] implement-increment -> origin/implement-increment
* [new branch] increment-node-ids -> origin/increment-node-ids
* [new branch] magic-numbers -> origin/magic-numbers
d69763e..ee88ccd master -> origin/master
* [new branch] max-id-patch -> origin/max-id-patch
* [new branch] packed-increment -> origin/packed-increment
* [new branch] pg-edge-count -> origin/pg-edge-count
* [new branch] sort-for-vectorization -> origin/sort-for-vectorization
* [new branch] use-submodules -> origin/use-submodules
Fetching submodule deps/libhandlegraph
From https://github.com/vgteam/libhandlegraph
* [new branch] include-path -> origin/include-path
* [new branch] increment-node-ids -> origin/increment-node-ids
* [new branch] magic-numbers -> origin/magic-numbers
541b973..df7c37a master -> origin/master
* [new branch] optional-magic-numbers -> origin/optional-magic-numbers
* [new branch] portable -> origin/portable
* [new branch] reassign-ids -> origin/reassign-ids
* [new branch] totals -> origin/totals
Fetching submodule deps/libvgio
From https://github.com/vgteam/libvgio
a369fb1..0b82391 master -> origin/master
* [new branch] multi-magic -> origin/multi-magic
* [new branch] no-sniff-eof -> origin/no-sniff-eof
* [new branch] parameters -> origin/parameters
* [new branch] sniff-proto-stream -> origin/sniff-proto-stream
Fetching submodule deps/pinchesAndCacti
From https://github.com/benedictpaten/pinchesAndCacti
817f664..467882b master -> origin/master
* [new branch] thread-safety -> origin/thread-safety
Fetching submodule deps/sha1
From https://github.com/vog/sha1
68a0990..767836a master -> origin/master
* [new tag] 1.3 -> 1.3
Fetching submodule deps/sonLib
From https://github.com/benedictpaten/sonLib
1decb75..63b0301 master -> origin/master
2105969..8e403f6 tpesout -> origin/tpesout
Fetching submodule deps/structures
From https://github.com/vgteam/structures
bfbb939..70c3e25 master -> origin/master
Fetching submodule deps/vcflib
Fetching submodule deps/xg
From https://github.com/vgteam/xg
* [new branch] canonicalize-for-indexing -> origin/canonicalize-for-indexing
* [new branch] describe-order -> origin/describe-order
* [new branch] fast-stats -> origin/fast-stats
* [new branch] fix-vectorization -> origin/fix-vectorization
fb89754..69e1ea0 master -> origin/master
* [new branch] new-serialization -> origin/new-serialization
* [new branch] portable -> origin/portable
* [new branch] steps-bug -> origin/steps-bug
* [new branch] update-submodules -> origin/update-submodules
From https://github.com/vgteam/vcflib
* branch 7ae6c38815f46dcbcdd5e9e723e37f487136418e -> FETCH_HEAD
Fetching submodule deps/vcflib/filevercmp
From https://github.com/ekg/filevercmp
cccb6ba..df20dcc master -> origin/master
Fetching submodule deps/vcflib/intervaltree
From https://github.com/ekg/intervaltree
e8082c7..b90527f master -> origin/master
Fetching submodule deps/vcflib/multichoose
From https://github.com/ekg/multichoose
86ab28f..e1f94ae master -> origin/master
Fetching submodule deps/vcflib/tabixpp
From https://github.com/ekg/tabixpp
6bbe690..eaf0dff master -> origin/master
* [new tag] v1.1.0 -> v1.1.0
fatal: exec 'rev-list': cd to 'htslib' failed: No such file or directory
Fetching submodule deps/vcflib/tabixpp/htslib
From https://github.com/samtools/htslib
f8512fb..9a10355 develop -> origin/develop
1832d3a..fd0f895 master -> origin/master
* [new tag] 1.10.2 -> 1.10.2
* [new tag] 1.10 -> 1.10
* [new tag] 1.10.1 -> 1.10.1
From https://github.com/vgteam/htslib
* branch fd0f89554459b78c07303e2c8a42acacd6851b46 -> FETCH_HEAD
Updating 1ac878e5d..9cd9ba375
Fast-forward
.github/ISSUE_TEMPLATE/report-a-bug.md | 43 +
.github/ISSUE_TEMPLATE/support-request.md | 14 +
.gitlab-ci.yml | 7 +-
.gitmodules | 8 +-
.travis.yml | 14 +-
Dockerfile | 61 +-
ISSUE_TEMPLATE.md | 10 -
Makefile | 43 +-
README.md | 21 +-
deps/BBHash | 2 +-
deps/gbwt | 2 +-
deps/gbwtgraph | 2 +-
deps/gssw | 2 +-
deps/htslib | 2 +-
deps/libbdsg | 2 +-
deps/libhandlegraph | 2 +-
deps/libvgio | 2 +-
deps/pinchesAndCacti | 2 +-
deps/sha1 | 2 +-
deps/sonLib | 2 +-
deps/structures | 2 +-
deps/vcflib | 2 +-
deps/xg | 2 +-
doc/asciidoc/man/vg-gaffe.adoc | 203 +++
doc/asciidoc/man/vg-test.adoc | 154 ++
doc/asciidoc/man/vg-version.adoc | 67 +
ontology/vg.html | 164 +-
ontology/vg.ttl | 28 +-
scripts/giraffe-facts.py | 29 +-
scripts/giraffe-wrangler.sh | 239 ++-
src/algorithms/copy_graph.cpp | 45 +
src/algorithms/copy_graph.hpp | 32 +
src/algorithms/coverage_depth.cpp | 266 +++
src/algorithms/coverage_depth.hpp | 66 +
src/algorithms/k_widest_paths.cpp | 256 +++
src/algorithms/k_widest_paths.hpp | 41 +
src/algorithms/kmer.cpp | 114 ++
src/algorithms/kmer.hpp | 46 +
src/algorithms/merge.cpp | 159 ++
src/algorithms/merge.hpp | 24 +
src/algorithms/normalize.cpp | 57 +
src/algorithms/normalize.hpp | 24 +
src/algorithms/simplify_siblings.cpp | 284 +++
src/algorithms/simplify_siblings.hpp | 31 +
src/algorithms/strongly_connected_components.hpp | 3 +-
src/algorithms/subgraph.cpp | 48 +-
src/algorithms/subgraph.hpp | 6 +-
src/algorithms/unchop.cpp | 479 +++++
src/algorithms/unchop.hpp | 24 +
src/algorithms/walk.cpp | 115 ++
src/algorithms/walk.hpp | 48 +
src/aligner.cpp | 170 +-
src/aligner.hpp | 36 +-
src/alignment.cpp | 384 +++-
src/alignment.hpp | 25 +-
src/alignment_emitter.cpp | 259 ++-
src/alignment_emitter.hpp | 45 +-
src/annotation.hpp | 13 +
src/augment.cpp | 552 ++++--
src/augment.hpp | 68 +-
src/cactus.cpp | 16 +-
src/cactus.hpp | 5 +-
src/chunker.cpp | 166 +-
src/chunker.hpp | 20 +-
src/cluster.cpp | 34 +-
src/cluster.hpp | 13 +-
src/constructor.cpp | 187 +-
src/constructor.hpp | 76 +-
src/convert_handle.cpp | 32 +
src/crash.cpp | 1 +
src/dagified_graph.cpp | 353 ++++
src/dagified_graph.hpp | 150 ++
src/gapless_extender.cpp | 245 ++-
src/gapless_extender.hpp | 28 +-
src/gbwt_helper.cpp | 38 +
src/gbwt_helper.hpp | 35 +
src/genotypekit.hpp | 3 +-
src/genotyper.hpp | 2 +-
src/gfa.cpp | 15 +
src/graph_caller.cpp | 662 ++++---
src/graph_caller.hpp | 91 +-
src/handle.hpp | 8 +
src/haplotype_indexer.cpp | 524 ++++++
src/haplotype_indexer.hpp | 189 ++
src/identity_overlay.cpp | 6 +-
src/identity_overlay.hpp | 26 +-
src/index_manager.cpp | 495 ++++++
src/index_manager.hpp | 198 +++
src/indexed_vg.hpp | 14 +-
src/io/load_proto_to_graph.cpp | 394 +++++
src/io/load_proto_to_graph.hpp | 44 +
src/io/register_loader_saver_hash_graph.cpp | 26 +-
src/io/register_loader_saver_odgi.cpp | 6 +-
src/io/register_loader_saver_packed_graph.cpp | 2 +-
src/io/register_loader_saver_vg.cpp | 2 +-
src/io/register_loader_saver_xg.cpp | 15 +-
src/io/save_handle_graph.hpp | 85 +
src/main.cpp | 4 +
src/mapper.cpp | 26 +-
src/mapper.hpp | 44 +-
src/min_distance.cpp | 1604 +++++++++--------
src/min_distance.hpp | 47 +-
src/minimizer_mapper.cpp | 2799 +++++++++++++++++++++++++-----
src/minimizer_mapper.hpp | 270 ++-
src/multipath_alignment.cpp | 14 +
src/multipath_alignment.hpp | 8 +
src/multipath_alignment_graph.cpp | 135 +-
src/multipath_alignment_graph.hpp | 46 +-
src/multipath_mapper.cpp | 698 +++++---
src/multipath_mapper.hpp | 54 +-
src/packer.cpp | 418 ++++-
src/packer.hpp | 105 +-
src/path.cpp | 85 +-
src/path.hpp | 12 +-
src/path_index.cpp | 10 +-
src/phase_unfolder.cpp | 26 +-
src/prune.cpp | 172 +-
src/prune.hpp | 5 +-
src/readfilter.cpp | 23 +-
src/readfilter.hpp | 14 +-
src/reverse_graph.cpp | 2 +-
src/sampler.cpp | 107 +-
src/sampler.hpp | 19 +-
src/seed_clusterer.cpp | 1443 ++++++++-------
src/seed_clusterer.hpp | 119 +-
src/snarl_caller.cpp | 796 +++++----
src/snarl_caller.hpp | 258 +--
src/snarls.cpp | 113 +-
src/snarls.hpp | 41 +-
src/statistics.cpp | 567 ++++++
src/{distributions.hpp => statistics.hpp} | 487 ++++--
src/subcommand/align_main.cpp | 41 +-
src/subcommand/augment_main.cpp | 138 +-
src/subcommand/call_main.cpp | 86 +-
src/subcommand/chunk_main.cpp | 344 +++-
src/subcommand/circularize_main.cpp | 45 +-
src/subcommand/cluster_main.cpp | 21 +-
src/subcommand/combine_main.cpp | 162 ++
src/subcommand/construct_main.cpp | 62 +-
src/subcommand/convert_main.cpp | 17 +-
src/subcommand/depth_main.cpp | 222 +++
src/subcommand/explode_main.cpp | 88 +-
src/subcommand/filter_main.cpp | 4 +-
src/subcommand/find_main.cpp | 71 +-
src/subcommand/gaffe_main.cpp | 480 +++--
src/subcommand/gbwt_main.cpp | 466 +++--
src/subcommand/help_main.cpp | 2 +
src/subcommand/ids_main.cpp | 71 +-
src/subcommand/index_main.cpp | 616 +------
src/subcommand/minimizer_main.cpp | 23 +-
src/subcommand/mod_main.cpp | 303 ++--
src/subcommand/mpmap_main.cpp | 180 +-
src/subcommand/msga_main.cpp | 23 +-
src/subcommand/pack_main.cpp | 61 +-
src/subcommand/paths_main.cpp | 173 +-
src/subcommand/prune_main.cpp | 138 +-
src/subcommand/rna_main.cpp | 132 +-
src/subcommand/sim_main.cpp | 86 +-
src/subcommand/snarls_main.cpp | 80 +-
src/subcommand/stats_main.cpp | 216 ++-
src/subcommand/surject_main.cpp | 31 +-
src/subcommand/validate_main.cpp | 16 +-
src/subcommand/view_main.cpp | 150 +-
src/subgraph_overlay.cpp | 209 +++
src/subgraph_overlay.hpp | 215 +++
src/surjector.cpp | 835 +++++++--
src/surjector.hpp | 66 +-
src/transcriptome.cpp | 1137 ++++++++----
src/transcriptome.hpp | 155 +-
src/traversal_finder.cpp | 80 +-
src/traversal_finder.hpp | 68 +-
src/traversal_support.cpp | 495 ++++++
src/traversal_support.hpp | 161 ++
src/unittest/chunker.cpp | 12 +
src/unittest/constructor.cpp | 88 +
src/unittest/dagified_graph.cpp | 460 +++++
src/unittest/dijkstra.cpp | 1 -
src/unittest/distributions.cpp | 2 +-
src/unittest/gapless_extender.cpp | 84 +-
src/unittest/genotypekit.cpp | 4 +-
src/unittest/k_widest_paths.cpp | 260 +++
src/unittest/mcmc_genotyper.cpp | 8 +-
src/unittest/min_distance.cpp | 423 ++++-
src/unittest/multipath_alignment_graph.cpp | 6 +-
src/unittest/multipath_mapper.cpp | 10 +-
src/unittest/sampler.cpp | 6 +-
src/unittest/seed_clusterer.cpp | 487 +++---
src/unittest/statistics.cpp | 158 ++
src/unittest/surject.cpp | 120 ++
src/unittest/traversal_support.cpp | 165 ++
src/unittest/vg.cpp | 16 +-
src/unittest/vg_algorithms.cpp | 79 +
src/unittest/vpkg.cpp | 39 +-
src/unittest/xg.cpp | 171 ++
src/utility.cpp | 221 ++-
src/utility.hpp | 174 +-
src/variant_recall.hpp | 2 +-
src/version.cpp | 5 +-
src/vg.cpp | 988 +----------
src/vg.hpp | 70 +-
src/vg_set.cpp | 300 ++--
src/vg_set.hpp | 10 +-
test/graphs/normalize_me.norm.gfa | 19 +
test/msgas/inv-mess-normalized.gfa | 12 +-
test/msgas/inv-mess-unchopped.gfa | 2 +-
test/reads/small.middle.ref.fq | 4 +
test/small/x.v4.3.vcf.gz | Bin 0 -> 541 bytes
test/small/x.v4.3.vcf.gz.tbi | Bin 0 -> 102 bytes
test/t/02_vg_construct.t | 6 +-
test/t/03_vg_view.t | 22 +-
test/t/04_vg_align.t | 4 +-
test/t/05_vg_find.t | 12 +-
test/t/06_vg_index.t | 4 +-
test/t/07_vg_map.t | 2 +-
test/t/08_vg_ids.t | 16 +-
test/t/100_code_quality.t | 11 +
test/t/10_vg_stats.t | 14 +-
test/t/11_vg_paths.t | 7 +-
test/t/14_vg_mod.t | 21 +-
test/t/15_vg_surject.t | 5 +-
test/t/16_vg_msga.t | 2 +-
test/t/17_vg_augment.t | 134 +-
test/t/18_vg_call.t | 43 +-
test/t/26_deconstruct.t | 6 +-
test/t/27_vg_genotype.t | 4 +-
test/t/30_vg_chunk.t | 47 +-
test/t/32_vg_snarls.t | 14 +-
test/t/33_vg_mpmap.t | 20 +-
test/t/34_vg_pack.t | 14 +-
test/t/37_vg_gbwt.t | 32 +-
test/t/38_vg_prune.t | 43 +-
test/t/43_vg_simplify.t | 4 +-
test/t/49_vg_depth.t | 21 +
test/t/50_vg_gaffe.t | 46 +
vgci/Dockerfile.vgci | 37 -
vgci/test-list.txt | 3 -
vgci/vgci.py | 145 +-
vgci/vgci.sh | 74 +-
238 files changed, 24550 insertions(+), 8268 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE/report-a-bug.md
create mode 100644 .github/ISSUE_TEMPLATE/support-request.md
delete mode 100644 ISSUE_TEMPLATE.md
create mode 100644 doc/asciidoc/man/vg-gaffe.adoc
create mode 100644 doc/asciidoc/man/vg-test.adoc
create mode 100644 doc/asciidoc/man/vg-version.adoc
create mode 100644 src/algorithms/copy_graph.cpp
create mode 100644 src/algorithms/copy_graph.hpp
create mode 100644 src/algorithms/coverage_depth.cpp
create mode 100644 src/algorithms/coverage_depth.hpp
create mode 100644 src/algorithms/k_widest_paths.cpp
create mode 100644 src/algorithms/k_widest_paths.hpp
create mode 100644 src/algorithms/kmer.cpp
create mode 100644 src/algorithms/kmer.hpp
create mode 100644 src/algorithms/merge.cpp
create mode 100644 src/algorithms/merge.hpp
create mode 100644 src/algorithms/normalize.cpp
create mode 100644 src/algorithms/normalize.hpp
create mode 100644 src/algorithms/simplify_siblings.cpp
create mode 100644 src/algorithms/simplify_siblings.hpp
create mode 100644 src/algorithms/unchop.cpp
create mode 100644 src/algorithms/unchop.hpp
create mode 100644 src/algorithms/walk.cpp
create mode 100644 src/algorithms/walk.hpp
create mode 100644 src/dagified_graph.cpp
create mode 100644 src/dagified_graph.hpp
create mode 100644 src/haplotype_indexer.cpp
create mode 100644 src/haplotype_indexer.hpp
create mode 100644 src/index_manager.cpp
create mode 100644 src/index_manager.hpp
create mode 100644 src/io/load_proto_to_graph.cpp
create mode 100644 src/io/load_proto_to_graph.hpp
create mode 100644 src/io/save_handle_graph.hpp
create mode 100644 src/statistics.cpp
rename src/{distributions.hpp => statistics.hpp} (66%)
create mode 100644 src/subcommand/combine_main.cpp
create mode 100644 src/subcommand/depth_main.cpp
create mode 100644 src/subgraph_overlay.cpp
create mode 100644 src/subgraph_overlay.hpp
create mode 100644 src/traversal_support.cpp
create mode 100644 src/traversal_support.hpp
create mode 100644 src/unittest/dagified_graph.cpp
create mode 100644 src/unittest/k_widest_paths.cpp
create mode 100644 src/unittest/statistics.cpp
create mode 100644 src/unittest/surject.cpp
create mode 100644 src/unittest/traversal_support.cpp
create mode 100644 test/graphs/normalize_me.norm.gfa
create mode 100644 test/reads/small.middle.ref.fq
create mode 100644 test/small/x.v4.3.vcf.gz
create mode 100644 test/small/x.v4.3.vcf.gz.tbi
create mode 100644 test/t/100_code_quality.t
create mode 100644 test/t/49_vg_depth.t
create mode 100644 test/t/50_vg_gaffe.t
delete mode 100644 vgci/Dockerfile.vgci
Now everything has to be built again I guess.
. ./source_me.sh && make
And we end up with errors, yay…
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/main.o src/main.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/stream_sorter.o src/stream_sorter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/path.o src/path.cpp
In file included from src/position.hpp:9:0,
from src/path.hpp:16,
from src/path.cpp:1:
src/handle.hpp:9:53: fatal error: handlegraph/serializable_handle_graph.hpp: No such file or directory
compilation terminated.
Makefile:702: recipe for target 'obj/path.o' failed
make: *** [obj/path.o] Error 1
OK, so in include/handlegraph/ a file is missing, which means that libhandlegraph wasn’t made as required.
libhandlegraph
cd deps/libhandlegraph/
make
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg/deps/libhandlegraph
Scanning dependencies of target handlegraph_objs
[ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o
[ 33%] Built target handlegraph_objs
Scanning dependencies of target handlegraph_static
[ 66%] Linking CXX static library libhandlegraph.a
[ 66%] Built target handlegraph_static
Scanning dependencies of target handlegraph_shared
[100%] Linking CXX shared library libhandlegraph.so
[100%] Built target handlegraph_shared
No problems here, great.
cd ../../
. ./source_me.sh && make
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/path.o src/path.cpp
In file included from src/position.hpp:9:0,
from src/path.hpp:16,
from src/path.cpp:1:
src/handle.hpp:9:53: fatal error: handlegraph/serializable_handle_graph.hpp: No such file or directory
compilation terminated.
Makefile:702: recipe for target 'obj/path.o' failed
make: *** [obj/path.o] Error 1
I think I’ll just fake this file, then…
touch include/handlegraph/serializable_handle_graph.hpp
. ./source_me.sh && make
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/path.o src/path.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/readfilter.o src/readfilter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/graph.o src/graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/snarls.o src/snarls.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/version.o src/version.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg/include -I. -I/data3/genome_graphs/vg/src -I/data3/genome_graphs/vg/src/unittest -I/data3/genome_graphs/vg/src/subcommand -I/data3/genome_graphs/vg/include/dynamic -I/data3/genome_graphs/vg/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c -o obj/mapper.o src/mapper.cpp
src/mapper.cpp: In constructor ‘vg::BaseMapper::BaseMapper(vg::PathPositionHandleGraph*, gcsa::GCSA*, gcsa::LCPArray*, haplo::ScoreProvider*)’:
src/mapper.cpp:37:35: error: ‘using PathPositionHandleGraph = class handlegraph::PathPositionHandleGraph {aka class handlegraph::PathPositionHandleGraph}’ has no member named get_total_length’
avg_node_length = xindex->get_total_length() / xindex->get_node_count();
^
Makefile:702: recipe for target 'obj/mapper.o' failed
make: *** [obj/mapper.o] Error 1
OK, something is not right with libhandlegraph. Time for a complete update.
cd deps/libhandlegraph/
git pull origin master
From https://github.com/vgteam/libhandlegraph
* branch master -> FETCH_HEAD
Updating 541b973..df7c37a
Fast-forward
src/handle.cpp | 24 +++++++
src/include/handlegraph/expanding_overlay_graph.hpp | 2 +-
src/include/handlegraph/handle_graph.hpp | 28 +++-----
src/include/handlegraph/mutable_handle_graph.hpp | 14 +++-
src/include/handlegraph/serializable_handle_graph.hpp | 92 +++++++++++++++++++++++++++
5 files changed, 138 insertions(+), 22 deletions(-)
create mode 100644 src/include/handlegraph/serializable_handle_graph.hpp
Aha!
I better remove the empty file I created, just to be sure I’ll get a new one made now.
rm ../../include/handlegraph/serializable_handle_graph.hpp
make
cd ../../
. ./source_me.sh && make
. ./source_me.sh && cd deps/libhandlegraph && cmake . && make && cp libhandlegraph.a /data3/genome_graphs/vg/lib && cp -r src/include/handlegraph /data3/genome_graphs/vg/include
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg/deps/libhandlegraph
make[1]: Entering directory '/data3/genome_graphs/vg/deps/libhandlegraph'
make[2]: Entering directory '/data3/genome_graphs/vg/deps/libhandlegraph'
make[3]: Entering directory '/data3/genome_graphs/vg/deps/libhandlegraph'
make[3]: Leaving directory '/data3/genome_graphs/vg/deps/libhandlegraph'
[ 33%] Built target handlegraph_objs
make[3]: Entering directory '/data3/genome_graphs/vg/deps/libhandlegraph'
make[3]: Leaving directory '/data3/genome_graphs/vg/deps/libhandlegraph'
[ 66%] Built target handlegraph_static
make[3]: Entering directory '/data3/genome_graphs/vg/deps/libhandlegraph'
make[3]: Leaving directory '/data3/genome_graphs/vg/deps/libhandlegraph'
[100%] Built target handlegraph_shared
make[2]: Leaving directory '/data3/genome_graphs/vg/deps/libhandlegraph'
make[1]: Leaving directory '/data3/genome_graphs/vg/deps/libhandlegraph'
. ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /data3/genome_graphs/vg/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /data3/genome_graphs/vg/lib
make[1]: Entering directory '/data3/genome_graphs/vg/deps/gbwtgraph'
rm -f utils.o gfa2gbwt.o gfa.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt
make[1]: Leaving directory '/data3/genome_graphs/vg/deps/gbwtgraph'
make[1]: Entering directory '/data3/genome_graphs/vg/deps/gbwtgraph'
/usr/bin/g++ -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg/include -c gbwtgraph.cpp
In file included from /data3/genome_graphs/vg/include/gbwtgraph/gbwtgraph.h:9:0,
from gbwtgraph.cpp:1:
/data3/genome_graphs/vg/include/gbwtgraph/utils.h:29:46: error: ‘SerializableHandleGrap ’ in namespace ‘handlegraph’ does not name a type
using SerializableHandleGraph = handlegraph::SerializableHandleGraph;
^
In file included from gbwtgraph.cpp:1:0:
/data3/genome_graphs/vg/include/gbwtgraph/gbwtgraph.h:32:1: error: expected class-name before ‘{’ token
{
^
Makefile:45: recipe for target 'gbwtgraph.o' failed
make[1]: *** [gbwtgraph.o] Error 1
make[1]: Leaving directory '/data3/genome_graphs/vg/deps/gbwtgraph'
Makefile:429: recipe for target 'lib/libgbwtgraph.a' failed
make: *** [lib/libgbwtgraph.a] Error 2
gbwtgraph
And on we go…
cd deps/gbwtgraph/
git pull origin master
From https://github.com/jltsiren/gbwtgraph
* branch master -> FETCH_HEAD
Updating acf690d..afc5097
Fast-forward
.gitignore | 3 +
CMakeLists.txt | 2 +-
LICENSE | 2 +-
Makefile | 2 +-
README.md | 3 +
gbwtgraph.cpp | 18 ++-
include/gbwtgraph/gbwtgraph.h | 22 ++-
include/gbwtgraph/minimizer.h | 266 +++++++++++++++++++++++++++++++-
include/gbwtgraph/path_cover.h | 95 ++++++++++++
include/gbwtgraph/utils.h | 3 +-
minimizer.cpp | 43 +++++-
path_cover.cpp | 631 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
tests/Makefile | 12 +-
tests/components.gfa | 30 ++++
tests/shared.h | 102 +++++++++++++
tests/test_gbwtgraph.cpp | 232 +---------------------------
tests/test_gfa.cpp | 68 +++++++++
tests/test_index.cpp | 104 +++++++++++++
tests/test_minimizer.cpp | 366 ++++++++++++++++++++++++++++++++++++--------
tests/test_path_cover.cpp | 324 +++++++++++++++++++++++++++++++++++++++
20 files changed, 2014 insertions(+), 314 deletions(-)
create mode 100644 include/gbwtgraph/path_cover.h
create mode 100644 path_cover.cpp
create mode 100644 tests/components.gfa
create mode 100644 tests/shared.h
create mode 100644 tests/test_gfa.cpp
create mode 100644 tests/test_index.cpp
create mode 100644 tests/test_path_cover.cpp
make
cd ../../
. ./source_me.sh && make
/usr/bin/g++ -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg/include -c gbwtgraph.cpp
In file included from /data3/genome_graphs/vg/include/gbwtgraph/gbwtgraph.h:9:0,
from gbwtgraph.cpp:1:
/data3/genome_graphs/vg/include/gbwtgraph/utils.h:29:46: error: ‘SerializableHandleGraph’ in namespace ‘handlegrap ’ does not name a type
using SerializableHandleGraph = handlegraph::SerializableHandleGraph;
^
In file included from gbwtgraph.cpp:1:0:
/data3/genome_graphs/vg/include/gbwtgraph/gbwtgraph.h:32:1: error: expected class-name before ‘{’ token
{
^
gbwtgraph.cpp:353:31: error: no ‘uint32_t gbwtgraph::GBWTGraph::get_magic_number() const’ member function declared in class ‘gbwtgraph::GBWTGraph’
GBWTGraph::get_magic_number() const {
^
gbwtgraph.cpp:361:49: error: no ‘void gbwtgraph::GBWTGraph::serialize_members(std::ostream&) const’ member function declared in class ‘gbwtgraph::GBWTGraph’
GBWTGraph::serialize_members(std::ostream& out) const
^
gbwtgraph.cpp:381:48: error: no ‘void gbwtgraph::GBWTGraph::deserialize_members(std::istream&)’ member function declared in class ‘gbwtgraph::GBWTGraph’
GBWTGraph::deserialize_members(std::istream& in)
^
Makefile:45: recipe for target 'gbwtgraph.o' failed
make: *** [gbwtgraph.o] Error 1
OK, that was obviously not the one that’s incomplete. This is definitely not the best approach.
Dependencies
Maybe I should have started with the dependencies again.
cd ../../
make get-deps
sudo apt-get install -qq -y build-essential git protobuf-compiler libprotoc-dev libjansson-dev libbz2-dev libncurses5-dev automake libtool jq rs samtools curl unzip redland-utils librdf-dev cmake pkg-config wget bc gtk-doc-tools raptor2-utils rasqal-utils bison flex gawk libgoogle-perftools-dev liblz4-dev liblzma-dev libcairo2-dev libpixman-1-dev libffi-dev libcairo-dev libprotobuf-dev
[sudo] password for spo12:
(Reading database ... 292364 files and directories currently installed.)
Removing linuxbrew-wrapper (20150804-3) ...
dpkg: libcurl4-openssl-dev:amd64: dependency problems, but removing anyway as you requested:
libdap-dev:amd64 depends on libcurl4-gnutls-dev | libcurl-dev; however:
Package libcurl4-gnutls-dev is not installed.
Package libcurl-dev is not installed.
Package libcurl4-openssl-dev:amd64 which provides libcurl-dev is to be removed.
libnetcdf-dev depends on libcurl4-gnutls-dev | libcurl-ssl-dev; however:
Package libcurl4-gnutls-dev is not installed.
Package libcurl-ssl-dev is not installed.
Package libcurl4-openssl-dev:amd64 which provides libcurl-ssl-dev is to be removed.
libgdal-dev depends on libcurl4-gnutls-dev | libcurl-ssl-dev; however:
Package libcurl4-gnutls-dev is not installed.
Package libcurl-ssl-dev is not installed.
Package libcurl4-openssl-dev:amd64 which provides libcurl-ssl-dev is to be removed.
Removing libcurl4-openssl-dev:amd64 (7.47.0-1ubuntu2.14) ...
Processing triggers for man-db (2.7.5-1) ...
Selecting previously unselected package libcurl4-gnutls-dev:amd64.
(Reading database ... 292331 files and directories currently installed.)
Preparing to unpack .../libcurl4-gnutls-dev_7.47.0-1ubuntu2.14_amd64.deb ...
Unpacking libcurl4-gnutls-dev:amd64 (7.47.0-1ubuntu2.14) ...
Selecting previously unselected package libxslt1-dev:amd64.
Preparing to unpack .../libxslt1-dev_1.1.28-2.1ubuntu0.3_amd64.deb ...
Unpacking libxslt1-dev:amd64 (1.1.28-2.1ubuntu0.3) ...
Selecting previously unselected package libyajl-dev:amd64.
Preparing to unpack .../libyajl-dev_2.1.0-2_amd64.deb ...
Unpacking libyajl-dev:amd64 (2.1.0-2) ...
Selecting previously unselected package libraptor2-dev.
Preparing to unpack .../libraptor2-dev_2.0.14-1_amd64.deb ...
Unpacking libraptor2-dev (2.0.14-1) ...
Selecting previously unselected package librasqal3-dev.
Preparing to unpack .../librasqal3-dev_0.9.32-1_amd64.deb ...
Unpacking librasqal3-dev (0.9.32-1) ...
Selecting previously unselected package librdf0-dev.
Preparing to unpack .../librdf0-dev_1.0.17-1build1_amd64.deb ...
Unpacking librdf0-dev (1.0.17-1build1) ...
Selecting previously unselected package rs.
Preparing to unpack .../rs_20140609-3_amd64.deb ...
Unpacking rs (20140609-3) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libcurl4-gnutls-dev:amd64 (7.47.0-1ubuntu2.14) ...
Setting up libxslt1-dev:amd64 (1.1.28-2.1ubuntu0.3) ...
Setting up libyajl-dev:amd64 (2.1.0-2) ...
Setting up libraptor2-dev (2.0.14-1) ...
Setting up librasqal3-dev (0.9.32-1) ...
Setting up librdf0-dev (1.0.17-1build1) ...
Setting up rs (20140609-3) ...
Since the include/ directory seems to be the one that is generated with make, I’m going to rename the current one to make sure that the whole process is running and it doesn’t start somewhere in the middle because some files already exist.
mv include/ include-old
. ./source_me.sh && make
. ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /data3/genome_graphs/vg/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /data3/genome_graphs/vg/lib
make[1]: Entering directory '/data3/genome_graphs/vg/deps/gbwtgraph'
rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt
make[1]: Leaving directory '/data3/genome_graphs/vg/deps/gbwtgraph'
make[1]: Entering directory '/data3/genome_graphs/vg/deps/gbwtgraph'
/usr/bin/g++ -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg/include -c gbwtgraph.cpp
In file included from gbwtgraph.cpp:1:0:
/data3/genome_graphs/vg/include/gbwtgraph/gbwtgraph.h:6:30: fatal error: gbwt/cached_gbwt.h: No such file or directory
compilation terminated.
Makefile:45: recipe for target 'gbwtgraph.o' failed
make[1]: *** [gbwtgraph.o] Error 1
make[1]: Leaving directory '/data3/genome_graphs/vg/deps/gbwtgraph'
Makefile:429: recipe for target 'lib/libgbwtgraph.a' failed
make: *** [lib/libgbwtgraph.a] Error 2
Nevertheless, the make process did not start at the beginning. How can I force that?
Never mind, I’m just going to do a clean install in a different directory, and if it works I can delete the current one.
Clean install
cd ..
git clone --recursive https://github.com/vgteam/vg.git vg-rotella
I don’t think the cloning produced that much output when I first installed vg… I’m copying it all here to have something to compare against next time:
-> click here for the cloning output <-
Cloning into 'vg-rotella'...
remote: Enumerating objects: 87201, done.
remote: Total 87201 (delta 0), reused 0 (delta 0), pack-reused 87201
Receiving objects: 100% (87201/87201), 77.23 MiB | 7.21 MiB/s, done.
Resolving deltas: 100% (73248/73248), done.
Submodule 'vgteam_bbhash' (https://github.com/vgteam/BBHash.git) registered for path 'deps/BBHash'
Submodule 'deps/DYNAMIC' (https://github.com/vgteam/DYNAMIC) registered for path 'deps/DYNAMIC'
Submodule 'deps/FlameGraph' (https://github.com/brendangregg/FlameGraph) registered for path 'deps/FlameGraph'
Submodule 'deps/backward-cpp' (https://github.com/adamnovak/backward-cpp.git) registered for path 'deps/backward-cpp'
Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'deps/bash-tap'
Submodule 'deps/boost-subset' (https://github.com/vgteam/boost-subset.git) registered for path 'deps/boost-subset'
Submodule 'deps/dozeu' (https://github.com/ocxtal/dozeu.git) registered for path 'deps/dozeu'
Submodule 'deps/elfutils' (git://sourceware.org/git/elfutils.git) registered for path 'deps/elfutils'
Submodule 'fastahack' (https://github.com/vgteam/fastahack.git) registered for path 'deps/fastahack'
Submodule 'deps/fermi-lite' (https://github.com/edawson/fermi-lite.git) registered for path 'deps/fermi-lite'
Submodule 'deps/gbwt' (https://github.com/jltsiren/gbwt.git) registered for path 'deps/gbwt'
Submodule 'deps/gbwtgraph' (https://github.com/jltsiren/gbwtgraph.git) registered for path 'deps/gbwtgraph'
Submodule 'gcsa2' (https://github.com/jltsiren/gcsa2.git) registered for path 'deps/gcsa2'
Submodule 'gfakluge' (https://github.com/vgteam/gfakluge.git) registered for path 'deps/gfakluge'
Submodule 'gssw' (https://github.com/ekg/gssw.git) registered for path 'deps/gssw'
Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'deps/htslib'
Submodule 'deps/ips4o' (https://github.com/vgteam/ips4o.git) registered for path 'deps/ips4o'
Submodule 'deps/jemalloc' (https://github.com/jemalloc/jemalloc.git) registered for path 'deps/jemalloc'
Submodule 'deps/libVCFH' (https://github.com/edawson/libVCFH.git) registered for path 'deps/libVCFH'
Submodule 'deps/libbdsg' (https://github.com/vgteam/libbdsg.git) registered for path 'deps/libbdsg'
Submodule 'deps/libdeflate' (https://github.com/ebiggers/libdeflate.git) registered for path 'deps/libdeflate'
Submodule 'deps/libhandlegraph' (https://github.com/vgteam/libhandlegraph.git) registered for path 'deps/libhandlegraph'
Submodule 'deps/libvgio' (https://github.com/vgteam/libvgio.git) registered for path 'deps/libvgio'
Submodule 'lru_cache' (https://github.com/ekg/lru_cache.git) registered for path 'deps/lru_cache'
Submodule 'deps/mmmultimap' (https://github.com/ekg/mmmultimap.git) registered for path 'deps/mmmultimap'
Submodule 'deps/pinchesAndCacti' (https://github.com/benedictpaten/pinchesAndCacti.git) registered for path 'deps/pinchesAndCacti'
Submodule 'progress_bar' (https://github.com/vgteam/cpp_progress_bar.git) registered for path 'deps/progress_bar'
Submodule 'deps/raptor' (https://github.com/vgteam/raptor.git) registered for path 'deps/raptor'
Submodule 'deps/rocksdb' (https://github.com/facebook/rocksdb.git) registered for path 'deps/rocksdb'
Submodule 'sdsl-lite' (https://github.com/simongog/sdsl-lite) registered for path 'deps/sdsl-lite'
Submodule 'sha1' (https://github.com/vog/sha1.git) registered for path 'deps/sha1'
Submodule 'deps/snappy' (https://github.com/google/snappy.git) registered for path 'deps/snappy'
Submodule 'deps/sonLib' (https://github.com/benedictpaten/sonLib.git) registered for path 'deps/sonLib'
Submodule 'deps/sparsehash' (https://github.com/sparsehash/sparsehash.git) registered for path 'deps/sparsehash'
Submodule 'deps/sparsepp' (https://github.com/greg7mdp/sparsepp.git) registered for path 'deps/sparsepp'
Submodule 'deps/Complete-Striped-Smith-Waterman-Library' (https://github.com/vgteam/Complete-Striped-Smith-Waterman-Library.git) registered for path 'deps/ssw'
Submodule 'deps/structures' (https://github.com/vgteam/structures.git) registered for path 'deps/structures'
Submodule 'deps/sublinear-Li-Stephens' (https://github.com/yoheirosen/sublinear-Li-Stephens.git) registered for path 'deps/sublinear-Li-Stephens'
Submodule 'vcflib' (https://github.com/vcflib/vcflib.git) registered for path 'deps/vcflib'
Submodule 'deps/vowpal_wabbit' (https://github.com/JohnLangford/vowpal_wabbit.git) registered for path 'deps/vowpal_wabbit'
Submodule 'deps/xg' (https://github.com/vgteam/xg.git) registered for path 'deps/xg'
Cloning into '/data3/genome_graphs/vg-rotella/deps/BBHash'...
remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 523 (delta 0), reused 1 (delta 0), pack-reused 518
Receiving objects: 100% (523/523), 222.76 KiB | 1009.00 KiB/s, done.
Resolving deltas: 100% (303/303), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/DYNAMIC'...
remote: Enumerating objects: 183, done.
remote: Counting objects: 100% (183/183), done.
remote: Compressing objects: 100% (63/63), done.
remote: Total 1134 (delta 125), reused 169 (delta 120), pack-reused 951
Receiving objects: 100% (1134/1134), 37.82 MiB | 7.10 MiB/s, done.
Resolving deltas: 100% (752/752), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/FlameGraph'...
remote: Enumerating objects: 1063, done.
remote: Total 1063 (delta 0), reused 0 (delta 0), pack-reused 1063
Receiving objects: 100% (1063/1063), 1.86 MiB | 3.47 MiB/s, done.
Resolving deltas: 100% (610/610), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/backward-cpp'...
remote: Enumerating objects: 564, done.
remote: Total 564 (delta 0), reused 0 (delta 0), pack-reused 564
Receiving objects: 100% (564/564), 475.90 KiB | 1.47 MiB/s, done.
Resolving deltas: 100% (348/348), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/bash-tap'...
remote: Enumerating objects: 52, done.
remote: Total 52 (delta 0), reused 0 (delta 0), pack-reused 52
Cloning into '/data3/genome_graphs/vg-rotella/deps/boost-subset'...
remote: Enumerating objects: 4733, done.
remote: Total 4733 (delta 0), reused 0 (delta 0), pack-reused 4733
Receiving objects: 100% (4733/4733), 5.16 MiB | 4.65 MiB/s, done.
Resolving deltas: 100% (1534/1534), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/dozeu'...
remote: Enumerating objects: 496, done.
remote: Total 496 (delta 0), reused 0 (delta 0), pack-reused 496
Receiving objects: 100% (496/496), 330.74 KiB | 1.04 MiB/s, done.
Resolving deltas: 100% (313/313), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/elfutils'...
remote: Enumerating objects: 33333, done.
remote: Counting objects: 100% (33333/33333), done.
remote: Compressing objects: 100% (6301/6301), done.
remote: Total 33333 (delta 27860), reused 32350 (delta 26996)
Receiving objects: 100% (33333/33333), 19.29 MiB | 1.39 MiB/s, done.
Resolving deltas: 100% (27860/27860), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/fastahack'...
remote: Enumerating objects: 227, done.
remote: Total 227 (delta 0), reused 0 (delta 0), pack-reused 227
Receiving objects: 100% (227/227), 51.19 KiB | 546.00 KiB/s, done.
Resolving deltas: 100% (128/128), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/fermi-lite'...
remote: Enumerating objects: 262, done.
remote: Total 262 (delta 0), reused 0 (delta 0), pack-reused 262
Receiving objects: 100% (262/262), 279.69 KiB | 917.00 KiB/s, done.
Resolving deltas: 100% (167/167), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/gbwt'...
remote: Enumerating objects: 146, done.
remote: Counting objects: 100% (146/146), done.
remote: Compressing objects: 100% (80/80), done.
remote: Total 1583 (delta 82), reused 106 (delta 50), pack-reused 1437
Receiving objects: 100% (1583/1583), 539.51 KiB | 1.59 MiB/s, done.
Resolving deltas: 100% (1100/1100), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/gbwtgraph'...
remote: Enumerating objects: 151, done.
remote: Counting objects: 100% (151/151), done.
remote: Compressing objects: 100% (68/68), done.
remote: Total 464 (delta 86), reused 112 (delta 61), pack-reused 313
Receiving objects: 100% (464/464), 154.25 KiB | 892.00 KiB/s, done.
Resolving deltas: 100% (263/263), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/gcsa2'...
remote: Enumerating objects: 44, done.
remote: Counting objects: 100% (44/44), done.
remote: Compressing objects: 100% (32/32), done.
remote: Total 1813 (delta 15), reused 26 (delta 9), pack-reused 1769
Receiving objects: 100% (1813/1813), 980.74 KiB | 2.32 MiB/s, done.
Resolving deltas: 100% (1302/1302), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/gfakluge'...
remote: Enumerating objects: 1528, done.
remote: Total 1528 (delta 0), reused 0 (delta 0), pack-reused 1528
Receiving objects: 100% (1528/1528), 1.83 MiB | 3.04 MiB/s, done.
Resolving deltas: 100% (995/995), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/gssw'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 1690 (delta 0), reused 1 (delta 0), pack-reused 1686
Receiving objects: 100% (1690/1690), 6.44 MiB | 4.75 MiB/s, done.
Resolving deltas: 100% (1127/1127), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/htslib'...
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 12963 (delta 0), reused 1 (delta 0), pack-reused 12960
Receiving objects: 100% (12963/12963), 9.58 MiB | 5.41 MiB/s, done.
Resolving deltas: 100% (9302/9302), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/ips4o'...
remote: Enumerating objects: 64, done.
remote: Total 64 (delta 0), reused 0 (delta 0), pack-reused 64
Cloning into '/data3/genome_graphs/vg-rotella/deps/jemalloc'...
remote: Enumerating objects: 175, done.
remote: Counting objects: 100% (175/175), done.
remote: Compressing objects: 100% (159/159), done.
remote: Total 22083 (delta 106), reused 35 (delta 15), pack-reused 21908
Receiving objects: 100% (22083/22083), 9.35 MiB | 5.33 MiB/s, done.
Resolving deltas: 100% (16016/16016), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/libVCFH'...
remote: Enumerating objects: 53, done.
remote: Total 53 (delta 0), reused 0 (delta 0), pack-reused 53
Cloning into '/data3/genome_graphs/vg-rotella/deps/libbdsg'...
remote: Enumerating objects: 284, done.
remote: Counting objects: 100% (284/284), done.
remote: Compressing objects: 100% (155/155), done.
remote: Total 4750 (delta 183), reused 200 (delta 120), pack-reused 4466
Receiving objects: 100% (4750/4750), 8.21 MiB | 5.23 MiB/s, done.
Resolving deltas: 100% (2746/2746), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/libdeflate'...
remote: Enumerating objects: 88, done.
remote: Counting objects: 100% (88/88), done.
remote: Compressing objects: 100% (63/63), done.
remote: Total 1623 (delta 41), reused 56 (delta 25), pack-reused 1535
Receiving objects: 100% (1623/1623), 774.64 KiB | 2.08 MiB/s, done.
Resolving deltas: 100% (1052/1052), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'...
remote: Enumerating objects: 52, done.
remote: Counting objects: 100% (52/52), done.
remote: Compressing objects: 100% (32/32), done.
remote: Total 866 (delta 20), reused 36 (delta 12), pack-reused 814
Receiving objects: 100% (866/866), 138.23 KiB | 799.00 KiB/s, done.
Resolving deltas: 100% (448/448), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/libvgio'...
remote: Enumerating objects: 821, done.
remote: Counting objects: 100% (821/821), done.
remote: Compressing objects: 100% (237/237), done.
remote: Total 821 (delta 511), reused 781 (delta 480), pack-reused 0
Receiving objects: 100% (821/821), 202.26 KiB | 1.06 MiB/s, done.
Resolving deltas: 100% (511/511), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/lru_cache'...
remote: Enumerating objects: 37, done.
remote: Total 37 (delta 0), reused 0 (delta 0), pack-reused 37
Cloning into '/data3/genome_graphs/vg-rotella/deps/mmmultimap'...
remote: Enumerating objects: 192, done.
remote: Counting objects: 100% (192/192), done.
remote: Compressing objects: 100% (122/122), done.
remote: Total 192 (delta 112), reused 144 (delta 66), pack-reused 0
Receiving objects: 100% (192/192), 41.91 KiB | 499.00 KiB/s, done.
Resolving deltas: 100% (112/112), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti'...
remote: Enumerating objects: 16, done.
remote: Counting objects: 100% (16/16), done.
remote: Compressing objects: 100% (15/15), done.
remote: Total 1277 (delta 4), reused 7 (delta 0), pack-reused 1261
Receiving objects: 100% (1277/1277), 605.58 KiB | 1.66 MiB/s, done.
Resolving deltas: 100% (818/818), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/progress_bar'...
remote: Enumerating objects: 131, done.
remote: Total 131 (delta 0), reused 0 (delta 0), pack-reused 131
Receiving objects: 100% (131/131), 62.89 KiB | 723.00 KiB/s, done.
Resolving deltas: 100% (70/70), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/raptor'...
remote: Enumerating objects: 34378, done.
remote: Total 34378 (delta 0), reused 0 (delta 0), pack-reused 34378
Receiving objects: 100% (34378/34378), 26.85 MiB | 5.75 MiB/s, done.
Resolving deltas: 100% (20887/20887), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/rocksdb'...
remote: Enumerating objects: 24, done.
remote: Counting objects: 100% (24/24), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 84557 (delta 6), reused 9 (delta 3), pack-reused 84533
Receiving objects: 100% (84557/84557), 144.02 MiB | 7.35 MiB/s, done.
Resolving deltas: 100% (63897/63897), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sdsl-lite'...
remote: Enumerating objects: 14003, done.
remote: Total 14003 (delta 0), reused 0 (delta 0), pack-reused 14003
Receiving objects: 100% (14003/14003), 9.30 MiB | 5.88 MiB/s, done.
Resolving deltas: 100% (8148/8148), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sha1'...
remote: Enumerating objects: 7, done.
remote: Counting objects: 100% (7/7), done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 152 (delta 1), reused 4 (delta 1), pack-reused 145
Receiving objects: 100% (152/152), 30.03 KiB | 361.00 KiB/s, done.
Resolving deltas: 100% (82/82), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/snappy'...
remote: Enumerating objects: 963, done.
remote: Total 963 (delta 0), reused 0 (delta 0), pack-reused 963
Receiving objects: 100% (963/963), 2.42 MiB | 3.82 MiB/s, done.
Resolving deltas: 100% (656/656), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sonLib'...
remote: Enumerating objects: 21, done.
remote: Counting objects: 100% (21/21), done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 5101 (delta 3), reused 7 (delta 0), pack-reused 5080
Receiving objects: 100% (5101/5101), 1.57 MiB | 3.15 MiB/s, done.
Resolving deltas: 100% (3280/3280), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sparsehash'...
remote: Enumerating objects: 1404, done.
remote: Total 1404 (delta 0), reused 0 (delta 0), pack-reused 1404
Receiving objects: 100% (1404/1404), 807.81 KiB | 1.93 MiB/s, done.
Resolving deltas: 100% (1002/1002), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sparsepp'...
remote: Enumerating objects: 35, done.
remote: Counting objects: 100% (35/35), done.
remote: Compressing objects: 100% (27/27), done.
remote: Total 686 (delta 15), reused 18 (delta 6), pack-reused 651
Receiving objects: 100% (686/686), 417.52 KiB | 1.36 MiB/s, done.
Resolving deltas: 100% (431/431), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/ssw'...
remote: Enumerating objects: 1567, done.
remote: Total 1567 (delta 0), reused 0 (delta 0), pack-reused 1567
Receiving objects: 100% (1567/1567), 12.17 MiB | 5.38 MiB/s, done.
Resolving deltas: 100% (976/976), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/structures'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 271 (delta 0), reused 0 (delta 0), pack-reused 267
Receiving objects: 100% (271/271), 84.87 KiB | 653.00 KiB/s, done.
Resolving deltas: 100% (146/146), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens'...
remote: Enumerating objects: 1171, done.
remote: Total 1171 (delta 0), reused 0 (delta 0), pack-reused 1171
Receiving objects: 100% (1171/1171), 3.44 MiB | 761.00 KiB/s, done.
Resolving deltas: 100% (897/897), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib'...
remote: Enumerating objects: 32, done.
remote: Counting objects: 100% (32/32), done.
remote: Compressing objects: 100% (26/26), done.
remote: Total 3669 (delta 13), reused 16 (delta 6), pack-reused 3637
Receiving objects: 100% (3669/3669), 27.96 MiB | 6.93 MiB/s, done.
Resolving deltas: 100% (2306/2306), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit'...
remote: Enumerating objects: 11, done.
remote: Counting objects: 100% (11/11), done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 62231 (delta 1), reused 3 (delta 0), pack-reused 62220
Receiving objects: 100% (62231/62231), 124.16 MiB | 6.96 MiB/s, done.
Resolving deltas: 100% (46407/46407), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg'...
remote: Enumerating objects: 6, done.
remote: Counting objects: 100% (6/6), done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 384 (delta 0), reused 2 (delta 0), pack-reused 378
Receiving objects: 100% (384/384), 143.78 KiB | 813.00 KiB/s, done.
Resolving deltas: 100% (204/204), done.
Submodule path 'deps/BBHash': checked out '36e4fe3eaeef762c831c49cdc01f1a3a2c7a97a4'
Submodule path 'deps/DYNAMIC': checked out '0da557fbd0613377bbde26dd60ded655bea58d3b'
Submodule path 'deps/FlameGraph': checked out '1b1c6deede9c33c5134c920bdb7a44cc5528e9a7'
Submodule path 'deps/backward-cpp': checked out '58f21c22d310d1c2078aad1a71254749d6f588df'
Submodule path 'deps/bash-tap': checked out 'c38fbfa401600cc81ccda66bfc0da3ea56288d03'
Submodule path 'deps/boost-subset': checked out '53ee8d82dbd2ae54825b49606d8a24d9d45bb142'
Submodule path 'deps/dozeu': checked out '6740461d9181cd4f4311947dda86ff53289ed3de'
Submodule path 'deps/elfutils': checked out 'd08c68fec94b26663257d24dbb8d94f2ed8935cd'
Submodule path 'deps/fastahack': checked out '8e886558959b4283dde8d31144f277716157884a'
Submodule path 'deps/fermi-lite': checked out 'cde7871d5a6658be61a7c3995a56ac21fbacf4f4'
Submodule path 'deps/gbwt': checked out 'fad85c93b150e385adf5eabb26f851320af49324'
Submodule path 'deps/gbwtgraph': checked out '1de86fbebf55b9a7ca1b05ffeea0b6e1b4301f43'
Submodule path 'deps/gcsa2': checked out 'cdebe96d2fbd88d56eccb5c283272ac7a3853425'
Submodule path 'deps/gfakluge': checked out '2341ed4ed1b0113f45a0aa2a9cfe87cc746e9b44'
Submodule 'GFA-spec' (https://github.com/GFA-spec/GFA-spec) registered for path 'deps/gfakluge/GFA-spec'
Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'deps/gfakluge/bash-tap'
Cloning into '/data3/genome_graphs/vg-rotella/deps/gfakluge/GFA-spec'...
remote: Enumerating objects: 409, done.
remote: Total 409 (delta 0), reused 0 (delta 0), pack-reused 409
Receiving objects: 100% (409/409), 1.10 MiB | 2.31 MiB/s, done.
Resolving deltas: 100% (233/233), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/gfakluge/bash-tap'...
remote: Enumerating objects: 52, done.
remote: Total 52 (delta 0), reused 0 (delta 0), pack-reused 52
Submodule path 'deps/gfakluge/GFA-spec': checked out '4b216c79c91702a96f94c2def6f056fbe496dcbf'
Submodule path 'deps/gfakluge/bash-tap': checked out 'd7db4e882a5bc8b141333a81f9fc640ec0784661'
Submodule path 'deps/gssw': checked out '9f8efbca6dbfa3b7a4e6a65d0ef7cf5009e4aca1'
Submodule path 'deps/htslib': checked out 'fd0f89554459b78c07303e2c8a42acacd6851b46'
Submodule path 'deps/ips4o': checked out '22069381cc1bf2df07ee1ff47f6b6073fcfb4508'
Submodule path 'deps/jemalloc': checked out '40a3435b8dc225ad61329aca89d9c8d0dfbc03ab'
Submodule path 'deps/libVCFH': checked out '615a06b5de21f59294d7d806e9f505162ae8c2c1'
Submodule path 'deps/libbdsg': checked out 'e4efb4bf6131a32395c40c779ae1cfb68c3092d0'
Submodule path 'deps/libdeflate': checked out '2b6689d8aa30175712a1e697adeac884fc3720dc'
Submodule path 'deps/libhandlegraph': checked out '962018b84d8525ca93e79efd5f3726a0683bcfdf'
Submodule path 'deps/libvgio': checked out 'fc9523feb660815b02a932e8e7f58467d462455e'
Submodule path 'deps/lru_cache': checked out '98c5eacfb2bf60debd2f9c3a3faf814e8821458c'
Submodule path 'deps/mmmultimap': checked out '38d5d70f4f9e10aae4548b022c2a7d55024c5e99'
Submodule path 'deps/pinchesAndCacti': checked out '467882b2d7c9a5bba233f4a9ae0d0345ba8f3ba9'
Submodule path 'deps/progress_bar': checked out 'e20ae5296b278bb6afb287a2e078a33c88f1c528'
Submodule path 'deps/raptor': checked out '64188142ab2c1b5459ca93eac9320ff38722bffa'
Submodule path 'deps/rocksdb': checked out 'acef93ed65f0cab701565a5d21edc1dea894130c'
Submodule path 'deps/sdsl-lite': checked out 'ddb0fbbc33bb183baa616f17eb48e261ac2a3672'
Submodule 'external/googletest' (https://github.com/google/googletest.git) registered for path 'deps/sdsl-lite/external/googletest'
Submodule 'external/libdivsufsort' (https://github.com/simongog/libdivsufsort.git) registered for path 'deps/sdsl-lite/external/libdivsufsort'
Cloning into '/data3/genome_graphs/vg-rotella/deps/sdsl-lite/external/googletest'...
remote: Enumerating objects: 34, done.
remote: Counting objects: 100% (34/34), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 19878 (delta 14), reused 18 (delta 4), pack-reused 19844
Receiving objects: 100% (19878/19878), 7.35 MiB | 4.51 MiB/s, done.
Resolving deltas: 100% (14684/14684), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/sdsl-lite/external/libdivsufsort'...
remote: Enumerating objects: 213, done.
remote: Total 213 (delta 0), reused 0 (delta 0), pack-reused 213
Receiving objects: 100% (213/213), 99.34 KiB | 578.00 KiB/s, done.
Resolving deltas: 100% (131/131), done.
Submodule path 'deps/sdsl-lite/external/googletest': checked out 'c2d90bddc6a2a562ee7750c14351e9ca16a6a37a'
Submodule path 'deps/sdsl-lite/external/libdivsufsort': checked out '0f24acd8de208464769c782119dacf158647f7ed'
Submodule path 'deps/sha1': checked out '011accb73af23c2703bd6801cd4285728c264d94'
Submodule path 'deps/snappy': checked out '2b9152d9c5bed71dffb7f7f6c7a3ec48b058ff2d'
Submodule path 'deps/sonLib': checked out '63b0301bce3861f247684c804fd204c452b8faf2'
Submodule path 'deps/sparsehash': checked out 'a61a6ba7adbc4e3a7545843a72c530bf35604dae'
Submodule path 'deps/sparsepp': checked out '7ac6088af04358843bb1816e8be69974d1973a20'
Submodule path 'deps/ssw': checked out 'd27667cbb93bab73de3c31bf0a265fd8e8632e72'
Submodule path 'deps/structures': checked out '70c3e256584a9ab6b8a13a6e57155f48ecaeaa2c'
Submodule path 'deps/sublinear-Li-Stephens': checked out '4efb2f3933ea8c684fe289e8f07f626f0747436e'
Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'deps/sublinear-Li-Stephens/deps/htslib'
Cloning into '/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib'...
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 12963 (delta 0), reused 1 (delta 0), pack-reused 12960
Receiving objects: 100% (12963/12963), 9.57 MiB | 5.33 MiB/s, done.
Resolving deltas: 100% (9302/9302), done.
Submodule path 'deps/sublinear-Li-Stephens/deps/htslib': checked out '6d2bfb7031c3237507815a72e917f1f20bff1288'
Submodule path 'deps/vcflib': checked out '7ae6c38815f46dcbcdd5e9e723e37f487136418e'
Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'deps/vcflib/fastahack'
Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'deps/vcflib/filevercmp'
Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'deps/vcflib/fsom'
Submodule 'googletest' (https://github.com/google/googletest.git) registered for path 'deps/vcflib/googletest'
Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'deps/vcflib/intervaltree'
Submodule 'libVCFH' (https://github.com/edawson/libVCFH.git) registered for path 'deps/vcflib/libVCFH'
Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'deps/vcflib/multichoose'
Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'deps/vcflib/smithwaterman'
Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'deps/vcflib/tabixpp'
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/fastahack'...
remote: Enumerating objects: 227, done.
remote: Total 227 (delta 0), reused 0 (delta 0), pack-reused 227
Receiving objects: 100% (227/227), 51.19 KiB | 419.00 KiB/s, done.
Resolving deltas: 100% (128/128), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/filevercmp'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 30 (delta 0), reused 0 (delta 0), pack-reused 26
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/fsom'...
remote: Enumerating objects: 42, done.
remote: Total 42 (delta 0), reused 0 (delta 0), pack-reused 42
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/googletest'...
remote: Enumerating objects: 34, done.
remote: Counting objects: 100% (34/34), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 19878 (delta 14), reused 18 (delta 4), pack-reused 19844
Receiving objects: 100% (19878/19878), 7.35 MiB | 5.15 MiB/s, done.
Resolving deltas: 100% (14684/14684), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/intervaltree'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 176 (delta 0), reused 0 (delta 0), pack-reused 172
Receiving objects: 100% (176/176), 121.35 KiB | 710.00 KiB/s, done.
Resolving deltas: 100% (97/97), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/libVCFH'...
remote: Enumerating objects: 53, done.
remote: Total 53 (delta 0), reused 0 (delta 0), pack-reused 53
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/multichoose'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 109 (delta 0), reused 0 (delta 0), pack-reused 105
Receiving objects: 100% (109/109), 24.75 KiB | 1.13 MiB/s, done.
Resolving deltas: 100% (54/54), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/smithwaterman'...
remote: Enumerating objects: 312, done.
remote: Total 312 (delta 0), reused 0 (delta 0), pack-reused 312
Receiving objects: 100% (312/312), 90.24 KiB | 210.00 KiB/s, done.
Resolving deltas: 100% (197/197), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'...
remote: Enumerating objects: 10, done.
remote: Counting objects: 100% (10/10), done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 145 (delta 3), reused 3 (delta 1), pack-reused 135
Receiving objects: 100% (145/145), 88.51 KiB | 642.00 KiB/s, done.
Resolving deltas: 100% (56/56), done.
Submodule path 'deps/vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
Submodule path 'deps/vcflib/filevercmp': checked out 'df20dcc4a2a772de56e804e8fbbcdef1ac068bbe'
Submodule path 'deps/vcflib/fsom': checked out 'a6ef318fbd347c53189384aef7f670c0e6ce89a3'
Submodule path 'deps/vcflib/googletest': checked out 'd225acc90bc3a8c420a9bcd1f033033c1ccd7fe0'
Submodule path 'deps/vcflib/intervaltree': checked out 'b90527f9e6d51cd36ecbb50429e4524d3a418ea5'
Submodule path 'deps/vcflib/libVCFH': checked out '615a06b5de21f59294d7d806e9f505162ae8c2c1'
Submodule path 'deps/vcflib/multichoose': checked out 'e1f94aeb5d52542b000287fd8e0204c78906897e'
Submodule path 'deps/vcflib/smithwaterman': checked out '84c08d7eae7211d87fbcb1871dae20e6c2041e96'
Submodule path 'deps/vcflib/tabixpp': checked out 'eaf0dffd383e8620a39eb85e4ab6fd8d78178fd1'
Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'deps/vcflib/tabixpp/htslib'
Cloning into '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp/htslib'...
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 12963 (delta 0), reused 1 (delta 0), pack-reused 12960
Receiving objects: 100% (12963/12963), 9.58 MiB | 3.36 MiB/s, done.
Resolving deltas: 100% (9302/9302), done.
Submodule path 'deps/vcflib/tabixpp/htslib': checked out '746549da5371c7689ebd81f693c9bd10aa984623'
Submodule path 'deps/vowpal_wabbit': checked out '0105bbc11baf24db25490b0a9a808b18a8a846e3'
Submodule path 'deps/xg': checked out '0cf6eaeb563d57d9c08c4934258a09510269edf3'
Submodule 'deps/BBHash' (https://github.com/vgteam/BBHash.git) registered for path 'deps/xg/deps/BBHash'
Submodule 'deps/args' (https://github.com/Taywee/args.git) registered for path 'deps/xg/deps/args'
Submodule 'deps/gfakluge' (https://github.com/vgteam/gfakluge.git) registered for path 'deps/xg/deps/gfakluge'
Submodule 'deps/ips4o' (https://github.com/SaschaWitt/ips4o.git) registered for path 'deps/xg/deps/ips4o'
Submodule 'deps/libhandlegraph' (https://github.com/vgteam/libhandlegraph.git) registered for path 'deps/xg/deps/libhandlegraph'
Submodule 'deps/mmmultimap' (https://github.com/ekg/mmmultimap.git) registered for path 'deps/xg/deps/mmmultimap'
Submodule 'deps/sdsl-lite' (https://github.com/simongog/sdsl-lite.git) registered for path 'deps/xg/deps/sdsl-lite'
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/BBHash'...
remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 523 (delta 0), reused 1 (delta 0), pack-reused 518
Receiving objects: 100% (523/523), 222.76 KiB | 1004.00 KiB/s, done.
Resolving deltas: 100% (303/303), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/args'...
remote: Enumerating objects: 17, done.
remote: Counting objects: 100% (17/17), done.
remote: Compressing objects: 100% (17/17), done.
remote: Total 3901 (delta 8), reused 2 (delta 0), pack-reused 3884
Receiving objects: 100% (3901/3901), 2.16 MiB | 3.48 MiB/s, done.
Resolving deltas: 100% (3323/3323), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/gfakluge'...
remote: Enumerating objects: 1528, done.
remote: Total 1528 (delta 0), reused 0 (delta 0), pack-reused 1528
Receiving objects: 100% (1528/1528), 1.83 MiB | 3.29 MiB/s, done.
Resolving deltas: 100% (995/995), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/ips4o'...
remote: Enumerating objects: 28, done.
remote: Counting objects: 100% (28/28), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 80 (delta 12), reused 21 (delta 8), pack-reused 52
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/libhandlegraph'...
remote: Enumerating objects: 52, done.
remote: Counting objects: 100% (52/52), done.
remote: Compressing objects: 100% (32/32), done.
remote: Total 866 (delta 20), reused 36 (delta 12), pack-reused 814
Receiving objects: 100% (866/866), 138.23 KiB | 760.00 KiB/s, done.
Resolving deltas: 100% (448/448), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/mmmultimap'...
remote: Enumerating objects: 192, done.
remote: Counting objects: 100% (192/192), done.
remote: Compressing objects: 100% (122/122), done.
remote: Total 192 (delta 112), reused 144 (delta 66), pack-reused 0
Receiving objects: 100% (192/192), 41.91 KiB | 650.00 KiB/s, done.
Resolving deltas: 100% (112/112), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/sdsl-lite'...
remote: Enumerating objects: 14003, done.
remote: Total 14003 (delta 0), reused 0 (delta 0), pack-reused 14003
Receiving objects: 100% (14003/14003), 9.30 MiB | 5.36 MiB/s, done.
Resolving deltas: 100% (8148/8148), done.
Submodule path 'deps/xg/deps/BBHash': checked out '36e4fe3eaeef762c831c49cdc01f1a3a2c7a97a4'
Submodule path 'deps/xg/deps/args': checked out '78e27faf75ff7d20f232f11ffcef65cde43c449d'
Submodule path 'deps/xg/deps/gfakluge': checked out 'd65e688b6f2d301ad953da578f3cf35e68feb452'
Submodule 'GFA-spec' (https://github.com/GFA-spec/GFA-spec) registered for path 'deps/xg/deps/gfakluge/GFA-spec'
Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'deps/xg/deps/gfakluge/bash-tap'
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/gfakluge/GFA-spec'...
remote: Enumerating objects: 409, done.
remote: Total 409 (delta 0), reused 0 (delta 0), pack-reused 409
Receiving objects: 100% (409/409), 1.10 MiB | 2.36 MiB/s, done.
Resolving deltas: 100% (233/233), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/gfakluge/bash-tap'...
remote: Enumerating objects: 52, done.
remote: Total 52 (delta 0), reused 0 (delta 0), pack-reused 52
Submodule path 'deps/xg/deps/gfakluge/GFA-spec': checked out '4b216c79c91702a96f94c2def6f056fbe496dcbf'
Submodule path 'deps/xg/deps/gfakluge/bash-tap': checked out 'd7db4e882a5bc8b141333a81f9fc640ec0784661'
Submodule path 'deps/xg/deps/ips4o': checked out '840c0d80cb9c8b5e805f9d5693104bcda3ea5e31'
Submodule path 'deps/xg/deps/libhandlegraph': checked out 'f261c36d0343ca1643bbf4d3ca5ef66a381708ef'
Submodule path 'deps/xg/deps/mmmultimap': checked out '88c734c36563048b0f3acc04dd8856f19e02b75f'
Submodule path 'deps/xg/deps/sdsl-lite': checked out 'c32874cb2d8524119f25f3b501526fe692df29f4'
Submodule 'external/googletest' (https://github.com/google/googletest.git) registered for path 'deps/xg/deps/sdsl-lite/external/googletest'
Submodule 'external/libdivsufsort' (https://github.com/simongog/libdivsufsort.git) registered for path 'deps/xg/deps/sdsl-lite/external/libdivsufsort'
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/sdsl-lite/external/googletest'...
remote: Enumerating objects: 34, done.
remote: Counting objects: 100% (34/34), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 19878 (delta 14), reused 18 (delta 4), pack-reused 19844
Receiving objects: 100% (19878/19878), 7.35 MiB | 5.68 MiB/s, done.
Resolving deltas: 100% (14684/14684), done.
Cloning into '/data3/genome_graphs/vg-rotella/deps/xg/deps/sdsl-lite/external/libdivsufsort'...
remote: Enumerating objects: 213, done.
remote: Total 213 (delta 0), reused 0 (delta 0), pack-reused 213
Receiving objects: 100% (213/213), 99.34 KiB | 605.00 KiB/s, done.
Resolving deltas: 100% (131/131), done.
Submodule path 'deps/xg/deps/sdsl-lite/external/googletest': checked out 'c2d90bddc6a2a562ee7750c14351e9ca16a6a37a'
Submodule path 'deps/xg/deps/sdsl-lite/external/libdivsufsort': checked out '0f24acd8de208464769c782119dacf158647f7ed'
cd vg-rotella
make get-deps
. ./source_me.sh && make
Since I already ran make get-deps there was nothing new to install, so I directly continued with source_me.sh and make.
-> click here for the make output <-
. ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 ./install.sh /data3/genome_graphs/vg-rotella
Library will be installed in '/data3/genome_graphs/vg-rotella'
WARNING: .git/hooks directory does not exists.
The pre-commit hook is not installed.
-- The CXX compiler identification is GNU 5.4.0
-- The C compiler identification is GNU 5.4.0
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Compiler is recent enough to support C++11.
-- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG
-- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success
-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS
-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success
-- Performing Test HAVE_CXA_DEMANGLE
-- Performing Test HAVE_CXA_DEMANGLE - Success
-- Compiler supports DEMANGLE.
-- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE
-- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success
-- Found Git: /usr/bin/miniconda3/bin/git (found version "2.25.0")
git found: /usr/bin/miniconda3/bin/git
CMake Warning (dev) at external/libdivsufsort/CMakeLists.txt:7 (project):
Policy CMP0048 is not set: project() command manages VERSION variables.
Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The following variable(s) would be set to empty:
PROJECT_VERSION
PROJECT_VERSION_MAJOR
PROJECT_VERSION_MINOR
PROJECT_VERSION_PATCH
This warning is for project developers. Use -Wno-dev to suppress it.
-- Performing Test HAVE_GCC_WALL
-- Performing Test HAVE_GCC_WALL - Success
-- Performing Test HAVE_GCC_FOMIT_FRAME_POINTER
-- Performing Test HAVE_GCC_FOMIT_FRAME_POINTER - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Looking for memory.h
-- Looking for memory.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Performing Test HAVE_INLINE
-- Performing Test HAVE_INLINE - Success
-- Performing Test HAVE___INLINE
-- Performing Test HAVE___INLINE - Success
-- Performing Test HAVE___INLINE__
-- Performing Test HAVE___INLINE__ - Success
-- Performing Test HAVE___DECLSPEC_DLLEXPORT_
-- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed
-- Performing Test HAVE___DECLSPEC_DLLIMPORT_
-- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Looking for PRId32
-- Looking for PRId32 - found
-- Check size of int64_t
-- Check size of int64_t - done
-- Looking for PRId64
-- Looking for PRId64 - found
CMake Warning (dev) at external/googletest/googletest/CMakeLists.txt:47 (project):
Policy CMP0048 is not set: project() command manages VERSION variables.
Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The following variable(s) would be set to empty:
PROJECT_VERSION
PROJECT_VERSION_MAJOR
PROJECT_VERSION_MINOR
PROJECT_VERSION_PATCH
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /usr/bin/miniconda3/bin/python (found version "2.7.15")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include cstdio
-- Looking for C++ include cstdio - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
-- Generating done
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-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/lcp_vlc.hpp
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-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/sorted_multi_stack_support.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/sorted_stack_support.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/structure_tree.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/suffix_array_algorithm.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/suffix_array_helper.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/suffix_arrays.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/suffix_tree_algorithm.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/suffix_tree_helper.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/suffix_trees.hpp
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-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/vectors.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/vlc_vector.hpp
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-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/wt_huff.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/wt_hutu.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/wt_int.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/wt_pc.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/sdsl/wt_rlmn.hpp
-- Installing: /data3/genome_graphs/vg-rotella/lib/libsdsl.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sdsl-lite/build'
SUCCESS: sdsl was installed successfully!
The sdsl include files are located in '/data3/genome_graphs/vg-rotella/include'.
The library files are located in '/data3/genome_graphs/vg-rotella/lib'.
Sample programs can be found in the examples-directory.
A program 'example.cpp' can be compiled with the command:
g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
-I/data3/genome_graphs/vg-rotella/include -L/data3/genome_graphs/vg-rotella/lib \
example.cpp -lsdsl -ldivsufsort -ldivsufsort64
Tests in the test-directory
A cheat sheet in the extras/cheatsheet-directory.
Have fun!
. ./source_me.sh && cd deps/ssw/src && make && ar rs /data3/genome_graphs/vg-rotella/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /data3/genome_graphs/vg-rotella/lib
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/ssw/src'
gcc -c -o ssw.o ssw.c -Wall -pipe -O3
gcc -o ssw_test ssw.o main.c -Wall -pipe -O3 -lm -lz
gcc -o example_c ssw.o example.c -Wall -pipe -O3 -lm -lz
g++ -c -o ssw_cpp.o ssw_cpp.cpp -Wall -pipe -O3
g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -Wall -pipe -O3 -lm -lz
gcc -Wall -pipe -O3 -fPIC -shared -o libssw.so ssw.c
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/ssw/src'
ar: creating /data3/genome_graphs/vg-rotella/lib/libssw.a
. ./source_me.sh && cd deps/snappy && ./autogen.sh && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2" ./configure --prefix=/data3/genome_graphs/vg-rotella && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2" make libsnappy.la && cp .libs/libsnappy.a /data3/genome_graphs/vg-rotella/lib/ && cp snappy-c.h snappy-sinksource.h snappy-stubs-public.h snappy.h /data3/genome_graphs/vg-rotella/include/
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:16: installing './compile'
configure.ac:16: installing './config.guess'
configure.ac:16: installing './config.sub'
configure.ac:14: installing './install-sh'
configure.ac:14: installing './missing'
Makefile.am: installing './INSTALL'
/usr/share/automake-1.15/am/ltlibrary.am: warning: 'libsnappy.la': linking libtool libraries using a non-POSIX
/usr/share/automake-1.15/am/ltlibrary.am: archiver requires 'AM_PROG_AR' in 'configure.ac'
Makefile.am:4: while processing Libtool library 'libsnappy.la'
Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
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checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
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checking dependency style of /usr/bin/gcc... gcc3
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checking if /usr/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking dependency style of /usr/bin/g++... gcc3
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking for ld used by /usr/bin/g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/g++ option to produce PIC... -fPIC -DPIC
checking if /usr/bin/g++ PIC flag -fPIC -DPIC works... yes
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checking if /usr/bin/g++ supports -c -o file.o... (cached) yes
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checking dynamic linker characteristics... (cached) GNU/Linux ld.so
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no
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configure: creating ./config.status
config.status: creating Makefile
config.status: creating snappy-stubs-public.h
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/snappy'
/bin/bash ./libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c -o snappy.lo snappy.cc
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c snappy.cc -fPIC -DPIC -o .libs/snappy.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c snappy.cc -o snappy.o >/dev/null 2>&1
mv -f .deps/snappy.Tpo .deps/snappy.Plo
/bin/bash ./libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-sinksource.lo -MD -MP -MF .deps/snappy-sinksource.Tpo -c -o snappy-sinksource.lo snappy-sinksource.cc
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-sinksource.lo -MD -MP -MF .deps/snappy-sinksource.Tpo -c snappy-sinksource.cc -fPIC -DPIC -o .libs/snappy-sinksource.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-sinksource.lo -MD -MP -MF .deps/snappy-sinksource.Tpo -c snappy-sinksource.cc -o snappy-sinksource.o >/dev/null 2>&1
mv -f .deps/snappy-sinksource.Tpo .deps/snappy-sinksource.Plo
/bin/bash ./libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-stubs-internal.lo -MD -MP -MF .deps/snappy-stubs-internal.Tpo -c -o snappy-stubs-internal.lo snappy-stubs-internal.cc
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-stubs-internal.lo -MD -MP -MF .deps/snappy-stubs-internal.Tpo -c snappy-stubs-internal.cc -fPIC -DPIC -o .libs/snappy-stubs-internal.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-stubs-internal.lo -MD -MP -MF .deps/snappy-stubs-internal.Tpo -c snappy-stubs-internal.cc -o snappy-stubs-internal.o >/dev/null 2>&1
mv -f .deps/snappy-stubs-internal.Tpo .deps/snappy-stubs-internal.Plo
/bin/bash ./libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c -o snappy-c.lo snappy-c.cc
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c snappy-c.cc -fPIC -DPIC -o .libs/snappy-c.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c snappy-c.cc -o snappy-c.o >/dev/null 2>&1
mv -f .deps/snappy-c.Tpo .deps/snappy-c.Plo
/bin/bash ./libtool --tag=CXX --mode=link /usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -version-info 4:0:3 -o libsnappy.la -rpath /data3/genome_graphs/vg-rotella/lib snappy.lo snappy-sinksource.lo snappy-stubs-internal.lo snappy-c.lo
libtool: link: /usr/bin/g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o .libs/snappy.o .libs/snappy-sinksource.o .libs/snappy-stubs-internal.o .libs/snappy-c.o -L/data3/genome_graphs/vg-rotella/lib/../lib -L/data3/genome_graphs/vg/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/data3/genome_graphs/vg-rotella/lib -L/data3/genome_graphs/vg/lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -O3 -ggdb -g -msse4.2 -Wl,-soname -Wl,libsnappy.so.1 -o .libs/libsnappy.so.1.3.0
libtool: link: (cd ".libs" && rm -f "libsnappy.so.1" && ln -s "libsnappy.so.1.3.0" "libsnappy.so.1")
libtool: link: (cd ".libs" && rm -f "libsnappy.so" && ln -s "libsnappy.so.1.3.0" "libsnappy.so")
libtool: link: ar cru .libs/libsnappy.a snappy.o snappy-sinksource.o snappy-stubs-internal.o snappy-c.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libsnappy.a
libtool: link: ( cd ".libs" && rm -f "libsnappy.la" && ln -s "../libsnappy.la" "libsnappy.la" )
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/snappy'
. ./source_me.sh && cd deps/rocksdb && PORTABLE=1 DISABLE_JEMALLOC=1 make static_lib && mv librocksdb.a /data3/genome_graphs/vg-rotella/lib/ && cp -r include/* /data3/genome_graphs/vg-rotella/include/
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/rocksdb'
Makefile:155: Warning: /data3/genome_graphs/vg/include/dynamic dont exist
Makefile:155: Warning: /data3/genome_graphs/vg-rotella/include/dynamic dont exist
GEN util/build_version.cc
Makefile:155: Warning: /data3/genome_graphs/vg/include/dynamic dont exist
Makefile:155: Warning: /data3/genome_graphs/vg-rotella/include/dynamic dont exist
GEN util/build_version.cc
CC cache/clock_cache.o
CC cache/lru_cache.o
CC cache/sharded_cache.o
CC db/builder.o
CC db/c.o
CC db/column_family.o
CC db/compacted_db_impl.o
CC db/compaction.o
CC db/compaction_iterator.o
CC db/compaction_job.o
CC db/compaction_picker.o
CC db/compaction_picker_universal.o
CC db/convenience.o
CC db/db_filesnapshot.o
CC db/db_impl.o
CC db/db_impl_write.o
CC db/db_impl_compaction_flush.o
CC db/db_impl_files.o
CC db/db_impl_open.o
CC db/db_impl_debug.o
CC db/db_impl_experimental.o
CC db/db_impl_readonly.o
CC db/db_info_dumper.o
CC db/db_iter.o
CC db/dbformat.o
CC db/event_helpers.o
CC db/experimental.o
CC db/external_sst_file_ingestion_job.o
CC db/file_indexer.o
CC db/flush_job.o
CC db/flush_scheduler.o
CC db/forward_iterator.o
CC db/internal_stats.o
CC db/log_reader.o
CC db/log_writer.o
CC db/malloc_stats.o
CC db/managed_iterator.o
CC db/memtable.o
CC db/memtable_list.o
CC db/merge_helper.o
CC db/merge_operator.o
CC db/range_del_aggregator.o
CC db/repair.o
CC db/snapshot_impl.o
CC db/table_cache.o
CC db/table_properties_collector.o
CC db/transaction_log_impl.o
CC db/version_builder.o
CC db/version_edit.o
CC db/version_set.o
CC db/wal_manager.o
CC db/write_batch.o
CC db/write_batch_base.o
CC db/write_controller.o
CC db/write_thread.o
CC env/env.o
CC env/env_chroot.o
CC env/env_encryption.o
CC env/env_hdfs.o
CC env/env_posix.o
CC env/io_posix.o
CC env/mock_env.o
CC memtable/alloc_tracker.o
CC memtable/hash_cuckoo_rep.o
CC memtable/hash_linklist_rep.o
CC memtable/hash_skiplist_rep.o
CC memtable/skiplistrep.o
CC memtable/vectorrep.o
CC memtable/write_buffer_manager.o
CC monitoring/histogram.o
CC monitoring/histogram_windowing.o
CC monitoring/instrumented_mutex.o
CC monitoring/iostats_context.o
CC monitoring/perf_context.o
CC monitoring/perf_level.o
CC monitoring/statistics.o
CC monitoring/thread_status_impl.o
CC monitoring/thread_status_updater.o
CC monitoring/thread_status_updater_debug.o
CC monitoring/thread_status_util.o
CC monitoring/thread_status_util_debug.o
CC options/cf_options.o
CC options/db_options.o
CC options/options.o
CC options/options_helper.o
CC options/options_parser.o
CC options/options_sanity_check.o
CC port/port_posix.o
CC port/stack_trace.o
CC table/adaptive_table_factory.o
CC table/block.o
CC table/block_based_filter_block.o
CC table/block_based_table_builder.o
CC table/block_based_table_factory.o
CC table/block_based_table_reader.o
CC table/block_builder.o
CC table/block_prefix_index.o
CC table/bloom_block.o
CC table/cuckoo_table_builder.o
CC table/cuckoo_table_factory.o
CC table/cuckoo_table_reader.o
CC table/flush_block_policy.o
CC table/format.o
CC table/full_filter_block.o
CC table/get_context.o
CC table/index_builder.o
CC table/iterator.o
CC table/merging_iterator.o
CC table/meta_blocks.o
CC table/partitioned_filter_block.o
CC table/persistent_cache_helper.o
CC table/plain_table_builder.o
CC table/plain_table_factory.o
CC table/plain_table_index.o
CC table/plain_table_key_coding.o
CC table/plain_table_reader.o
CC table/sst_file_writer.o
CC table/table_properties.o
CC table/two_level_iterator.o
CC tools/dump/db_dump_tool.o
CC util/arena.o
CC util/auto_roll_logger.o
CC util/bloom.o
CC util/build_version.o
CC util/coding.o
CC util/compaction_job_stats_impl.o
CC util/comparator.o
CC util/concurrent_arena.o
CC util/crc32c.o
CC util/delete_scheduler.o
CC util/dynamic_bloom.o
CC util/event_logger.o
CC util/file_reader_writer.o
CC util/file_util.o
CC util/filename.o
CC util/filter_policy.o
CC util/hash.o
CC util/log_buffer.o
CC util/murmurhash.o
CC util/random.o
CC util/rate_limiter.o
CC util/slice.o
CC util/sst_file_manager_impl.o
CC util/status.o
CC util/status_message.o
CC util/string_util.o
CC util/sync_point.o
CC util/thread_local.o
CC util/threadpool_imp.o
CC util/transaction_test_util.o
CC util/xxhash.o
CC utilities/backupable/backupable_db.o
CC utilities/blob_db/blob_db.o
CC utilities/blob_db/blob_db_impl.o
CC utilities/blob_db/blob_db_options_impl.o
CC utilities/blob_db/blob_file.o
CC utilities/blob_db/blob_log_reader.o
CC utilities/blob_db/blob_log_writer.o
CC utilities/blob_db/blob_log_format.o
CC utilities/blob_db/ttl_extractor.o
CC utilities/checkpoint/checkpoint_impl.o
CC utilities/compaction_filters/remove_emptyvalue_compactionfilter.o
CC utilities/convenience/info_log_finder.o
CC utilities/date_tiered/date_tiered_db_impl.o
CC utilities/debug.o
CC utilities/document/document_db.o
CC utilities/document/json_document.o
CC utilities/document/json_document_builder.o
CC utilities/env_mirror.o
CC utilities/env_timed.o
CC utilities/geodb/geodb_impl.o
CC utilities/leveldb_options/leveldb_options.o
CC utilities/lua/rocks_lua_compaction_filter.o
CC utilities/memory/memory_util.o
CC utilities/merge_operators/cassandra/format.o
CC utilities/merge_operators/cassandra/merge_operator.o
CC utilities/merge_operators/max.o
CC utilities/merge_operators/put.o
CC utilities/merge_operators/string_append/stringappend.o
CC utilities/merge_operators/string_append/stringappend2.o
CC utilities/merge_operators/uint64add.o
CC utilities/option_change_migration/option_change_migration.o
CC utilities/options/options_util.o
CC utilities/persistent_cache/block_cache_tier.o
CC utilities/persistent_cache/block_cache_tier_file.o
CC utilities/persistent_cache/block_cache_tier_metadata.o
CC utilities/persistent_cache/persistent_cache_tier.o
CC utilities/persistent_cache/volatile_tier_impl.o
CC utilities/redis/redis_lists.o
CC utilities/simulator_cache/sim_cache.o
CC utilities/spatialdb/spatial_db.o
CC utilities/table_properties_collectors/compact_on_deletion_collector.o
CC utilities/transactions/optimistic_transaction_db_impl.o
CC utilities/transactions/optimistic_transaction_impl.o
CC utilities/transactions/transaction_base.o
CC utilities/transactions/transaction_db_impl.o
CC utilities/transactions/transaction_db_mutex_impl.o
CC utilities/transactions/transaction_impl.o
CC utilities/transactions/transaction_lock_mgr.o
CC utilities/transactions/transaction_util.o
CC utilities/ttl/db_ttl_impl.o
CC utilities/write_batch_with_index/write_batch_with_index.o
CC utilities/write_batch_with_index/write_batch_with_index_internal.o
CC tools/ldb_cmd.o
CC tools/ldb_tool.o
CC tools/sst_dump_tool.o
CC utilities/blob_db/blob_dump_tool.o
AR librocksdb.a
ar: creating librocksdb.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/rocksdb'
. ./source_me.sh && cp -r deps/gcsa2/include/gcsa /data3/genome_graphs/vg-rotella/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /data3/genome_graphs/vg-rotella/lib
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/gcsa2'
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c algorithms.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c dbg.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c files.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c gcsa.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c internal.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c lcp.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c path_graph.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c support.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c utils.cpp
ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/gcsa2'
. ./source_me.sh && cp -r deps/gbwt/include/gbwt /data3/genome_graphs/vg-rotella/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /data3/genome_graphs/vg-rotella/lib
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/gbwt'
rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq utils.o build_gbwt.o variants.o algorithms.o dynamic_gbwt.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o benchmark.o gbwt.o bwtmerge.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/gbwt'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/gbwt'
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c algorithms.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c bwtmerge.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c cached_gbwt.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c dynamic_gbwt.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c files.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c gbwt.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c internal.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c metadata.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c support.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c utils.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c variants.cpp
ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o files.o gbwt.o internal.o metadata.o support.o utils.o variants.o
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c build_gbwt.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -o build_gbwt build_gbwt.o libgbwt.a -L/data3/genome_graphs/vg-rotella/lib -lsdsl -ldivsufsort -ldivsufsort64
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c merge_gbwt.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/data3/genome_graphs/vg-rotella/lib -lsdsl -ldivsufsort -ldivsufsort64
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c benchmark.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -o benchmark benchmark.o libgbwt.a -L/data3/genome_graphs/vg-rotella/lib -lsdsl -ldivsufsort -ldivsufsort64
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c metadata_tool.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -o metadata_tool metadata_tool.o libgbwt.a -L/data3/genome_graphs/vg-rotella/lib -lsdsl -ldivsufsort -ldivsufsort64
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c remove_seq.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -o remove_seq remove_seq.o libgbwt.a -L/data3/genome_graphs/vg-rotella/lib -lsdsl -ldivsufsort -ldivsufsort64
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/gbwt'
. ./source_me.sh && cd deps/libhandlegraph && cmake . && make && cp libhandlegraph.a /data3/genome_graphs/vg-rotella/lib && cp -r src/include/handlegraph /data3/genome_graphs/vg-rotella/include
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/libhandlegraph
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
Scanning dependencies of target handlegraph_objs
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
[ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
[ 33%] Built target handlegraph_objs
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
Scanning dependencies of target handlegraph_static
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
[ 66%] Linking CXX static library libhandlegraph.a
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
[ 66%] Built target handlegraph_static
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
Scanning dependencies of target handlegraph_shared
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
[100%] Linking CXX shared library libhandlegraph.so
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
[100%] Built target handlegraph_shared
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libhandlegraph'
. ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /data3/genome_graphs/vg-rotella/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /data3/genome_graphs/vg-rotella/lib
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/gbwtgraph'
rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/gbwtgraph'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/gbwtgraph'
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c gbwtgraph.cpp
In file included from /usr/include/arpa/inet.h:22:0,
from /data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/utils.h:5,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/gbwtgraph.h:9,
from gbwtgraph.cpp:1:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp: In member function ‘void handlegraph::SerializableHandleGraph::deserialize(std::istream&)’:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:70:60: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
uint32_t magic_number = ntohl(*((uint32_t*) magic_bytes));
^
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c gfa.cpp
In file included from /usr/include/arpa/inet.h:22:0,
from /data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/utils.h:5,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/gfa.h:8,
from gfa.cpp:1:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp: In member function ‘void handlegraph::SerializableHandleGraph::deserialize(std::istream&)’:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:70:60: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
uint32_t magic_number = ntohl(*((uint32_t*) magic_bytes));
^
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c minimizer.cpp
In file included from /usr/include/arpa/inet.h:22:0,
from /data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/utils.h:5,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/minimizer.h:15,
from minimizer.cpp:1:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp: In member function ‘void handlegraph::SerializableHandleGraph::deserialize(std::istream&)’:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:70:60: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
uint32_t magic_number = ntohl(*((uint32_t*) magic_bytes));
^
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c path_cover.cpp
In file included from /usr/include/arpa/inet.h:22:0,
from /data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/utils.h:5,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/gbwtgraph.h:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/path_cover.h:6,
from path_cover.cpp:1:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp: In member function ‘void handlegraph::SerializableHandleGraph::deserialize(std::istream&)’:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:70:60: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
uint32_t magic_number = ntohl(*((uint32_t*) magic_bytes));
^
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c utils.cpp
In file included from /usr/include/arpa/inet.h:22:0,
from /data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/utils.h:5,
from utils.cpp:1:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp: In member function ‘void handlegraph::SerializableHandleGraph::deserialize(std::istream&)’:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:70:60: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
uint32_t magic_number = ntohl(*((uint32_t*) magic_bytes));
^
ar rcs libgbwtgraph.a gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -c gfa2gbwt.cpp
In file included from /usr/include/arpa/inet.h:22:0,
from /data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:9,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/utils.h:5,
from /data3/genome_graphs/vg-rotella/include/gbwtgraph/gbwtgraph.h:9,
from gfa2gbwt.cpp:6:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp: In member function ‘void handlegraph::SerializableHandleGraph::deserialize(std::istream&)’:
/data3/genome_graphs/vg-rotella/include/handlegraph/serializable_handle_graph.hpp:70:60: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
uint32_t magic_number = ntohl(*((uint32_t*) magic_bytes));
^
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg-rotella/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/data3/genome_graphs/vg-rotella/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/gbwtgraph'
. ./source_me.sh && cd deps/libdeflate && V=1 make && cp libdeflate.a /data3/genome_graphs/vg-rotella/lib && cp libdeflate.h /data3/genome_graphs/vg-rotella/include
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libdeflate'
/usr/bin/gcc -o lib/aligned_malloc.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/aligned_malloc.c
/usr/bin/gcc -o lib/deflate_decompress.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/deflate_decompress.c
/usr/bin/gcc -o lib/arm/cpu_features.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/arm/cpu_features.c
/usr/bin/gcc -o lib/x86/cpu_features.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/x86/cpu_features.c
/usr/bin/gcc -o lib/deflate_compress.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/deflate_compress.c
/usr/bin/gcc -o lib/adler32.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/adler32.c
/usr/bin/gcc -o lib/zlib_decompress.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/zlib_decompress.c
/usr/bin/gcc -o lib/zlib_compress.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/zlib_compress.c
/usr/bin/gcc -o lib/crc32.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/crc32.c
/usr/bin/gcc -o lib/gzip_decompress.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/gzip_decompress.c
/usr/bin/gcc -o lib/gzip_compress.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE lib/gzip_compress.c
ar cr libdeflate.a lib/aligned_malloc.o lib/deflate_decompress.o lib/arm/cpu_features.o lib/x86/cpu_features.o lib/deflate_compress.o lib/adler32.o lib/zlib_decompress.o lib/zlib_compress.o lib/crc32.o lib/gzip_decompress.o lib/gzip_compress.o
/usr/bin/gcc -o lib/aligned_malloc.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/aligned_malloc.c
/usr/bin/gcc -o lib/deflate_decompress.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/deflate_decompress.c
/usr/bin/gcc -o lib/arm/cpu_features.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/arm/cpu_features.c
/usr/bin/gcc -o lib/x86/cpu_features.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/x86/cpu_features.c
/usr/bin/gcc -o lib/deflate_compress.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/deflate_compress.c
/usr/bin/gcc -o lib/adler32.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/adler32.c
/usr/bin/gcc -o lib/zlib_decompress.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/zlib_decompress.c
/usr/bin/gcc -o lib/zlib_compress.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/zlib_compress.c
/usr/bin/gcc -o lib/crc32.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/crc32.c
/usr/bin/gcc -o lib/gzip_decompress.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/gzip_decompress.c
/usr/bin/gcc -o lib/gzip_compress.shlib.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -fPIC -DLIBDEFLATE_DLL lib/gzip_compress.c
/usr/bin/gcc -o libdeflate.so -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -fvisibility=hidden -D_ANSI_SOURCE -shared lib/aligned_malloc.shlib.o lib/deflate_decompress.shlib.o lib/arm/cpu_features.shlib.o lib/x86/cpu_features.shlib.o lib/deflate_compress.shlib.o lib/adler32.shlib.o lib/zlib_decompress.shlib.o lib/zlib_compress.shlib.o lib/crc32.shlib.o lib/gzip_decompress.shlib.o lib/gzip_compress.shlib.o
CC="/usr/bin/gcc" CFLAGS=" -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H" programs/detect.sh > programs/config.h
/usr/bin/gcc -o programs/gzip.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/gzip.c
/usr/bin/gcc -o programs/prog_util.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/prog_util.c
/usr/bin/gcc -o programs/tgetopt.o -c -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/tgetopt.c
/usr/bin/gcc -o gzip -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O2 -fomit-frame-pointer -std=c99 -I. -Icommon -Wall -Wundef -Wpedantic -Wdeclaration-after-statement -Wmissing-prototypes -Wstrict-prototypes -Wvla -D_POSIX_C_SOURCE=200809L -D_FILE_OFFSET_BITS=64 -DHAVE_CONFIG_H programs/gzip.o programs/prog_util.o programs/tgetopt.o libdeflate.a
ln -f gzip gunzip
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libdeflate'
cd deps/libdeflate && cp libdeflate.so /data3/genome_graphs/vg-rotella/lib
touch /data3/genome_graphs/vg-rotella/lib/libdeflate.so
. ./source_me.sh && cd deps/htslib && rm -Rf /data3/genome_graphs/vg-rotella/include/htslib /data3/genome_graphs/vg-rotella/lib/libhts* && autoheader && autoconf && CFLAGS="-I/data3/genome_graphs/vg-rotella/include" LDFLAGS="-L/data3/genome_graphs/vg-rotella/lib" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=/data3/genome_graphs/vg-rotella && make clean && make && make install
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/htslib'
rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f hts-object-files
rm -f libhts.so libhts.so.*
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/sam test/test_bgzf test/test_kstring test/test_realn test/test-regidx test/test_str2int test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/htslib'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/htslib'
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o kfunc.o kfunc.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o knetfile.o knetfile.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o kstring.o kstring.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o bgzf.o bgzf.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o errmod.o errmod.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o faidx.o faidx.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o header.o header.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o hfile.o hfile.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION_TEXT "1.10.2"' > version.h
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o hts.o hts.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o hts_os.o hts_os.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o md5.o md5.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o multipart.o multipart.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o probaln.o probaln.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o realn.o realn.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o regidx.o regidx.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o region.o region.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o sam.o sam.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o tbx.o tbx.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o textutils.o textutils.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o vcf.o vcf.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/rANS_static.o cram/rANS_static.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o
ranlib libhts.a
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o knetfile.pico knetfile.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o header.pico header.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o hfile_net.pico hfile_net.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o region.pico region.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
/usr/bin/gcc -shared -Wl,-soname,libhts.so.3 -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico -ldeflate -llzma -lbz2 -lz -lm -lpthread
ln -sf libhts.so libhts.so.3
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o bgzip.o bgzip.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o htsfile.o htsfile.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o tabix.o tabix.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/sam.o test/sam.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test_str2int test/test_str2int.o
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lpthread
/usr/bin/gcc -Wall -I/data3/genome_graphs/vg-rotella/include -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
/usr/bin/gcc -L/data3/genome_graphs/vg-rotella/lib -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lpthread
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/htslib'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/htslib'
mkdir -p -m 755 /data3/genome_graphs/vg-rotella/bin /data3/genome_graphs/vg-rotella/include /data3/genome_graphs/vg-rotella/include/htslib /data3/genome_graphs/vg-rotella/lib /data3/genome_graphs/vg-rotella/share/man/man1 /data3/genome_graphs/vg-rotella/share/man/man5 /data3/genome_graphs/vg-rotella/share/man/man7 /data3/genome_graphs/vg-rotella/lib/pkgconfig
if test -n ""; then mkdir -p -m 755 ; fi
install -p -m 644 libhts.so /data3/genome_graphs/vg-rotella/lib/libhts.so.1.10.2
ln -sf libhts.so.1.10.2 /data3/genome_graphs/vg-rotella/lib/libhts.so
ln -sf libhts.so.1.10.2 /data3/genome_graphs/vg-rotella/lib/libhts.so.3
sed -e 's#@-includedir@#/data3/genome_graphs/vg-rotella/include#g;s#@-libdir@#/data3/genome_graphs/vg-rotella/lib#g;s#@-PACKAGE_VERSION@#1.10.2#g' htslib.pc.tmp > /data3/genome_graphs/vg-rotella/lib/pkgconfig/htslib.pc
chmod 644 /data3/genome_graphs/vg-rotella/lib/pkgconfig/htslib.pc
install -p bgzip htsfile tabix /data3/genome_graphs/vg-rotella/bin
if test -n ""; then install -p ; fi
install -p -m 644 htslib/*.h /data3/genome_graphs/vg-rotella/include/htslib
install -p -m 644 libhts.a /data3/genome_graphs/vg-rotella/lib/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /data3/genome_graphs/vg-rotella/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /data3/genome_graphs/vg-rotella/share/man/man5
install -p -m 644 htslib-s3-plugin.7 /data3/genome_graphs/vg-rotella/share/man/man7
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/htslib'
. ./source_me.sh && cd deps/vcflib && make clean && HTS_LIB="/data3/genome_graphs/vg-rotella/lib/libhts.a" HTS_INCLUDES="-I/data3/genome_graphs/vg-rotella/include" HTS_LDFLAGS="-L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz" make libvcflib.a && cp lib/* /data3/genome_graphs/vg-rotella/lib/ && cp include/* /data3/genome_graphs/vg-rotella/include/ && cp intervaltree/*.h /data3/genome_graphs/vg-rotella/include/ && cp src/*.h* /data3/genome_graphs/vg-rotella/include/
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib'
rm -f bin/vcfecho bin/vcfnormalizesvs bin/dumpContigsFromHeader bin/bFst bin/pVst bin/hapLrt bin/popStats bin/wcFst bin/iHS bin/segmentFst bin/segmentIhs bin/genotypeSummary bin/sequenceDiversity bin/pFst bin/smoother bin/vcfld bin/plotHaps bin/abba-baba bin/permuteGPAT++ bin/permuteSmooth bin/normalize-iHS bin/meltEHH bin/vcfaltcount bin/vcfhetcount bin/vcfhethomratio bin/vcffilter bin/vcf2tsv bin/vcfgenotypes bin/vcfannotategenotypes bin/vcfcommonsamples bin/vcfremovesamples bin/vcfkeepsamples bin/vcfsamplenames bin/vcfgenotypecompare bin/vcffixup bin/vcfclassify bin/vcfsamplediff bin/vcfremoveaberrantgenotypes bin/vcfrandom bin/vcfparsealts bin/vcfstats bin/vcfflatten bin/vcfprimers bin/vcfnumalt bin/vcfcleancomplex bin/vcfintersect bin/vcfannotate bin/vcfallelicprimitives bin/vcfoverlay bin/vcfaddinfo bin/vcfkeepinfo bin/vcfkeepgeno bin/vcfafpath bin/vcfcountalleles bin/vcflength bin/vcfdistance bin/vcfrandomsample bin/vcfentropy bin/vcfglxgt bin/vcfroc bin/vcfcheck bin/vcfstreamsort bin/vcfuniq bin/vcfuniqalleles bin/vcfremap bin/vcf2fasta bin/vcfsitesummarize bin/vcfbreakmulti bin/vcfcreatemulti bin/vcfevenregions bin/vcfcat bin/vcfgenosummarize bin/vcfgenosamplenames bin/vcfgeno2haplo bin/vcfleftalign bin/vcfcombine bin/vcfgeno2alleles bin/vcfindex bin/vcf2dag bin/vcfsample2info bin/vcfqual2info bin/vcfinfo2qual bin/vcfglbound bin/vcfunphase bin/vcfnull2ref bin/vcfinfosummarize src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o
rm -f ssw_cpp.o ssw.o
rm -f libvcflib.a
rm -f -r bin
rm -f -r lib
rm -f -r include
rm -f -r obj
make clean -C tabixpp
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
rm -fr gmon.out *.o a.out *.dSYM tabix++ *~ *.a tabix.aux tabix.log \
tabix.pdf *.class libtabix.*.dylib libtabix.so*
cd htslib && make clean
make[4]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp/htslib'
rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.so libhts.so.*
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/sam test/test_bgzf test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/test-bcf-translate test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6
make[4]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp/htslib'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
make clean -C smithwaterman
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/smithwaterman'
Cleaning up.
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/smithwaterman'
make clean -C fastahack
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/fastahack'
rm -f fastahack *.o
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/fastahack'
make clean -C multichoose
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/multichoose'
rm -f cmultichoose
rm -f multichoose
rm -f multipermute
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/multichoose'
make clean -C fsom
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/fsom'
rm -f *.o fsom
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/fsom'
make clean -C libVCFH
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/libVCFH'
rm -f -f *.o
rm -f -f example.exe
rm -f -f *.a
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/libVCFH'
make clean -C test
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/test'
rm -f tests/main
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/test'
make clean -C filevercmp
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/filevercmp'
rm -f filevercmp main.o filevercmp.o
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/filevercmp'
make clean -C intervaltree
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/intervaltree'
rm -rf interval_tree_test stage
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/intervaltree'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib'
if [ ! -d bin ]; then mkdir -p bin; fi
if [ ! -d lib ]; then mkdir -p lib; fi
if [ ! -d include ]; then mkdir -p include; fi
if [ ! -d obj ]; then mkdir -p obj; fi
cd tabixpp && INCLUDES="-I/data3/genome_graphs/vg-rotella/include" LIBPATH="-L. -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz" HTSLIB="/data3/genome_graphs/vg-rotella/lib/libhts.a" make && cp -f *.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c tabix.cpp -I/data3/genome_graphs/vg-rotella/include
tabix.cpp: In constructor ‘Tabix::Tabix(std::__cxx11::string&)’:
tabix.cpp:15:10: warning: ‘int bgzf_is_bgzf(const char*)’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if ( bgzf_is_bgzf(cfilename)!=1 )
^
In file included from tabix.hpp:4:0,
from tabix.cpp:1:
/data3/genome_graphs/vg-rotella/include/htslib/bgzf.h:264:9: note: declared here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^
tabix.cpp:15:10: warning: ‘int bgzf_is_bgzf(const char*)’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if ( bgzf_is_bgzf(cfilename)!=1 )
^
In file included from tabix.hpp:4:0,
from tabix.cpp:1:
/data3/genome_graphs/vg-rotella/include/htslib/bgzf.h:264:9: note: declared here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^
tabix.cpp:15:32: warning: ‘int bgzf_is_bgzf(const char*)’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if ( bgzf_is_bgzf(cfilename)!=1 )
^
In file included from tabix.hpp:4:0,
from tabix.cpp:1:
/data3/genome_graphs/vg-rotella/include/htslib/bgzf.h:264:9: note: declared here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -o tabix++ main.cpp tabix.o -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lhts -lpthread -lm -lbz2 -llzma -lz
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/tabixpp'
cd multichoose && make && cp -f *.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/multichoose'
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x multichoose.cpp -o multichoose
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x multipermute.cpp -o multipermute
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/multichoose'
cd smithwaterman && make && cp -f *.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/ && cp -f *.o /data3/genome_graphs/vg-rotella/deps/vcflib/obj/
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/smithwaterman'
/usr/bin/g++ -O3 -c -o disorder.o disorder.cpp -I.
/usr/bin/g++ -O3 -c -o smithwaterman.o smithwaterman.cpp -I.
/usr/bin/g++ -O3 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I.
/usr/bin/g++ -O3 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I.
/usr/bin/g++ -O3 -c -o LeftAlign.o LeftAlign.cpp -I.
/usr/bin/g++ -O3 -c -o Repeats.o Repeats.cpp -I.
/usr/bin/g++ -O3 -c -o IndelAllele.o IndelAllele.cpp -I.
/usr/bin/g++ -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman
ld -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L.
#/usr/bin/g++ -O3 -c -o smithwaterman.cpp disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -I.
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/smithwaterman'
cd filevercmp && make && cp -f *.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/ && cp -f *.o /data3/genome_graphs/vg-rotella/deps/vcflib/include/
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/filevercmp'
/usr/bin/gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c main.c
/usr/bin/gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c filevercmp.c
/usr/bin/gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -o filevercmp main.o filevercmp.o
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/filevercmp'
cd fastahack && make && cp -f *.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/ && cp -f Fasta.o /data3/genome_graphs/vg-rotella/deps/vcflib/obj/
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vcflib/fastahack'
g++ -O3 -D_FILE_OFFSET_BITS=64 -c Fasta.cpp
Fasta.cpp: In member function ‘std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)’:
Fasta.cpp:254:43: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(seq, sizeof(char), seqlen, file);
^
Fasta.cpp: In member function ‘std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)’:
Fasta.cpp:301:51: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(seq, sizeof(char), (off_t) seqlen, file);
^
g++ -O3 -D_FILE_OFFSET_BITS=64 -c split.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -c disorder.c
g++ -O3 -D_FILE_OFFSET_BITS=64 Fasta.o FastaHack.cpp split.o disorder.o -o fastahack
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib/fastahack'
/usr/bin/g++ -c -o src/Variant.o src/Variant.cpp -I/data3/genome_graphs/vg-rotella/include -Iinclude -Llib -lvcflib -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lpthread -lz -lm -llzma -lbz2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x && cp -f src/*.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
/usr/bin/g++ -c -o src/rnglib.o src/rnglib.cpp -I/data3/genome_graphs/vg-rotella/include -Iinclude -Llib -lvcflib -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lpthread -lz -lm -llzma -lbz2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x && cp -f src/*.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
/usr/bin/g++ -c -o src/var.o src/var.cpp -I/data3/genome_graphs/vg-rotella/include -Iinclude -Llib -lvcflib -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lpthread -lz -lm -llzma -lbz2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x && cp -f src/*.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
/usr/bin/g++ -c -o src/pdflib.o src/pdflib.cpp -I/data3/genome_graphs/vg-rotella/include -Iinclude -Llib -lvcflib -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lpthread -lz -lm -llzma -lbz2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x && cp -f src/*.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
/usr/bin/g++ -c -o src/cdflib.o src/cdflib.cpp -I/data3/genome_graphs/vg-rotella/include -Iinclude -Llib -lvcflib -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lpthread -lz -lm -llzma -lbz2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x && cp -f src/*.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
/usr/bin/g++ -c -o src/split.o src/split.cpp -I/data3/genome_graphs/vg-rotella/include -Iinclude -Llib -lvcflib -L/data3/genome_graphs/vg-rotella/lib -Wl,-Bstatic -lhts -ldeflate -Wl,-Bdynamic -lpthread -lm -lbz2 -llzma -lz -lpthread -lz -lm -llzma -lbz2 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x && cp -f src/*.h* /data3/genome_graphs/vg-rotella/deps/vcflib/include/
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o smithwaterman/disorder.o smithwaterman/disorder.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw.o src/ssw.cpp
/usr/bin/g++ -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -c -o src/ssw_cpp.o src/ssw_cpp.cpp
ar rs libvcflib.a src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o smithwaterman/sw.o fastahack/Fasta.o src/ssw.o src/ssw_cpp.o filevercmp/filevercmp.o tabixpp/tabix.o
ar: creating libvcflib.a
cp -f libvcflib.a lib
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vcflib'
. ./source_me.sh && cd deps/gssw && make && cp lib/* /data3/genome_graphs/vg-rotella/lib/ && cp obj/* /data3/genome_graphs/vg-rotella/obj && cp src/*.h /data3/genome_graphs/vg-rotella/include
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/gssw'
gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -Wall -O3 -msse4 -g -c -o obj/gssw.o src/gssw.c
# Make dest directory
gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -Wall -O3 -msse4 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz
gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -Wall -O3 -msse4 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz
gcc -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -Wall -O3 -msse4 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz
ar rvs lib/libgssw.a obj/gssw.o
ar: creating lib/libgssw.a
a - obj/gssw.o
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/gssw'
. ./source_me.sh && cd ./deps/libVCFH && make && cp libvcfh.a /data3/genome_graphs/vg-rotella/lib/ && cp vcfheader.hpp /data3/genome_graphs/vg-rotella/include/
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libVCFH'
g++ -O3 -std=c++11 -c -o vcfheader.o vcfheader.cpp -I./ -L./
ar -rs libvcfh.a vcfheader.o
ar: creating libvcfh.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libVCFH'
. ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /data3/genome_graphs/vg-rotella/lib/libsonlib.a && mkdir -p /data3/genome_graphs/vg-rotella/include/sonLib && cp lib/*.h /data3/genome_graphs/vg-rotella/include/sonLib
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sonLib'
cd externalTools && make all
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sonLib/externalTools'
cd cutest && make all
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sonLib/externalTools/cutest'
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c
ar rc cuTest.a *.o
ranlib cuTest.a
rm -f *.o
mv cuTest.a ../../lib/
cp CuTest.h ../../lib/
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sonLib/externalTools/cutest'
cd quicktree_1.1 && make all CC="/usr/bin/gcc -std=c99"
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sonLib/externalTools/quicktree_1.1'
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/align.o ./src/align.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/cluster.o ./src/cluster.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/distancemat.o ./src/distancemat.c
./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’:
./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%s", identifier );
^
./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%lf", &dist);
^
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/options.o ./src/options.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/util.o ./src/util.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/sequence.o ./src/sequence.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/quicktree.o ./src/quicktree.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/buildtree.o ./src/buildtree.c
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -c -I./include -O3 -Wall -o ./obj/tree.o ./src/tree.c
./src/tree.c: In function ‘read_newhampshire_Tnode’:
./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c);
^
./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c); /* should be , */
^
./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c); /* should be ) */
^
./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c); /* should be : */
^
./src/tree.c: In function ‘read_newhampshire_Tree’:
./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "(");
^
./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c ); /* should be , */
^
./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c ); /* should be , */
^
./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c);
^
./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf( handle, "%1s", &c);
^
/usr/bin/gcc -std=c99 -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sonLib/externalTools/quicktree_1.1'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sonLib/externalTools'
cd C && make all
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sonLib/C'
cp inc/stGraph.h ../lib/stGraph.h.tmp
mv ../lib/stGraph.h.tmp ../lib/stGraph.h
cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp
mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h
cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp
mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h
cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp
mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h
cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp
mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h
cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp
mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h
cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp
mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h
cp inc/stJson.h ../lib/stJson.h.tmp
mv ../lib/stJson.h.tmp ../lib/stJson.h
cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp
mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h
cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp
mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h
cp inc/bioioC.h ../lib/bioioC.h.tmp
mv ../lib/bioioC.h.tmp ../lib/bioioC.h
cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp
mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h
cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp
mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h
cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp
mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h
cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp
mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h
cp inc/commonC.h ../lib/commonC.h.tmp
mv ../lib/commonC.h.tmp ../lib/commonC.h
cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp
mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h
cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp
mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h
cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp
mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h
cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp
mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h
cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp
mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h
cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp
mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h
cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp
mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h
cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp
mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h
cp inc/jsmn.h ../lib/jsmn.h.tmp
mv ../lib/jsmn.h.tmp ../lib/jsmn.h
cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp
mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h
cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp
mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h
cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp
mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h
cp inc/avl.h ../lib/avl.h.tmp
mv ../lib/avl.h.tmp ../lib/avl.h
cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp
mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h
cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp
mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h
cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp
mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h
cp inc/stMatrix.h ../lib/stMatrix.h.tmp
mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h
cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp
mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h
cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp
mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h
cp inc/hashTableC.h ../lib/hashTableC.h.tmp
mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h
cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp
mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h
cp inc/sonLib.h ../lib/sonLib.h.tmp
mv ../lib/sonLib.h.tmp ../lib/sonLib.h
cp inc/stSafeC.h ../lib/stSafeC.h.tmp
mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h
cp inc/sonLibList.h ../lib/sonLibList.h.tmp
mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h
cp inc/sonLibString.h ../lib/sonLibString.h.tmp
mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I ../lib/ -c impl/*.c
/usr/bin/g++ -std=gnu++98 -O3 -g -Wall -funroll-loops -DNDEBUG -I inc -I ../lib/ -c impl/*.cpp
ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o
ranlib sonLib.a
rm *.o
mv sonLib.a ../lib/
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread
mv ../bin/sonLibTests.tmp ../bin/sonLibTests
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm
mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm
mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm
mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sonLib/C'
cp sonLib_daemonize.py ./bin/sonLib_daemonize.py
chmod +x ./bin/sonLib_daemonize.py
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sonLib'
. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /data3/genome_graphs/vg-rotella/./deps/sonLib && cp lib/stPinchesAndCacti.a /data3/genome_graphs/vg-rotella/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /data3/genome_graphs/vg-rotella/lib/lib3edgeconnected.a && mkdir -p /data3/genome_graphs/vg-rotella/include/sonLib && cp lib/*.h /data3/genome_graphs/vg-rotella/include/sonLib
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti'
cd externalTools && make all
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti/externalTools'
cd threeEdgeConnected && make all
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti/externalTools/threeEdgeConnected'
/usr/bin/gcc -std=c99 -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c
ar rc 3EdgeConnected.a *.o
ranlib 3EdgeConnected.a
rm *.o
mv 3EdgeConnected.a ../..//../sonLib/lib/
cp inc/*.h ../..//../sonLib/lib/
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti/externalTools/threeEdgeConnected'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti/externalTools'
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I .//../sonLib/lib/ -c impl/*.c
ar rc stPinchesAndCacti.a *.o
ranlib stPinchesAndCacti.a
rm *.o
mv stPinchesAndCacti.a .//../sonLib/lib/
cp inc/*.h .//../sonLib/lib/
/usr/bin/gcc -std=c99 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/pinchesAndCacti'
which bison
/usr/bin/bison
. ./source_me.sh && cd deps/raptor/build && rm -Rf CMakeCache.txt CMakeFiles CTestTestfile.cmake Makefile cmake_install.cmake src tests utils && cmake .. && rm -f src/turtle_parser.c && rm -f src/turtle_lexer.c && make turtle_lexer_tgt && make -f src/CMakeFiles/raptor2.dir/build.make src/turtle_lexer.c && sed -i.bak '/yycleanup/d' src/turtle_lexer.c && make && cp src/libraptor2.a /data3/genome_graphs/vg-rotella/lib
-- The C compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.47.0")
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.3")
-- Found LibXslt: /usr/lib/x86_64-linux-gnu/libxslt.so (found version "1.1.28")
-- Found Perl: /usr/bin/miniconda3/bin/perl (found version "5.26.2")
-- Found BISON: /usr/bin/bison (found suitable version "3.0.4", minimum required is "3")
-- Found FLEX: /usr/bin/flex (found version "2.6.0")
-- Looking for errno.h
-- Looking for errno.h - found
-- Looking for fcntl.h
-- Looking for fcntl.h - found
-- Looking for getopt.h
-- Looking for getopt.h - found
-- Looking for limits.h
-- Looking for limits.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for setjmp.h
-- Looking for setjmp.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for sys/param.h
-- Looking for sys/param.h - found
-- Looking for sys/stat.h
-- Looking for sys/stat.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for include files sys/time.h, time.h
-- Looking for include files sys/time.h, time.h - found
-- Looking for access
-- Looking for access - found
-- Looking for _access
-- Looking for _access - not found
-- Looking for getopt
-- Looking for getopt - found
-- Looking for getopt_long
-- Looking for getopt_long - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for isascii
-- Looking for isascii - found
-- Looking for setjmp
-- Looking for setjmp - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for _snprintf
-- Looking for _snprintf - not found
-- Looking for stat
-- Looking for stat - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for stricmp
-- Looking for stricmp - not found
-- Looking for _stricmp
-- Looking for _stricmp - not found
-- Looking for strtok_r
-- Looking for strtok_r - found
-- Looking for vasprintf
-- Looking for vasprintf - found
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Looking for _vsnprintf
-- Looking for _vsnprintf - not found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Check size of unsigned char
-- Check size of unsigned char - done
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Check size of unsigned int
-- Check size of unsigned int - done
-- Check size of unsigned long
-- Check size of unsigned long - done
-- Check size of unsigned long long
-- Check size of unsigned long long - done
-- Performing Test HAVE___FUNCTION__
-- Performing Test HAVE___FUNCTION__ - Success
-- Looking for xmlCtxtUseOptions
-- Looking for xmlCtxtUseOptions - found
-- Looking for xmlSAX2InternalSubset
-- Looking for xmlSAX2InternalSubset - found
-- Performing Test RAPTOR_LIBXML_ENTITY_NAME_LENGTH
-- Performing Test RAPTOR_LIBXML_ENTITY_NAME_LENGTH - Failed
-- Performing Test RAPTOR_LIBXML_ENTITY_ETYPE
-- Performing Test RAPTOR_LIBXML_ENTITY_ETYPE - Success
-- Performing Test RAPTOR_LIBXML_XMLSAXHANDLER_INITIALIZED
-- Performing Test RAPTOR_LIBXML_XMLSAXHANDLER_INITIALIZED - Success
-- Performing Test RAPTOR_LIBXML_XMLSAXHANDLER_EXTERNALSUBSET
-- Performing Test RAPTOR_LIBXML_XMLSAXHANDLER_EXTERNALSUBSET - Success
-- Performing Test RAPTOR_LIBXML_XML_PARSE_NONET
-- Performing Test RAPTOR_LIBXML_XML_PARSE_NONET - Success
-- Performing Test RAPTOR_LIBXML_HTML_PARSE_NONET
-- Performing Test RAPTOR_LIBXML_HTML_PARSE_NONET - Success
--
################################################################
Raptor Configuration Summary
################################################################
http://librdf.org/raptor/
Configured on host
host OS Linux
host architecture x86_64
General flags:
CC /usr/bin/gcc
CXX (not used)
CFLAGS -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg-rotella/include -I /data3/genome_graphs/vg/include
CXXFLAGS
LDFLAGS
Installation prefix: /usr/local
Dependencies (packages marked with *** are required):
*** Perl /usr/bin/miniconda3/bin/perl
*** Bison /usr/bin/bison
*** Flex /usr/bin/flex
*** libxml2 (lib) /usr/lib/x86_64-linux-gnu/libxml2.so
*** libxml2 (include) /usr/include/libxml2
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/raptor/build
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[4]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target turtle_flex_tgt
make[4]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[4]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[100%] Generating turtle_lexer.t
make[4]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[100%] Built target turtle_flex_tgt
make[4]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target turtle_lexer_tgt
make[4]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[100%] Built target turtle_lexer_tgt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Generating turtle_lexer.c
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target turtle_tables_tgt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 1%] Generating turtle_parser.tab.c
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 1%] Built target turtle_tables_tgt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target parsedate_tables_tgt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 1%] Generating parsedate.tab.c
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 1%] Built target parsedate_tables_tgt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target parsedate_tgt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 2%] Generating parsedate.c
[ 3%] Generating parsedate.h
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 3%] Built target parsedate_tgt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target turtle_parser_tgt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 4%] Generating turtle_parser.c
[ 5%] Generating turtle_parser.h
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 5%] Built target turtle_parser_tgt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 6%] Built target turtle_flex_tgt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 6%] Built target turtle_lexer_tgt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor2
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 6%] Building C object src/CMakeFiles/raptor2.dir/raptor_avltree.c.o
[ 7%] Building C object src/CMakeFiles/raptor2.dir/raptor_concepts.c.o
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[ 52%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/language.c.o
[ 52%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/lists.c.o
[ 53%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/namespace.c.o
[ 54%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/rdfa.c.o
[ 55%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/rdfa_utils.c.o
[ 56%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/strtok_r.c.o
[ 57%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/subject.c.o
[ 58%] Building C object src/CMakeFiles/raptor2.dir/__/librdfa/triple.c.o
[ 59%] Building C object src/CMakeFiles/raptor2.dir/parsedate.c.o
[ 60%] Linking C static library libraptor2.a
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 63%] Built target raptor2
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_sort_r_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 64%] Building C object src/CMakeFiles/raptor_sort_r_test.dir/sort_r.c.o
[ 64%] Linking C executable raptor_sort_r_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 64%] Built target raptor_sort_r_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_snprintf_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 65%] Building C object src/CMakeFiles/raptor_snprintf_test.dir/snprintf.c.o
[ 66%] Linking C executable raptor_snprintf_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 66%] Built target raptor_snprintf_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_permute_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 67%] Building C object src/CMakeFiles/raptor_permute_test.dir/raptor_permute_test.c.o
[ 67%] Linking C executable raptor_permute_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 67%] Built target raptor_permute_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_sequence_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 68%] Building C object src/CMakeFiles/raptor_sequence_test.dir/raptor_sequence.c.o
[ 69%] Linking C executable raptor_sequence_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 69%] Built target raptor_sequence_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_parse_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 70%] Building C object src/CMakeFiles/raptor_parse_test.dir/raptor_parse.c.o
[ 71%] Linking C executable raptor_parse_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 71%] Built target raptor_parse_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_iostream_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 72%] Building C object src/CMakeFiles/raptor_iostream_test.dir/raptor_iostream.c.o
[ 73%] Linking C executable raptor_iostream_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 73%] Built target raptor_iostream_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target turtle_parser_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 74%] Building C object src/CMakeFiles/turtle_parser_test.dir/turtle_parser.c.o
[ 75%] Linking C executable turtle_parser_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 76%] Built target turtle_parser_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_rfc2396_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 77%] Building C object src/CMakeFiles/raptor_rfc2396_test.dir/raptor_rfc2396.c.o
[ 78%] Linking C executable raptor_rfc2396_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 78%] Built target raptor_rfc2396_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_uri_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 79%] Building C object src/CMakeFiles/raptor_uri_test.dir/raptor_uri.c.o
[ 80%] Linking C executable raptor_uri_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 80%] Built target raptor_uri_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target turtle_lexer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 81%] Building C object src/CMakeFiles/turtle_lexer_test.dir/turtle_lexer.c.o
[ 82%] Linking C executable turtle_lexer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 82%] Built target turtle_lexer_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_namespace_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 83%] Building C object src/CMakeFiles/raptor_namespace_test.dir/raptor_namespace.c.o
[ 84%] Linking C executable raptor_namespace_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 84%] Built target raptor_namespace_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target strcasecmp_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 85%] Building C object src/CMakeFiles/strcasecmp_test.dir/strcasecmp.c.o
[ 86%] Linking C executable strcasecmp_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 86%] Built target strcasecmp_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_stringbuffer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 87%] Building C object src/CMakeFiles/raptor_stringbuffer_test.dir/raptor_stringbuffer.c.o
[ 88%] Linking C executable raptor_stringbuffer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 88%] Built target raptor_stringbuffer_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_term_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 89%] Building C object src/CMakeFiles/raptor_term_test.dir/raptor_term.c.o
[ 90%] Linking C executable raptor_term_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 90%] Built target raptor_term_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_www_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 90%] Building C object src/CMakeFiles/raptor_www_test.dir/raptor_www_test.c.o
[ 91%] Linking C executable raptor_www_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 91%] Built target raptor_www_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_xml_writer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 92%] Building C object src/CMakeFiles/raptor_xml_writer_test.dir/raptor_xml_writer.c.o
[ 93%] Linking C executable raptor_xml_writer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 93%] Built target raptor_xml_writer_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_turtle_writer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 94%] Building C object src/CMakeFiles/raptor_turtle_writer_test.dir/raptor_turtle_writer.c.o
[ 95%] Linking C executable raptor_turtle_writer_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 95%] Built target raptor_turtle_writer_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target raptor_avltree_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 95%] Building C object src/CMakeFiles/raptor_avltree_test.dir/raptor_avltree.c.o
[ 96%] Linking C executable raptor_avltree_test
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 96%] Built target raptor_avltree_test
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target rapper
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 97%] Building C object utils/CMakeFiles/rapper.dir/rapper.c.o
[ 98%] Linking C executable rapper
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 98%] Built target rapper
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
Scanning dependencies of target rdfdiff
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[ 99%] Building C object utils/CMakeFiles/rdfdiff.dir/rdfdiff.c.o
[100%] Linking C executable rdfdiff
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
[100%] Built target rdfdiff
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/raptor/build'
touch lib/libraptor2.a
. ./source_me.sh && cd deps/fermi-lite && make && cp *.h /data3/genome_graphs/vg-rotella/include/ && cp libfml.a /data3/genome_graphs/vg-rotella/lib/
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/fermi-lite'
gcc -c -g -Wall -O2 -Wno-unused-function kthread.c -o kthread.o
gcc -c -g -Wall -O2 -Wno-unused-function misc.c -o misc.o
misc.c: In function ‘fml_utg_print’:
misc.c:212:12: warning: variable ‘l’ set but not used [-Wunused-but-set-variable]
int i, j, l;
^
gcc -c -g -Wall -O2 -Wno-unused-function bseq.c -o bseq.o
gcc -c -g -Wall -O2 -Wno-unused-function htab.c -o htab.o
gcc -c -g -Wall -O2 -Wno-unused-function bfc.c -o bfc.o
bfc.c: In function ‘bfc_kmer_insert’:
bfc.c:86:17: warning: variable ‘hash’ set but not used [-Wunused-but-set-variable]
uint64_t y[2], hash;
^
gcc -c -g -Wall -O2 -Wno-unused-function rle.c -o rle.o
gcc -c -g -Wall -O2 -Wno-unused-function rope.c -o rope.o
gcc -c -g -Wall -O2 -Wno-unused-function mrope.c -o mrope.o
gcc -c -g -Wall -O2 -Wno-unused-function rld0.c -o rld0.o
rld0.c: In function ‘rld_restore’:
rld0.c:298:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(e->z[i], 8, RLD_LSIZE, fp);
^
rld0.c:299:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(e->z[i], 8, k, fp);
^
rld0.c:301:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(e->frame, 8 * e->asize1, e->n_frames, fp);
^
rld0.c: In function ‘rld_restore_header’:
rld0.c:256:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(magic, 1, 4, fp);
^
rld0.c:258:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&x, 4, 1, fp);
^
rld0.c:260:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(a, 8, 3, fp);
^
rld0.c:262:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(e->mcnt + 1, 8, e->asize, fp);
^
gcc -c -g -Wall -O2 -Wno-unused-function unitig.c -o unitig.o
unitig.c: In function ‘unitig1’:
unitig.c:325:16: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
int seed_len, ret, is_loop, contained;
^
gcc -c -g -Wall -O2 -Wno-unused-function mag.c -o mag.o
gcc -c -g -Wall -O2 -Wno-unused-function bubble.c -o bubble.o
gcc -c -g -Wall -O2 -Wno-unused-function ksw.c -o ksw.o
ar -csru libfml.a kthread.o misc.o bseq.o htab.o bfc.o rle.o rope.o mrope.o rld0.o unitig.o mag.o bubble.o ksw.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -c -g -Wall -O2 -Wno-unused-function example.c -o example.o
gcc -g -Wall -O2 -Wno-unused-function libfml.a example.o -o fml-asm -L. -lfml -lm -lz -lpthread
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/fermi-lite'
. ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/data3/genome_graphs/vg-rotella/include" make libs && cp lib/libsublinearLS.a /data3/genome_graphs/vg-rotella/lib/ && mkdir -p /data3/genome_graphs/vg-rotella/include/sublinearLS && cp src/*.hpp /data3/genome_graphs/vg-rotella/include/sublinearLS/
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens'
rm -f /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/bin/* /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/*.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/test/*.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/lib/*
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens'
if [ ! -d /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj; fi
if [ ! -d /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/test; fi
if [ ! -d /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/bin; fi
if [ ! -d /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/lib; fi
if [ ! -d /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps; fi
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/math.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/math.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/reference.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/reference.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/probability.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/probability.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/input_haplotype.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/delay_multiplier.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/DP_map.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/penalty_set.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/allele.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/allele.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/row_set.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/row_set.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/haplotype_manager.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/set_of_extensions.o
g++ -std=c++11 -g -I/data3/genome_graphs/vg-rotella/include -L. -L/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/reference_sequence.o
ar rc /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/math.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/reference.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/probability.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/input_haplotype.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/DP_map.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/penalty_set.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/allele.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/row_set.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/obj/reference_sequence.o
ranlib /data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens/lib/libsublinearLS.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sublinear-Li-Stephens'
. ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /data3/genome_graphs/vg-rotella/lib/ && cp -r src/include/structures /data3/genome_graphs/vg-rotella/include/
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/structures'
if [ ! -d bin ]; then mkdir -p bin; fi
if [ ! -d obj ]; then mkdir -p obj; fi
if [ ! -d lib ]; then mkdir -p lib; fi
find bin obj lib -type f -delete
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/structures'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/structures'
if [ ! -d bin ]; then mkdir -p bin; fi
if [ ! -d obj ]; then mkdir -p obj; fi
if [ ! -d lib ]; then mkdir -p lib; fi
g++ -std=c++11 -m64 -g -O3 -Isrc/include -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c src/union_find.cpp -o obj/union_find.o
g++ -std=c++11 -m64 -g -O3 -Isrc/include -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c src/suffix_tree.cpp -o obj/suffix_tree.o
g++ -std=c++11 -m64 -g -O3 -Isrc/include -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2 -c src/stable_double.cpp -o obj/stable_double.o
rm -f lib/libstructures.a
ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o
ar: creating lib/libstructures.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/structures'
. ./source_me.sh && cd deps/boost-subset && ./bootstrap.sh --with-libraries=program_options --libdir=/data3/genome_graphs/vg-rotella/lib --includedir=/data3/genome_graphs/vg-rotella/include && ./b2 --ignore-site-config --link=static cxxflags="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2" linkflags="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -fopenmp -msse4.2" install
Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help
- Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html
- Boost.Build documentation:
http://www.boost.org/build/doc/html/index.html
/data3/genome_graphs/vg-rotella/deps/boost-subset/libs/predef/check/../tools/check/predef.jam:46: Unescaped special character in argument $(language)::$(expression)
Performing configuration checks
- default address-model : 64-bit
- default architecture : x86
Component configuration:
- atomic : not building
- chrono : not building
- filesystem : not building
- program_options : building
- regex : not building
- system : not building
- test : not building
- timer : not building
...patience...
...found 6135 targets...
...updating 2702 targets...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc551/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/list.hpp
...on 100th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/value_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/value_at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/size_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/prior_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/next_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/equal_to_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/distance_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/deref_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/detail/advance_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/value_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/value_of_data_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/next_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/key_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/deref_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/deref_data_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/value_at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/size_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/segments_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/segmented_iterator_range.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/is_segmented_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/detail/at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_tie50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_tie40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_tie30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_tie20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_tie10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_tie.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple50_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple40_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple30_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple20_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple10_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/make_tuple50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/make_tuple40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/make_tuple30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/make_tuple20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/make_tuple10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/preprocessed/make_tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/io/detail/out.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/io/detail/manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/io/detail/in.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/detail/segmented_size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/detail/segmented_end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/detail/segmented_end.hpp
...on 200th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/detail/segmented_begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/detail/segmented_begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/detail/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/detail/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/detail/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/detail/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/detail/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/detail/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/value_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/value_at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/prior_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/next_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/equal_to_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/distance_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/deref_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/advance_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/value_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/value_at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/reverse_cons.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/next_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/equal_to_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/empty_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/deref_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/value_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/value_at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/size_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/is_view_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/is_sequence_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/extension.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/deref_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/category_of_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/adapt_is_tpl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/adapt_base_attr_filler.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/adapt_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/adapt_auto.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/mpl/detail/end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/mpl/detail/begin_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/win/thread_clock.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/win/process_cpu_clocks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/win/chrono.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/posix/thread_clock.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/posix/process_cpu_clocks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/posix/chrono.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/mac/thread_clock.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/mac/process_cpu_clocks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/mac/chrono.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector50_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector40_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector30_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector20_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector10_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/typeof_based/vector10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector50_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector40_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector30_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector20_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector10_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/plain/vector10.hpp
...on 300th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector50_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector40_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector30_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector20_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector10_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/preprocessed/no_ctps/vector10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list50_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list40_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list30_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list20_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list10_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/preprocessed/plain/list10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector_n_chooser.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector_n.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector_forward_ctor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector50_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector40_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector30_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector20_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector10_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/value_at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/limits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/list_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/limits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/detail/preprocessor/is_seq.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector50_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector40_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector30_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector20_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector10_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vvector10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_chooser50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_chooser40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_chooser30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_chooser20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_chooser10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector_chooser.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector50_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector40_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector30_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector20_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector10_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/detail/cpp03/preprocessed/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/preprocessed/list_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/preprocessed/list50_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/preprocessed/list40_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/preprocessed/list30_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/preprocessed/list20_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/detail/cpp03/preprocessed/list10_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/version_number.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/version.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/other.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/make.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/language.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/endian.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_uwp.h
...on 400th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_system.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_store.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_server.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_runtime.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_phone.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/windows_desktop.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/mingw64.h
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/cmdline.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/config_file.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/options_description.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/parsers.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/variables_map.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/value_semantic.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/positional_options.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/utf8_codecvt_facet.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/convert.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/winmain.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/split.o
gcc.archive bin.v2/libs/program_options/build/gcc-5.4.0/release/link-static/threading-multi/libboost_program_options.a
common.copy /data3/genome_graphs/vg-rotella/lib/libboost_program_options.a
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/mingw32.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/mingw.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/ios.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/platform/cloudabi.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/other/workaround.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/other/endian.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/windows.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/vms.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/unix.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/solaris.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/qnxnto.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/os400.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/macos.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/linux.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/irix.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/ios.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/hpux.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/haiku.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/cygwin.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/bsd.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/beos.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/android.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/amigaos.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/aix.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/language/stdcpp.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/language/stdc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/language/objc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/test_def.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/test.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/platform_detected.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/os_detected.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/endian_compat.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/comp_detected.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/_exception.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/detail/_cassert.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/watcom.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/visualc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/tendra.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/sunpro.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/sgi_mipspro.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/pgi.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/palm.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/mpw.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/microtec.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/metrowerks.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/metaware.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/llvm.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/kai.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/intel.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/ibm.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/iar.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/hp_acc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/greenhills.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/gcc_xml.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/gcc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/ekopath.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/edg.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/dignus.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/digitalmars.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/diab.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/compaq.h
...on 500th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/comeau.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/clang.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/compiler/borland.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/z.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/x86.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/sys390.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/sys370.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/superh.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/sparc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/rs6k.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/pyramid.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/ppc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/parisc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/mips.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/m68k.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/ia64.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/convex.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/blackfin.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/arm.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/alpha.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/bsd/open.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/bsd/net.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/bsd/free.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/bsd/dragonfly.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/os/bsd/bsdi.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/vacpp.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/stlport.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/stdcpp3.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/sgi.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/roguewave.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/msl.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/modena.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/libcomo.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/dinkumware.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/cxx.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/std/_prefix.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c/zos.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c/vms.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c/uc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c/gnu.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c/cloudabi.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/library/c/_prefix.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/x86_amd.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/x86.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/ppc.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/arm.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/x86/64.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/architecture/x86/32.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/x86_amd/versions.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/x86/versions.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/ppc/versions.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/predef/hardware/simd/arm/versions.h
common.copy /data3/genome_graphs/vg-rotella/include/boost/version.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/limits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/cxx11_char_types.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/cstdint.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/warning_disable.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/user.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/requires_threads.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/pragma_message.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/helper_macros.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/header_deprecated.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/auto_link.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/abi_suffix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/abi_prefix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/xlcpp_zos.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/vacpp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/stlport.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/sgi.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/roguewave.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/msl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/modena.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/libstdcpp3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/libcpp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/libcomo.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/stdlib/dinkumware.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/zos.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/win32.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/vxworks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/vms.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/symbian.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/solaris.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/qnxnto.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/macos.hpp
...on 600th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/linux.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/irix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/hpux.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/haiku.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/cygwin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/cray.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/cloudabi.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/bsd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/beos.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/amigaos.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/platform/aix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/no_tr1/utility.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/no_tr1/memory.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/no_tr1/functional.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/no_tr1/complex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/no_tr1/cmath.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/detail/suffix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/detail/select_stdlib_config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/detail/select_platform_config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/detail/select_compiler_config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/detail/posix_features.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/xlcpp_zos.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/xlcpp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/visualc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/vacpp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/sunpro_cc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/sgi_mipspro.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/pgi.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/pathscale.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/nvcc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/mpw.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/metrowerks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/kai.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/intel.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/hp_acc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/greenhills.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/gcc_xml.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/gcc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/digitalmars.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/diab.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/cray.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/compaq_cxx.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/common_edg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/comeau.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/codegear.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/clang.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/compiler/borland.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/abi/msvc_suffix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/abi/msvc_prefix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/abi/borland_suffix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/config/abi/borland_prefix.hpp
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/cmdline.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/config_file.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/options_description.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/parsers.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/variables_map.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/value_semantic.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/positional_options.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/utf8_codecvt_facet.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/convert.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/winmain.o
gcc.compile.c++ bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/split.o
gcc.link.dll bin.v2/libs/program_options/build/gcc-5.4.0/release/threading-multi/libboost_program_options.so.1.67.0
common.copy /data3/genome_graphs/vg-rotella/lib/libboost_program_options.so.1.67.0
ln-UNIX /data3/genome_graphs/vg-rotella/lib/libboost_program_options.so
common.copy /data3/genome_graphs/vg-rotella/include/boost/visit_each.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/tokenizer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/token_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/token_functions.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/timer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/throw_exception.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/swap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/static_assert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/shared_ptr.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/scoped_ptr.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/scoped_array.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ref.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/rational.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/operators.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/noncopyable.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/non_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/next_prior.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/memory_order.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mem_fn.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/make_shared.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/is_placeholder.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/io_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/integer_traits.hpp
...on 700th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/integer_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/integer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/get_pointer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/foreach_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/foreach.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/current_function.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/cstdlib.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/cregex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept_check.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/checked_delete.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/cerrno.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/call_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/assert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/array.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/any.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/aligned_storage.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/timers.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/time.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/local_memory.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/get_thread_times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/get_process_times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/get_last_error.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/get_current_thread.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/get_current_process.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/error_handling.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/error_codes.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/character_code_conversion.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/winapi/basic_types.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/value_init.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/swap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/result_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/identity_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/enable_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/declval.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/binary.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/base_from_member.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/addressof.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/vector200.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/vector150.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/vector100.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/unsupported.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/typeof_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/typeof.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/type_template_param.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/type_encoding.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/template_template_param.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/template_encoding.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/register_mem_functions.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/register_fundamental.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/register_functions_iterate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/register_functions.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/pointers_data_members.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/native.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/modifiers.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/message.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/integral_template_param.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/int_encoding.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/encode_decode_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/encode_decode.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/decltype.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/type_with_alignment.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/type_identity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_volatile.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_pointer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_extent.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_cv_ref.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_cv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_const.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/remove_bounds.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/make_void.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/make_unsigned.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/make_signed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_volatile.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_void.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_unsigned.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_union.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_signed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_scalar.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_same.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_rvalue_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_polymorphic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_pointer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_pod.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_nothrow_move_constructible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_member_pointer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_member_function_pointer.hpp
...on 800th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_lvalue_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_integral.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_fundamental.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_function.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_floating_point.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_float.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_destructible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_default_constructible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_copy_constructible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_convertible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_constructible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_const.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_complete.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_class.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_base_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_base_and_derived.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_assignable.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_array.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_arithmetic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/is_abstract.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/intrinsics.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/integral_constant.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_trivial_move_constructor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_trivial_destructor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_trivial_copy.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_trivial_constructor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_trivial_assign.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_right_shift.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_plus_assign.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_nothrow_copy.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_minus_assign.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/has_left_shift.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/function_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/declval.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/decay.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/cv_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/copy_cv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/conversion_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/conditional.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/composite_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/common_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/alignment_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/aligned_storage.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_volatile.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_rvalue_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_pointer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_lvalue_reference.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_cv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/add_const.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index/type_index_facade.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index/stl_type_index.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index/ctti_type_index.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/tuple/tuple_comparison.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/tuple/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/timer/timer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/timer/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/unit_test_suite.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/unit_test_parameters.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/unit_test_monitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/unit_test_log_formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/unit_test_log.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/unit_test.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/test_tools.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/test_framework_init_observer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/results_reporter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/results_collector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/progress_monitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/framework.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/execution_monitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/debug_config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/debug.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/system/system_error.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/system/error_code.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/system/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/system/api_config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/shared_ptr.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/scoped_ptr.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/scoped_array.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/make_shared_object.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/make_shared_array.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/make_shared.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/bad_weak_ptr.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/allocate_shared_array.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/user.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/regex_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/pattern_except.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/icu.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/config.hpp
...on 900th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/ratio_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/ratio.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/value_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/size_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/reverse_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/rend.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/rbegin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/range_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/mutable_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/iterator_range_io.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/iterator_range_core.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/iterator_range.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/has_range_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/functions.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/distance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/difference_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/const_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/concepts.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/as_literal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/version.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/variables_map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/value_semantic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/positional_options.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/parsers.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/options_description.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/option.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/errors.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/eof_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/environment_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/cmdline.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/stringize.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repeat_from_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repeat.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iterate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/inc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/identity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/expr_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/enum_shifted_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/enum_params_with_a_default.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/enum_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/dec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/comma_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/cat.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/void_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/void.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/tag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/size_t_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/size_t.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/size_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/sequence_tag_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/sequence_tag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/same_as.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/reverse_fold.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/remove_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/push_front_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/push_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/push_back_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/push_back.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/protect.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/prior.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/pop_front_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/pop_back_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/pair.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/numeric_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/not.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/next_prior.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/next.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/negate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/multiplies.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/long_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/long.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/logical.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/lambda_fwd.hpp
...on 1000th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/iterator_tags.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/iterator_range.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/iter_fold_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/iter_fold.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/is_sequence.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/is_placeholder.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/integral_c_tag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/integral_c_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/integral_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/int_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/int.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/inserter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/identity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/has_xxx.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/front_inserter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/front_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/for_each.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/fold.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/find_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/find.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/eval_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/empty_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/empty_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/distance_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/distance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/deref.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/contains_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/contains.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/comparison.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/clear_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/clear.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/bool_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/bool.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/begin_end_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/begin_end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/back_inserter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/back_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/at_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/at.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/assert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/arg_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/always.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/advance_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/advance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/O1_size_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/O1_size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/utility_core.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/core.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/try_lexical_convert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/bad_lexical_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/transform_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/reverse_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/minimum_category.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/iterator_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/iterator_facade.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/iterator_concepts.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/iterator_categories.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/iterator_adaptor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/interoperable.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/advance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/io/ios_state.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/integer/static_log2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/integer/common_factor_rt.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/functional/hash_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/functional/hash.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function_template.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function8.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function10.hpp
...on 1100th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/function0.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/string_file.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/path_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/path.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/operations.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/fstream.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/convenience.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/exception/get_error_info.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/exception/exception.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/exception/current_exception_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/utf8_codecvt_facet.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/utf8_codecvt_facet.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/sp_typeinfo.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/scoped_enum_emulation.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/no_exceptions_support.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/lightweight_test.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/lightweight_mutex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/lightweight_main.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/lcast_precision.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/indirect_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/fenv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/container_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/call_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/bitmask.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/basic_pointerbuf.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/typeinfo.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/swap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/scoped_enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/ref.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/noncopyable.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/no_exceptions_support.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/lightweight_test.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/is_same.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/ignore_unused.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/enable_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/demangle.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/checked_delete.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/core/addressof.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container_hash/hash_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container_hash/hash.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container_hash/extensions.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container/container_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/usage.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/assert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/time_point.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/thread_clock.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/system_clocks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/process_cpu_clocks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/duration.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/clock_string.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/chrono.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/storage.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/mem_fn_vw.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/mem_fn_template.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/mem_fn_cc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/mem_fn.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/bind_template.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/bind_mf_cc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/bind_mf2_cc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/bind_cc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/bind/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/fences.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/capabilities.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/atomic_flag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/align/is_aligned.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/utility/detail/result_of_iterate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/msvc/typeof_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/typeof/dmc/typeof_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/yes_no_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/mp_defer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/is_mem_fun_pointer_tester.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/is_mem_fun_pointer_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/is_likely_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/is_function_ptr_tester.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/is_function_ptr_helper.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/has_binary_operator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/composite_pointer_type.hpp
...on 1200th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/composite_member_pointer_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/common_type_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_traits/detail/common_arithmetic_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index/detail/stl_register_class.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index/detail/ctti_register_class.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/type_index/detail/compile_time_type_info.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/tuple/detail/tuple_basic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/xml_printer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/wrap_stringstream.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/trivial_singleton.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/string_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/setcolor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/rtti.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/named_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/lazy_ostream.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/is_forward_iterable.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/is_cstring.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/foreach.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/custom_manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/class_properties.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/assign_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/algorithm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/visitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/traverse.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/test_unit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/test_case_template.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/test_case_counter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/observer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/global_fixture.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/fixture.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/decorator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tree/auto_registration.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/output_test_stream.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/interface.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/fpc_tolerance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/fpc_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/floating_point_comparison.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/cstring_comparison_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/context.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/collection_comparison_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/assertion_result.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/assertion.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/output/xml_report_formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/output/xml_log_formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/output/plain_report_formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/output/junit_log_formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/output/compiler_log_formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/xml_report_formatter.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/xml_log_formatter.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/unit_test_parameters.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/unit_test_monitor.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/unit_test_main.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/unit_test_log.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/test_tree.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/test_tools.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/test_main.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/test_framework_init_observer.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/results_reporter.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/results_collector.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/progress_monitor.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/plain_report_formatter.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/junit_log_formatter.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/framework.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/execution_monitor.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/decorator.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/debug.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/cpp_main.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/impl/compiler_log_formatter.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/throw_exception.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/suppress_warnings.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/pp_variadic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/log_level.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/global_typedef.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/fwd_decl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/enable_warnings.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/detail/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/system/detail/local_free_on_destruction.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/system/detail/error_code.ipp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/yield_k.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_w32.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_sync.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_std_atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_pt.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_pool.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_nt.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock_gcc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/spinlock.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_nullptr_t.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_noexcept.hpp
...on 1300th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_interlocked.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_has_sync.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_disable_deprecated.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_w32.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_vacpp_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_std_atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_spin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_snc_ps3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_pt.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_nt.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_gcc_sparc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_gcc_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_gcc_mips.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_gcc_ia64.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_cw_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_clang.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_aix.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base_acc_ia64.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_counted_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/sp_convertible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/shared_count.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/quick_allocator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/operator_bool.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/lwm_win32_cs.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/lwm_pthreads.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/lwm_nop.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/local_sp_deleter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/local_counted_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/smart_ptr/detail/lightweight_mutex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/w32_regex_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/u32regex_token_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/u32regex_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/syntax_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/sub_match.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/states.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_traits_defaults.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_token_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_split.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_search.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_replace.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_raw_buffer.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_merge.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_match.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_grep.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex_format.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/regbase.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/protected_call.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/primary_transform.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/perl_matcher_recursive.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/perl_matcher_non_recursive.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/perl_matcher_common.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/perl_matcher.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/mem_block_cache.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/match_results.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/match_flags.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/iterator_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/iterator_category.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/instances.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/fileiter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/error_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/cregex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/cpp_regex_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/char_regex_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/c_regex_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/basic_regex_parser.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/basic_regex_creator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/v4/basic_regex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/pending/unicode_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/pending/static_mutex.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/pending/object_cache.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/config/cwchar.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/regex/config/borland.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/mpl/rational_c_tag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/detail/overflow_helpers.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/value_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/str_types.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/size_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/sfinae.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/safe_bool.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/remove_extent.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/msvc_has_iterator_workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/misc_concept.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/implementation_help.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/has_member_size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/extract_optional_type.hpp
...on 1400th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/detail_str.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/common.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/detail/as_literal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/range/algorithm/equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/detail/value_semantic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/detail/utf8_codecvt_facet.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/detail/parsers.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/detail/convert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/detail/config_file.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/program_options/detail/cmdline.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/variadic/to_seq.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/variadic/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/variadic/elem.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/to_seq.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/to_list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/rem.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/elem.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/eat.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/slot.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/transform.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/to_tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/subseq.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/seq.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/rest_n.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/push_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/for_each_i.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/for_each.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/fold_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/first_n.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/elem.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/cat.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/repeat_from_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/repeat.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/for.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_trailing_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_trailing.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_shifted_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_shifted.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_params_with_a_default.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum_binary_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/punctuation/paren.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/punctuation/is_begin_parens.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/punctuation/comma_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/punctuation/comma.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/not.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/compl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/bool.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/logical/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/reverse.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/for_each_i.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/fold_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/fold_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/adt.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/self.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/local.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/iterate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/overload.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/is_empty_variadic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/is_empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/is_1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/intercept.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/identity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/expand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/detail/split.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/detail/is_unary.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/detail/is_binary.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/detail/check.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/detail/auto_rec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/debug/error.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/while.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/iif.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/expr_iif.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/expr_if.hpp
...on 1500th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/deduce_d.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/config/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/comparison/not_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/comparison/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/comparison/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/comparison/equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/array/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/array/elem.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/array/data.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/arithmetic/sub.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/arithmetic/mod.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/arithmetic/inc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/arithmetic/dec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/arithmetic/add.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/udt_builtin_mixture_enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/sign_mixture_enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/numeric_cast_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/int_float_mixture_enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/converter_policies.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/converter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/conversion_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/bounds.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector50_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector40_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector30_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector20_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector10_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector0_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/vector0.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list50_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list50.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list40_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list40.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list30_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list30.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list20_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list10_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list0_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/list0.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/limits/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/limits/unrolling.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/limits/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/limits/arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/yes_no.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/value_wknd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/unwrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/type_wrapper.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/traits_lambda_spec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/template_arity_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/static_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/size_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/sequence_wrapper.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/reverse_fold_impl_body.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/push_front_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/push_back_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/numeric_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/numeric_cast_utils.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/nttp_decl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/nested_type_wknd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/na_spec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/na_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/na_assert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/na.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/msvc_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/msvc_never_true.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/msvc_is_class.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/msvc_eti_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/msvc_dtw.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/logical_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/largest_int.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/lambda_support.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/lambda_spec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/lambda_arity_param.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/iter_apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/is_msvc_eti_arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/integral_wrapper.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/inserter_algorithm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/include_preprocessed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/has_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/has_tag.hpp
...on 1600th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/has_size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/has_rebind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/has_begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/has_apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/fold_impl_body.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/find_if_pred.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/count_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/contains_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/comparison_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/common_name_wknd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/clear_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/begin_end_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/at_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/arity_spec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/arithmetic_op.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/arg_typedef.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/adl_barrier.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/O1_size_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/type_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/std_ns_end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/std_ns_begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/meta_utils_core.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/meta_utils.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/config_end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/move/detail/config_begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/user.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/toms748_solve.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/series.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/roots.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/real_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/rational.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/promotion.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/precision.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/fraction.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/convert_from_string.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/big_constant.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/zeta.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/trunc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/sqrt1pm1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/sin_pi.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/sign.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/powm1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/math_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/log1p.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/lanczos.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/gamma.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/fpclassify.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/factorials.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/expm1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/erf.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/digamma.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/bernoulli.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/policies/policy.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/policies/error_handling.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/constants/constants.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/constants/calculate_constants.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/widest_char.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/lcast_unsigned_converters.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/lcast_char_constants.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/is_character.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/inf_nan.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/converter_numeric.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/converter_lexical_streams.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/lexical_cast/detail/converter_lexical.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/detail/facade_iterator_category.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/detail/enable_if.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/detail/config_undef.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/iterator/detail/config_def.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/io/detail/quoted_manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/tuple_tie.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/tuple_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/make_tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/void.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/tag_of_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/tag_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/sequence_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/iterator_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/is_view.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/is_sequence.hpp
...on 1700th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/is_segmented.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/is_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/category_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/as_const.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/io.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/mpl/end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/mpl/begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/value_of_data.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/value_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/segmented_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/prior.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/next.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/key_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/iterator_facade.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/distance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/deref_data.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/deref.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/basic_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/advance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/include/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/include/std_pair.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/std_pair.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/detail/prologue.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/detail/maybe_include.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/function/detail/function_iterate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/filesystem/detail/utf8_codecvt_facet.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/exception/detail/type_info.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/exception/detail/shared_ptr.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/exception/detail/error_info_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/timers.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/time.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/get_thread_times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/get_process_times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/get_last_error.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/get_current_thread.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/get_current_process.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container_hash/detail/limits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container_hash/detail/hash_float.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container_hash/detail/float_functions.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/container/detail/std_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/msvc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/has_constraints.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/general.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/concept_undef.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/concept_def.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/borland.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/concept/detail/backward_compatibility.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/system.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/static_assert.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/is_evenly_divisible_by.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/string_ops.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/storage_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/platform.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/pause.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_windows.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_msvc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_msvc_common.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_msvc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_linux_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_x86_dcas.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_sync.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_sparc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_ppc_common.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_arm_common.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_gcc_alpha.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_extending_cas_based.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_emulated.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/ops_cas_based.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/operations_lockfree.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/operations_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/operations.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/lockpool.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/link.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/interlocked.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/integral_extend.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/int_sizes.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/hwcaps_gcc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/hwcaps_gcc_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/hwcaps_gcc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/fp_ops_generic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/fp_ops_emulated.hpp
...on 1800th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/fp_operations_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/fp_operations.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/float_sizes.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_msvc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_msvc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_generic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_gcc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_gcc_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_gcc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_ops_emulated.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_operations_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_operations.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_fp_ops_generic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_fp_ops_emulated.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_fp_operations_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/extra_fp_operations.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_windows.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_msvc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_msvc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_linux_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_x86.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_sync.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_sparc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_ppc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_atomic.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_arm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/caps_gcc_alpha.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/bitwise_fp_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/bitwise_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/atomic_template.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/atomic_flag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/addressof.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/align/detail/is_alignment.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/align/detail/is_aligned.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/yes_no_type.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/trim.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/std_containers_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/split.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/sequence_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/replace.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/predicate_facade.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/predicate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/join.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/iter_find.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/finder.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/find_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/find_format.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/find.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/erase.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/constants.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/config.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/concept.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/compare.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/classification.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/case_conv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/cxx11/all_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/parameter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/modifier.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/finalize.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/errors.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/argument_factory.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/argument.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/iterator/token_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/iterator/input_iterator_facade.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/basic_cstring/io.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/basic_cstring/compare.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/basic_cstring/basic_cstring_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/basic_cstring/basic_cstring.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/old/interface.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/old/impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/tolerance_manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/print_helper.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/per_element_manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/lexicographic_manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/it_pair.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/indirections.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/expression_holder.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/tools/detail/bitwise_manip.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/detail/mpl/sign.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/detail/mpl/lcm.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/detail/mpl/gcd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/ratio/detail/mpl/abs.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/tuple/detail/is_single_return.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/slot5.hpp
...on 1900th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/slot4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/slot3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/slot2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/slot1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/shared.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/def.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/slot/detail/counter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/detail/split.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/seq/detail/is_empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/detail/for.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/punctuation/detail/is_begin_parens.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/detail/fold_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/detail/fold_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/start.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/self.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/rlocal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/local.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/finish.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/facilities/detail/is_empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/detail/dmc/auto_rec.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/detail/while.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/arithmetic/detail/div_base.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/udt_builtin_mixture.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/sign_mixture.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/old_numeric_cast.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/numeric_cast_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/meta.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/is_subranged.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/int_float_mixture.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/converter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/conversion_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/bounds.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/vector0.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/tag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/push_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/push_back.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/pop_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/pop_back.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/numbered_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/numbered.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/item.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/include_preprocessed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/clear.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/begin_end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/back.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/at.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/vector/aux_/O1_size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/tag.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/push_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/push_back.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/pop_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/numbered_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/numbered.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/item.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/include_preprocessed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/clear.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/begin_end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/list/aux_/O1_size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/token_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/sub.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/repeat.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/range.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/partial_spec_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/is_seq.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/filter_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/ext_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/enum.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/default_params.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/def_params_tail.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessor/add.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/workaround.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/use_preprocessed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/typeof.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/ttp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/static_constant.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/preprocessor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/pp_counter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/overload_resolution.hpp
...on 2000th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/nttp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/msvc_typename.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/msvc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/intel.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/integral.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/has_xxx.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/has_apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/gpu.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/gcc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/forwarding.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/eti.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/dtp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/dmc_ambiguous_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/dependent_nttp.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/compiler.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/bcc.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/arrays.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/config/adl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_8.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_19.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_18.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_17.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_16.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_15.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_14.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_13.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_12.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_11.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner3_10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_8.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_19.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_18.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_17.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_16.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_15.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_14.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_13.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_12.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_11.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner2_10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_8.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_19.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_18.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_17.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_16.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_15.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_14.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_13.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_12.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_11.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/rational_horner1_10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_8.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_19.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_18.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_17.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_16.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_15.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_14.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_13.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_12.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_11.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner3_10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_8.hpp
...on 2100th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_19.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_18.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_17.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_16.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_15.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_14.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_13.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_12.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_11.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner2_10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_9.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_8.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_7.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_6.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_20.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_19.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_18.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_17.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_16.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_15.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_14.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_13.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_12.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_11.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/tools/detail/polynomial_horner1_10.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/unchecked_factorial.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/unchecked_bernoulli.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/round_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/lgamma_small.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/lanczos_sse2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/igamma_large.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/igamma_inverse.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/gamma_inva.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/fp_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/erf_inv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/math/special_functions/detail/bernoulli_details.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/single_view_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/single_view/single_view.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/joint_view_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/joint_view_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/joint_view/joint_view.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/view/iterator_range/iterator_range.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/tuple_tie.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/tuple_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/tuple_expand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/tuple/detail/make_tuple.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/segmented_fold_until_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/pp_round.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/mpl_iterator_category.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/is_view.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/is_mpl_sequence.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/index_sequence.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/enabler.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/category_of.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/as_fusion_element.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/support/detail/access.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/io/out.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/io/in.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/value_at.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/size.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/segments.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/end.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/empty.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/begin.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/intrinsic/at.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/sequence/comparison/enable_comparison.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/mpl/fusion_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/mpl/convert_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/segmented_next_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/segmented_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/segmented_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/segment_sequence.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/distance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/advance.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/adapt_value_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/iterator/detail/adapt_deref_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/vector_iterator.hpp
...on 2200th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/vector_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/vector/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/nil.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/list_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/cons_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/cons_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/list/cons.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/container/generation/ignore.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/algorithm/transformation/push_front.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/algorithm/transformation/push_back.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/struct/adapt_struct.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/fusion/adapted/mpl/mpl_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/detail/winapi/detail/deprecated_namespace.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/thread_clock.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/process_cpu_clocks.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/chrono/detail/inlined/chrono.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/make_unsigned.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/make_signed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/is_trivially_default_constructible.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/is_signed.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/is_integral.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/is_iec559.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/is_function.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/is_floating_point.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/integral_constant.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/atomic/detail/type_traits/conditional.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/std/string_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/std/slist_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/std/list_traits.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/util.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/trim.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/sequence.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/replace_storage.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/predicate.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/formatter.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/finder.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/find_iterator.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/find_format_store.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/find_format_all.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/find_format.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/classification.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/algorithm/string/detail/case_conv.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/env/fetch.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/cla/parser.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/test/utils/runtime/cla/argv_traverser.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/detail/msvc/for.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/detail/edg/for.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/repetition/detail/dmc/for.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/detail/edg/fold_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/detail/edg/fold_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/list/detail/dmc/fold_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/reverse5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/reverse4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/reverse3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/reverse2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/reverse1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/forward5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/forward4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/forward3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/forward2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/iter/forward1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/upper5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/upper4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/upper3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/upper2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/upper1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/lower5.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/lower4.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/lower3.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/lower2.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/iteration/detail/bounds/lower1.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/detail/msvc/while.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/detail/edg/while.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/preprocessor/control/detail/dmc/while.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/preprocessed/numeric_cast_traits_long_long.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/numeric/conversion/detail/preprocessed/numeric_cast_traits_common.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/unpack_args.hpp
...on 2300th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/plain/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ttp/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/shift_left.hpp
...on 2400th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/no_ctps/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/mwcw/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/reverse_fold_impl.hpp
...on 2500th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc70/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/msvc60/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/or.hpp
...on 2600th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/gcc/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/list_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/less.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/lambda_no_ctps.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/iter_fold_if_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/inherit.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/greater_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/greater.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/full_lambda.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/divides.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/deque.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/bitxor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/bitor.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/bitand.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/bind_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/basic_bind.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/arg.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/apply_wrap.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/apply_fwd.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/apply.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/and.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/advance_forward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/dmc/advance_backward.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/vector_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/vector.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/unpack_args.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/times.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/template_arity.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/shift_right.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/shift_left.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/set_c.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/set.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/reverse_iter_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/reverse_fold_impl.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/quote.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/plus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/placeholders.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/or.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/not_equal_to.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/modulus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/minus.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/map.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/list_c.hpp
...on 2700th target...
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/list.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/less_equal.hpp
common.copy /data3/genome_graphs/vg-rotella/include/boost/mpl/aux_/preprocessed/bcc_pre590/less.hpp
...updated 2702 targets...
. ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am
. ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am
. ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac
. ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am
. ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am
. ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2" ./autogen.sh || true
./autogen.sh: 22: ./autogen.sh: [[: not found
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'.
libtoolize: copying file 'acinclude.d/libtool.m4'
libtoolize: copying file 'acinclude.d/ltoptions.m4'
libtoolize: copying file 'acinclude.d/ltsugar.m4'
libtoolize: copying file 'acinclude.d/ltversion.m4'
libtoolize: copying file 'acinclude.d/lt~obsolete.m4'
configure.ac:15: installing './compile'
configure.ac:13: installing './config.guess'
configure.ac:13: installing './config.sub'
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
cluster/Makefile.am: installing './depcomp'
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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checking for C++ compiler default output file name... a.out
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checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
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checking how to truncate binary pipes... /usr/bin/miniconda3/bin/dd bs=4096 count=1
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checking if mt is a manifest tool... no
checking how to run the C preprocessor... /usr/bin/gcc -E
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checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking whether the Boost::Program_Options library is available... yes
configure: error: Could not find a version of the library!
. ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2" ./configure --with-boost=/data3/genome_graphs/vg-rotella
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
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checking dependency style of /usr/bin/g++... gcc3
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configure: creating ./config.status
config.status: creating Makefile
config.status: creating vowpalwabbit/Makefile
config.status: creating cluster/Makefile
config.status: creating library/Makefile
config.status: creating libvw.pc
config.status: creating vowpalwabbit/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
. ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2" make
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit'
Making all in vowpalwabbit
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit'
make all-am
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit'
depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1
depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1
depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread
libtool: link: /usr/bin/g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread -L/data3/genome_graphs/vg-rotella/lib/../lib -L/data3/genome_graphs/vg/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/data3/genome_graphs/vg/lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -msse4.2 -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0
libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0")
libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so")
libtool: link: ar cru .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/liballreduce.a
libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" )
depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1
depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1
depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1
depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1
depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1
depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1
depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1
depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1
depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1
depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1
depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1
depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1
depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1
depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1
depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1
depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1
depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1
depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1
depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1
depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1
depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1
depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1
depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1
depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1
depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1
depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1
depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1
depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1
depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1
depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1
depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1
depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1
depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1
depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1
depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1
depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1
depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1
depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1
depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1
depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1
depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1
depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1
depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1
depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1
depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1
depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1
depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1
depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1
depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1
depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1
depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1
depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1
depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1
depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1
depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1
depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1
depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1
depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1
depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1
depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1
depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1
depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1
depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1
depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1
depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1
depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1
depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1
depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1
depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1
depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1
depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1
depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1
depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1
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/bin/bash ../libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread
libtool: link: /usr/bin/g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit/.libs ./.libs/liballreduce.so -L/lib -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -lz -lpthread -L/data3/genome_graphs/vg-rotella/lib/../lib -L/data3/genome_graphs/vg/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/data3/genome_graphs/vg/lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -msse4.2 -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0")
libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so")
libtool: link: ar cru .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libvw.a
libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" )
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc
mv -f .deps/vw-main.Tpo .deps/vw-main.Po
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o vw vw-main.o libvw.la liballreduce.la -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread
libtool: link: /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o .libs/vw vw-main.o ./.libs/libvw.so -L/lib /data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit/.libs/liballreduce.so ./.libs/liballreduce.so -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -lz -lpthread
depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\
mv -f $depbase.Tpo $depbase.Po
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o active_interactor active_interactor.o -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread
libtool: link: /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I ../rapidjson/include -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o active_interactor active_interactor.o -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit'
Making all in cluster
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/cluster'
depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -I/data3/genome_graphs/vg-rotella/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -I/data3/genome_graphs/vg-rotella/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../vowpalwabbit/vw_exception.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -I/data3/genome_graphs/vg-rotella/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\
mv -f $depbase.Tpo $depbase.Po
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la
libtool: link: /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -L/data3/genome_graphs/vg-rotella/lib -L/lib ../vowpalwabbit/.libs/liballreduce.so -lboost_program_options -lz -lpthread
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/cluster'
Making all in library
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/library'
depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\
mv -f $depbase.Tpo $depbase.Po
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la
libtool: link: /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o .libs/library_example library_example.o -L/data3/genome_graphs/vg-rotella/lib -L/lib ../vowpalwabbit/.libs/libvw.so /data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit/.libs/liballreduce.so ../vowpalwabbit/.libs/liballreduce.so -lboost_program_options -lz -lpthread
depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\
mv -f $depbase.Tpo $depbase.Po
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la
libtool: link: /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o .libs/ezexample_train ezexample_train.o -L/data3/genome_graphs/vg-rotella/lib -L/lib ../vowpalwabbit/.libs/libvw.so /data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit/.libs/liballreduce.so ../vowpalwabbit/.libs/liballreduce.so -lboost_program_options -lz -lpthread
depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\
mv -f $depbase.Tpo $depbase.Po
/bin/bash ../libtool --tag=CXX --mode=link /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -L/data3/genome_graphs/vg-rotella/lib -lboost_program_options -L/lib -lz -lpthread -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la
libtool: link: /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I/include -I ../rapidjson/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -msse4.2 -o .libs/ezexample_predict ezexample_predict.o -L/data3/genome_graphs/vg-rotella/lib -L/lib ../vowpalwabbit/.libs/libvw.so /data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/vowpalwabbit/.libs/liballreduce.so ../vowpalwabbit/.libs/liballreduce.so -lboost_program_options -lz -lpthread
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit/library'
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/vowpal_wabbit'
. ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /data3/genome_graphs/vg-rotella/lib/
. ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /data3/genome_graphs/vg-rotella/include/vowpalwabbit
. ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /data3/genome_graphs/vg-rotella/include/vowpalwabbit/
rm -f lib/cleaned_old_protobuf*
rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc
rm -Rf include/google/protobuf deps/protobuf
touch lib/cleaned_old_protobuf_v003
rm -f /data3/genome_graphs/vg-rotella/include/vg.pb.h /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h
rm -Rf /data3/genome_graphs/vg-rotella/include/vg/io/
. ./source_me.sh && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/data3/genome_graphs/vg-rotella/lib/pkgconfig: cmake -DCMAKE_PREFIX_PATH=/data3/genome_graphs/vg-rotella -DCMAKE_LIBRARY_PATH=/data3/genome_graphs/vg-rotella/lib -DCMAKE_INSTALL_PREFIX=/data3/genome_graphs/vg-rotella -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install
-- The CXX compiler identification is GNU 5.4.0
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
CMake Warning at /usr/share/cmake-3.15/Modules/FindProtobuf.cmake:499 (message):
Protobuf compiler version 3.11.4 doesn't match library version 3.9.2
Call Stack (most recent call first):
CMakeLists.txt:14 (find_package)
-- Found Protobuf: /usr/local/lib/libprotobuf.so;-lpthread (found version "3.9.2")
-- Checking for module 'protobuf'
-- Found protobuf, version 3.9.2
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
-- Checking for module 'htslib'
-- Found htslib, version 1.10.2
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/libvgio
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
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/usr/bin/cmake -E cmake_progress_start /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
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cd /data3/genome_graphs/vg-rotella/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color=
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/depend.internal".
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/depend.internal".
Scanning dependencies of target link_target
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make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build
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/usr/bin/cmake -E create_symlink . vg
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make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend
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[ 3%] Running cpp protocol buffer compiler on deps/vg.proto
/usr/bin/miniconda3/bin/protoc --cpp_out /data3/genome_graphs/vg-rotella/deps/libvgio -I /data3/genome_graphs/vg-rotella/deps/libvgio/deps /data3/genome_graphs/vg-rotella/deps/libvgio/deps/vg.proto
cd /data3/genome_graphs/vg-rotella/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color=
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal".
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal".
Scanning dependencies of target vgio_static
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make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[ 7%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:12:2: error: #error This file was generated by a newer version of protoc which is
#error This file was generated by a newer version of protoc which is
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:13:2: error: #error incompatible with your Protocol Buffer headers. Please update
#error incompatible with your Protocol Buffer headers. Please update
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:14:2: error: #error your headers.
#error your headers.
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:256:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:254:15: error: ‘const char* vg::Graph::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:255:35: error: ‘google::protobuf::uint8* vg::Graph::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:433:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:431:15: error: ‘const char* vg::Node::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:432:35: error: ‘google::protobuf::uint8* vg::Node::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:597:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:595:15: error: ‘const char* vg::Edge::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:596:35: error: ‘google::protobuf::uint8* vg::Edge::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:769:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:767:15: error: ‘const char* vg::Edit::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:768:35: error: ‘google::protobuf::uint8* vg::Edit::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:926:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:924:15: error: ‘const char* vg::Mapping::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:925:35: error: ‘google::protobuf::uint8* vg::Mapping::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1091:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1089:15: error: ‘const char* vg::Position::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1090:35: error: ‘google::protobuf::uint8* vg::Position::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1259:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1257:15: error: ‘const char* vg::Path::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1258:35: error: ‘google::protobuf::uint8* vg::Path::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1436:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1434:15: error: ‘const char* vg::Alignment::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:1435:35: error: ‘google::protobuf::uint8* vg::Alignment::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2029:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2027:15: error: ‘const char* vg::MultipathAlignment::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2028:35: error: ‘google::protobuf::uint8* vg::MultipathAlignment::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2327:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2325:15: error: ‘const char* vg::Subpath::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2326:35: error: ‘google::protobuf::uint8* vg::Subpath::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2497:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2495:15: error: ‘const char* vg::KmerMatch::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2496:35: error: ‘google::protobuf::uint8* vg::KmerMatch::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2665:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2663:15: error: ‘const char* vg::BasePileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2664:35: error: ‘google::protobuf::uint8* vg::BasePileup::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2840:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2838:15: error: ‘const char* vg::NodePileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2839:35: error: ‘google::protobuf::uint8* vg::NodePileup::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2988:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2986:15: error: ‘const char* vg::EdgePileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:2987:35: error: ‘google::protobuf::uint8* vg::EdgePileup::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3162:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3160:15: error: ‘const char* vg::Pileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3161:35: error: ‘google::protobuf::uint8* vg::Pileup::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3319:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3317:15: error: ‘const char* vg::Snarl::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3318:35: error: ‘google::protobuf::uint8* vg::Snarl::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3560:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3558:15: error: ‘const char* vg::Visit::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3559:35: error: ‘google::protobuf::uint8* vg::Visit::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3716:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3714:15: error: ‘const char* vg::SnarlTraversal::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3715:35: error: ‘google::protobuf::uint8* vg::SnarlTraversal::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3871:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3869:15: error: ‘const char* vg::Locus::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:3870:35: error: ‘google::protobuf::uint8* vg::Locus::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4108:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4106:15: error: ‘const char* vg::Genotype::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4107:35: error: ‘google::protobuf::uint8* vg::Genotype::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4305:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4303:15: error: ‘const char* vg::Support::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4304:35: error: ‘google::protobuf::uint8* vg::Support::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4483:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4481:15: error: ‘const char* vg::LocationSupport::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4482:35: error: ‘google::protobuf::uint8* vg::LocationSupport::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4660:76: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const fina
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4658:15: error: ‘const char* vg::Translation::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’ marked ‘final’, but is not virtual
const char* _InternalParse(const char* ptr, ::PROTOBUF_NAMESPACE_ID::internal::ParseContext* ctx) final;
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:4659:35: error: ‘google::protobuf::uint8* vg::Translation::_InternalSerialize(google::protobuf::uint8*, int*) const’ marked ‘final’, but is not virtual
::PROTOBUF_NAMESPACE_ID::uint8* _InternalSerialize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:145:68: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_ListValue_google_2fprotobuf_2fstruct_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:159:141: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
OBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_BasePileup_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:173:135: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
::PROTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Edge_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:188:39: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Edge_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:202:135: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
::PROTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Edit_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:216:139: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
OTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Genotype_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:233:39: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Path_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:247:140: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
TOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_KmerMatch_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:263:39: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Edge_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:280:43: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Genotype_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:296:39: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Edit_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:312:68: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_ListValue_google_2fprotobuf_2fstruct_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:326:135: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
::PROTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Node_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:341:45: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_BasePileup_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:356:42: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Mapping_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:372:45: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_EdgePileup_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:386:139: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
OTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Position_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:406:136: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
:PROTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Snarl_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:421:40: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Snarl_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:436:39: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Path_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:450:138: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
ROTOBUF_NAMESPACE_ID::internal::SCCInfoBase::kUninitialized), 0, 0, InitDefaultsscc_info_Support_vg_2eproto}, {}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:465:39: error: too many initializers for ‘google::protobuf::internal::SCCInfoBase’
&scc_info_Path_vg_2eproto.base,}};
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Graph::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:974:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<10>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:986:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<18>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:998:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<26>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1007:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1022:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Graph::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1030:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1031:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1038:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1039:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1046:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1047:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1052:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Graph::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1089:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::Graph::InternalSwap(vg::Graph* ’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1145:35: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Node>’
node_.InternalSwap(&other->node_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1146:35: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Edge>’
edge_.InternalSwap(&other->edge_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1147:35: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Path>’
path_.InternalSwap(&other->path_);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Node::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc🔢85: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Node.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc🔢11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Node.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1243:81: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Node.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1243:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Node.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1260:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1275:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Node::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1286:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1296:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1302:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1307:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Node::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1344:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Edge::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1526:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1541:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Edge::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1548:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1554:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1560:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1566:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1572:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1577:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Edge::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1624:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Edit::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1796:85: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Edit.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1796:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Edit.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1806:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1821:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Edit::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1828:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1834:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1844:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1849:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Edit::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:1886:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Mapping::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2057:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<18>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2073:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2088:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Mapping::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2095:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2096:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2104:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2105:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2111:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2116:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Mapping::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2153:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::Mapping::InternalSwap(vg::Mapping*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2213:35: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Edit>’
edit_.InternalSwap(&other->edit_);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Position::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2322:85: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Position.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2322:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Position.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2332:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2347:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Position::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2354:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2360:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2366:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2376:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2381:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Position::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2423:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Path::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2581:81: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Path.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2581:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Path.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2594:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<18>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2617:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2632:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Path::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2643:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2650:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2651:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2657:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2663:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2668:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Path::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2710:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::Path::InternalSwap(vg::Path*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2774:41: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Mapping>’
mapping_.InternalSwap(&other->mapping_);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Alignment::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2998:90: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:2998:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3014:86: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3014:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3052:93: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.sample_name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3052:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.sample_name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3061:92: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.read_group"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3061:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.read_group"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3102:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<138>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3114:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<146>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3126:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<154>(ptr));
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3221:110: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.fragment_length_distribution"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3221:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Alignment.fragment_length_distribution"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3259:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3274:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Alignment::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3285:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3291:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3292:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3303:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3309:22: error: request for member ‘WriteBytesMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteBytesMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3315:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3321:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3327:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3337:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3347:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3353:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3354:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3361:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3362:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3369:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3375:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3382:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3383:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3390:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3391:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3398:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3399:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3405:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3411:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3417:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3423:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3429:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3435:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3441:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3447:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3453:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3461:24: error: request for member ‘WriteInt32Packed’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteInt32Packed(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3468:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3474:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3484:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3490:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3496:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3497:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3504:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3510:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3511:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3517:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Alignment::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3742:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::Alignment::InternalSwap(vg::Alignment*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3892:43: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Path>’
fragment_.InternalSwap(&other->fragment_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3893:37: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Locus>’
locus_.InternalSwap(&other->locus_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3894:39: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Position>’
refpos_.InternalSwap(&other->refpos_);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::MultipathAlignment::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4074:99: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4074:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4091:95: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4091:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4100:102: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.sample_name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4100:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.sample_name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4109:101: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.read_group"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4109:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.read_group"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4122:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<50>(ptr));
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4147:107: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.paired_read_name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4147:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.MultipathAlignment.paired_read_name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4164:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4179:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::MultipathAlignment::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4190:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4196:22: error: request for member ‘WriteBytesMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteBytesMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4206:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4216:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4226:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4233:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4234:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4240:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4248:24: error: request for member ‘WriteUInt32Packed’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteUInt32Packed(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4259:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4265:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4266:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4272:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::MultipathAlignment::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4366:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::MultipathAlignment::InternalSwap(vg::MultipathAlignment*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4451:41: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Subpath>’
subpath_.InternalSwap(&other->subpath_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Subpath::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4585:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4600:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Subpath::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4607:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4608:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4617:24: error: request for member ‘WriteUInt32Packed’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteUInt32Packed(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4624:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4629:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Subpath::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4674:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::KmerMatch::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4822:90: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.KmerMatch.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4822:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.KmerMatch.sequence"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4853:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4868:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::KmerMatch::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4879:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4885:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4891:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4897:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4902:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::KmerMatch::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4944:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::BasePileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5121:88: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.BasePileup.bases"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5121:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.BasePileup.bases"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5139:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5154:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::BasePileup::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5161:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5167:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5177:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5183:22: error: request for member ‘WriteBytesMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteBytesMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5188:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::BasePileup::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5232:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::NodePileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5390:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<18>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5399:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5414:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::NodePileup::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5421:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5428:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5429:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5434:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::NodePileup::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5464:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::NodePileup::InternalSwap(vg::NodePileup*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5521:49: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::BasePileup>’
base_pileup_.InternalSwap(&other->base_pileup_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::EdgePileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5655:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5670:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::EdgePileup::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5677:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5678:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5685:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5691:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5697:22: error: request for member ‘WriteBytesMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteBytesMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5702:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::EdgePileup::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5746:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Pileup::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5894:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<10>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5906:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<18>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5915:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5930:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Pileup::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5938:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5939:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5946:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5947:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5952:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Pileup::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:5982:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::Pileup::InternalSwap(vg::Pileup*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6037:51: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::NodePileup>’
node_pileups_.InternalSwap(&other->node_pileups_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6038:51: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::EdgePileup>’
edge_pileups_.InternalSwap(&other->edge_pileups_);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Snarl::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6204:82: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Snarl.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6204:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Snarl.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6242:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6257:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Snarl::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6264:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6271:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6272:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6279:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6280:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6287:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6288:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6299:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6305:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6311:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6317:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6323:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6328:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Snarl::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6398:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Visit::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6606:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6621:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Visit::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6628:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6634:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6635:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6642:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6647:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Visit::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6682:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::SnarlTraversal::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6829:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<10>(ptr));
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6837:91: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.SnarlTraversal.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6837:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.SnarlTraversal.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6847:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6862:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::SnarlTraversal::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6870:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6871:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6881:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6886:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::SnarlTraversal::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6916:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::SnarlTraversal::InternalSwap(vg::SnarlTraversal*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:6974:37: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Visit>’
visit_.InternalSwap(&other->visit_);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:16:0:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Locus::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7079:82: error: could not convert ‘str’ from ‘std::__cxx11::basic_string<char>*’ to ‘google::protobuf::StringPiece’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Locus.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7079:11: note: in expansion of macro ‘CHK_’
CHK_(::PROTOBUF_NAMESPACE_ID::internal::VerifyUTF8(str, "vg.Locus.name"));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7092:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<18>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7104:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<26>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7116:20: error: ‘ExpectTag’ is not a member of ‘google::protobuf::internal’
} while (::PROTOBUF_NAMESPACE_ID::internal::ExpectTag<34>(ptr));
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7142:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7157:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Locus::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7168:22: error: request for member ‘WriteStringMaybeAliased’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteStringMaybeAliased(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7175:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7176:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7183:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7184:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7191:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7192:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7198:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7199:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7206:22: error: request for member ‘WriteFixedPacked’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteFixedPacked(6, _internal_allele_log_likelihood(), target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7210:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Locus::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7276:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘void vg::Locus::InternalSwap(vg::Locus* ’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7340:39: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Path>’
allele_.InternalSwap(&other->allele_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7341:41: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Support>’
support_.InternalSwap(&other->support_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7342:43: error: ‘google::protobuf::internal::RepeatedPtrFieldBase’ is an inaccessible base of ‘google::protobuf::RepeatedPtrField<vg::Genotype>’
genotype_.InternalSwap(&other->genotype_);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Genotype::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7472:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7487:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Genotype::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7496:24: error: request for member ‘WriteInt32Packed’ in ‘* stream’, which is of non-class type ‘int’
target = stream->WriteInt32Packed(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7503:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7509:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7515:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7521:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7527:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7532:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Genotype::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7588:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Support::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7776:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7791:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Support::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7798:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7804:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7810:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7816:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7822:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7827:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Support::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:7868:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::LocationSupport::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8110:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8125:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::LocationSupport::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8132:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8133:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8140:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8141:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8148:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8153:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::LocationSupport::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8195:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘const char* vg::Translation::_InternalParse(const char*, google::protobuf::internal::ParseContext*)’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8388:68: error: no matching function for call to ‘UnknownFieldParse(google::protobuf::uint32&, google::protobuf::internal::InternalMetadataWithArena*, const char*&, google::protobuf::internal::ParseContext*&)’
ptr = UnknownFieldParse(tag, &_internal_metadata_, ptr, ctx);
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h:750:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, google::protobuf::internal::InternalMetadataWithArenaLite*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:750:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘google::protobuf::internal::InternalMetadataWithArenaLite*’
/usr/local/include/google/protobuf/parse_context.h:748:54: note: candidate: const char* google::protobuf::internal::UnknownFieldParse(google::protobuf::uint32, std::__cxx11::string*, const char*, google::protobuf::internal::ParseContext*)
PROTOBUF_EXPORT PROTOBUF_MUST_USE_RESULT const char* UnknownFieldParse(
^
/usr/local/include/google/protobuf/parse_context.h:748:54: note: no known conversion for argument 2 from ‘google::protobuf::internal::InternalMetadataWithArena*’ to ‘std::__cxx11::string* {aka std::__cxx11::basic_string<char>*}’
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: At global scope:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8403:74: error: ‘google::protobuf::io::EpsCopyOutputStream’ has not been declared
::PROTOBUF_NAMESPACE_ID::uint8* target, ::PROTOBUF_NAMESPACE_ID::io::EpsCopyOutputStream* stream) const {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘google::protobuf::uint8* vg::Translation::_InternalSerialize(google::protobuf::uint8*, int*) const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8410:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8411:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8418:22: error: request for member ‘EnsureSpace’ in ‘* strea ’, which is of non-class type ‘int’
target = stream->EnsureSpace(target);
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8419:14: error: ‘InternalWriteMessage’ is not a member of ‘google::protobuf::internal::WireFormatLite’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormatLite::
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8425:14: error: ‘InternalSerializeUnknownFieldsToArray’ is not a member of ‘google::protobuf::internal::WireFormat’
target = ::PROTOBUF_NAMESPACE_ID::internal::WireFormat::InternalSerializeUnknownFieldsToArray(
^
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc: In member function ‘virtual size_t vg::Translation::ByteSizeLong() const’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:8455:12: error: ‘ComputeUnknownFieldsSize’ is not a member of ‘google::protobuf::internal’
return ::PROTOBUF_NAMESPACE_ID::internal::ComputeUnknownFieldsSize(
^
In file included from /usr/local/include/google/protobuf/map_type_handler.h:34:0,
from /usr/local/include/google/protobuf/map.h:49,
from /usr/local/include/google/protobuf/generated_message_table_driven.h:34,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.h:26,
from /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:4:
/usr/local/include/google/protobuf/parse_context.h: In instantiation of ‘const char* google::protobuf::internal::ParseContext::ParseMessage(T*, const char*) [with T = google::protobuf::Struct]’:
/data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc:3249:70: required from here
/usr/local/include/google/protobuf/parse_context.h:578:7: error: ‘class google::protobuf::Struct’ has no member named ‘_InternalParse’
ptr = msg->_InternalParse(ptr, this);
^
CMakeFiles/vgio_static.dir/build.make:70: recipe for target 'CMakeFiles/vgio_static.dir/vg.pb.cc.o' failed
make[3]: *** [CMakeFiles/vgio_static.dir/vg.pb.cc.o] Error 1
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
CMakeFiles/Makefile2:109: recipe for target 'CMakeFiles/vgio_static.dir/all' failed
make[2]: *** [CMakeFiles/vgio_static.dir/all] Error 2
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
Makefile:129: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
Makefile:454: recipe for target 'lib/libvgio.a' failed
make: *** [lib/libvgio.a] Error 2
This went well for a very long time before it stopped working… The errors seem to be caused by incompatible protoc versions, so maybe I have to update that again. I wish the vg repo had been updated to reflect that, if it is true.
protobuf / protoc
protoc --version
libprotoc 3.11.4
Since only “Protobuf 3” is mentioned, I would have expected that that is enough, BUT:
export PATH=/usr/bin:$PATH
protoc --version
libprotoc 2.6.1
And there is also:
export PATH=/usr/local/bin:$PATH
protoc --version
libprotoc 3.9.2
This latter version is the one I installed when I first installed vg, so what about the other(s)?
which protoc
/usr/bin/miniconda3/bin/protoc
I see! The 3.11.4 version was installed via conda, so now we have three and they probably get confused somewhere during the vg make process.
cd deps/libvgio/
./install.sh /data3/genome_graphs/vg-rotella
Library will be installed in '/data3/genome_graphs/vg-rotella'
CMake Warning at /usr/share/cmake-3.15/Modules/FindProtobuf.cmake:499 (message):
Protobuf compiler version 3.11.4 doesn't match library version 3.9.2
Call Stack (most recent call first):
CMakeLists.txt:14 (find_package)
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/libvgio
make: *** No targets specified and no makefile found. Stop.
ERROR: Build failed.
I can’t just remove the protobuf version from miniconda, I don’t know who or what needs it. But how do I tell the installer where to look for the right version?
Apparently there is a way to edit the cmake cache and environment variables, and this seems to be done in certain files: CMakeLists.txt (I hope) and CMakeCache.txt.
In CMakeCache.txt in /deps/libvgio the protobuf libraries are listed as being located in /usr/local/lib/, which would be the 3.9.2 version, but for some reason in the same file, the executable is listed with the miniconda path. Maybe I can just change that to the other one?
./install.sh /data3/genome_graphs/vg-rotella
Library will be installed in '/data3/genome_graphs/vg-rotella'
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/libvgio
make: *** No targets specified and no makefile found. Stop.
ERROR: Build failed.
OK… The error is gone, but the build still failed? Let’s see what happens if I try to make vg again.
cd ../../
. ./source_me.sh && make
Sadly, nothing has changed and I still get the same long list of errors. Maybe I need the miniconda version of protobuf? Or the problem is that the executable path changed back to the miniconda one in CMakeCache.txt. CMakeLists.txt shows the code that looks for protobuf, and I think the problem is that it looks for protobuf twice:
# We need to find Protobuf normally to get the protobuf_generate_cpp command
find_package(Protobuf REQUIRED)
# But we also need to find it via pkg-config to get both the static and dynamic libraries.
# The default find_package implementation can only give us one or the other.
pkg_check_modules(Protobuf REQUIRED protobuf)
Maybe I’m looking at this the wrong way, maybe I should “just” make sure that both versions are the same…
cd ~
wget https://github.com/protocolbuffers/protobuf/releases/download/v3.11.4/protobuf-all-3.11.4.zip
unzip protobuf-all-3.11.4.zip
cd protobuf-3.11.4
./configure
make
make check
sudo make install
-> click here for the output of the above code <-
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1025' is supported by ustar format... yes
checking whether GID '100' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking whether /usr/bin/gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of /usr/bin/gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
checking dependency style of /usr/bin/g++... gcc3
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking C++ compiler flags...... use user-supplied: -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/miniconda3/bin/dd
checking how to truncate binary pipes... /usr/bin/miniconda3/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for /usr/bin/gcc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/gcc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/gcc static flag -static works... yes
checking if /usr/bin/gcc supports -c -o file.o... yes
checking if /usr/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking for ld used by /usr/bin/g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/g++ option to produce PIC... -fPIC -DPIC
checking if /usr/bin/g++ PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/g++ static flag -static works... yes
checking if /usr/bin/g++ supports -c -o file.o... yes
checking if /usr/bin/g++ supports -c -o file.o... (cached) yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether the linker supports version scripts... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking whether /usr/bin/g++ supports C++11 features by default... no
checking whether /usr/bin/g++ supports C++11 features with -std=c++11... yes
checking whether -latomic is needed... no
checking whether /usr/bin/gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating benchmarks/Makefile
config.status: creating conformance/Makefile
config.status: creating protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in third_party/googletest (/home/spo12/protobuf-3.11.4/third_party/googletest)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' 'CC=/usr/bin/gcc' 'CFLAGS=-I /data3/genome_graphs/vg-rotella/include ' 'CXX=/usr/bin/g++' 'CXXFLAGS=-I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic ' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
=== configuring in googletest (/home/spo12/protobuf-3.11.4/third_party/googletest/googletest)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' 'CC=/usr/bin/gcc' 'CFLAGS=-I /data3/genome_graphs/vg-rotella/include ' 'CXX=/usr/bin/g++' 'CXXFLAGS=-I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic ' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking whether /usr/bin/gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of /usr/bin/gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
checking dependency style of /usr/bin/g++... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/miniconda3/bin/dd
checking how to truncate binary pipes... /usr/bin/miniconda3/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for /usr/bin/gcc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/gcc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/gcc static flag -static works... yes
checking if /usr/bin/gcc supports -c -o file.o... yes
checking if /usr/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking for ld used by /usr/bin/g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/g++ option to produce PIC... -fPIC -DPIC
checking if /usr/bin/g++ PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/g++ static flag -static works... yes
checking if /usr/bin/g++ supports -c -o file.o... yes
checking if /usr/bin/g++ supports -c -o file.o... (cached) yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... /usr/bin/miniconda3/bin/python
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gtest-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in googlemock (/home/spo12/protobuf-3.11.4/third_party/googletest/googlemock)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' 'CC=/usr/bin/gcc' 'CFLAGS=-I /data3/genome_graphs/vg-rotella/include ' 'CXX=/usr/bin/g++' 'CXXFLAGS=-I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic ' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking whether /usr/bin/gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of /usr/bin/gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
checking dependency style of /usr/bin/g++... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/miniconda3/bin/dd
checking how to truncate binary pipes... /usr/bin/miniconda3/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for /usr/bin/gcc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/gcc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/gcc static flag -static works... yes
checking if /usr/bin/gcc supports -c -o file.o... yes
checking if /usr/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking for ld used by /usr/bin/g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/g++ option to produce PIC... -fPIC -DPIC
checking if /usr/bin/g++ PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/g++ static flag -static works... yes
checking if /usr/bin/g++ supports -c -o file.o... yes
checking if /usr/bin/g++ supports -c -o file.o... (cached) yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... /usr/bin/miniconda3/bin/python
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking for gtest-config... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gmock-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
spo12@CPI-SL64001:~/protobuf-3.11.4$ make
make all-recursive
make[1]: Entering directory '/home/spo12/protobuf-3.11.4'
Making all in .
make[2]: Entering directory '/home/spo12/protobuf-3.11.4'
make[2]: Leaving directory '/home/spo12/protobuf-3.11.4'
Making all in src
make[2]: Entering directory '/home/spo12/protobuf-3.11.4/src'
CXX google/protobuf/compiler/main.o
CXX google/protobuf/stubs/bytestream.lo
CXX google/protobuf/stubs/common.lo
CXX google/protobuf/stubs/int128.lo
CXX google/protobuf/io/io_win32.lo
CXX google/protobuf/stubs/status.lo
CXX google/protobuf/stubs/statusor.lo
CXX google/protobuf/stubs/stringpiece.lo
CXX google/protobuf/stubs/stringprintf.lo
CXX google/protobuf/stubs/structurally_valid.lo
CXX google/protobuf/stubs/strutil.lo
CXX google/protobuf/stubs/time.lo
CXX google/protobuf/any_lite.lo
CXX google/protobuf/arena.lo
CXX google/protobuf/extension_set.lo
CXX google/protobuf/generated_enum_util.lo
CXX google/protobuf/generated_message_util.lo
CXX google/protobuf/generated_message_table_driven_lite.lo
CXX google/protobuf/implicit_weak_message.lo
CXX google/protobuf/message_lite.lo
CXX google/protobuf/parse_context.lo
CXX google/protobuf/repeated_field.lo
CXX google/protobuf/wire_format_lite.lo
CXX google/protobuf/io/coded_stream.lo
CXX google/protobuf/io/strtod.lo
CXX google/protobuf/io/zero_copy_stream.lo
CXX google/protobuf/io/zero_copy_stream_impl.lo
CXX google/protobuf/io/zero_copy_stream_impl_lite.lo
CXX google/protobuf/any.pb.lo
CXX google/protobuf/api.pb.lo
CXX google/protobuf/any.lo
CXX google/protobuf/descriptor.lo
CXX google/protobuf/descriptor_database.lo
CXX google/protobuf/descriptor.pb.lo
CXX google/protobuf/duration.pb.lo
CXX google/protobuf/dynamic_message.lo
CXX google/protobuf/empty.pb.lo
CXX google/protobuf/extension_set_heavy.lo
CXX google/protobuf/field_mask.pb.lo
CXX google/protobuf/generated_message_reflection.lo
CXX google/protobuf/generated_message_table_driven.lo
CXX google/protobuf/map_field.lo
CXX google/protobuf/message.lo
CXX google/protobuf/reflection_ops.lo
CXX google/protobuf/service.lo
CXX google/protobuf/source_context.pb.lo
CXX google/protobuf/struct.pb.lo
CXX google/protobuf/stubs/substitute.lo
CXX google/protobuf/text_format.lo
CXX google/protobuf/timestamp.pb.lo
CXX google/protobuf/type.pb.lo
CXX google/protobuf/unknown_field_set.lo
CXX google/protobuf/wire_format.lo
CXX google/protobuf/wrappers.pb.lo
CXX google/protobuf/io/gzip_stream.lo
CXX google/protobuf/io/printer.lo
CXX google/protobuf/io/tokenizer.lo
CXX google/protobuf/compiler/importer.lo
CXX google/protobuf/compiler/parser.lo
CXX google/protobuf/util/delimited_message_util.lo
CXX google/protobuf/util/field_comparator.lo
CXX google/protobuf/util/field_mask_util.lo
CXX google/protobuf/util/internal/datapiece.lo
CXX google/protobuf/util/internal/default_value_objectwriter.lo
CXX google/protobuf/util/internal/error_listener.lo
CXX google/protobuf/util/internal/field_mask_utility.lo
CXX google/protobuf/util/internal/json_escaping.lo
CXX google/protobuf/util/internal/json_objectwriter.lo
CXX google/protobuf/util/internal/json_stream_parser.lo
CXX google/protobuf/util/internal/object_writer.lo
CXX google/protobuf/util/internal/protostream_objectsource.lo
CXX google/protobuf/util/internal/protostream_objectwriter.lo
CXX google/protobuf/util/internal/proto_writer.lo
CXX google/protobuf/util/internal/type_info.lo
CXX google/protobuf/util/internal/type_info_test_helper.lo
CXX google/protobuf/util/internal/utility.lo
CXX google/protobuf/util/json_util.lo
CXX google/protobuf/util/message_differencer.lo
CXX google/protobuf/util/time_util.lo
CXX google/protobuf/util/type_resolver_util.lo
CXXLD libprotobuf.la
ar: `u' modifier ignored since `D' is the default (see `U')
CXX google/protobuf/compiler/code_generator.lo
CXX google/protobuf/compiler/command_line_interface.lo
CXX google/protobuf/compiler/plugin.lo
CXX google/protobuf/compiler/plugin.pb.lo
CXX google/protobuf/compiler/subprocess.lo
CXX google/protobuf/compiler/zip_writer.lo
CXX google/protobuf/compiler/cpp/cpp_enum.lo
CXX google/protobuf/compiler/cpp/cpp_enum_field.lo
CXX google/protobuf/compiler/cpp/cpp_extension.lo
CXX google/protobuf/compiler/cpp/cpp_field.lo
CXX google/protobuf/compiler/cpp/cpp_file.lo
CXX google/protobuf/compiler/cpp/cpp_generator.lo
CXX google/protobuf/compiler/cpp/cpp_helpers.lo
CXX google/protobuf/compiler/cpp/cpp_map_field.lo
CXX google/protobuf/compiler/cpp/cpp_message.lo
CXX google/protobuf/compiler/cpp/cpp_message_field.lo
CXX google/protobuf/compiler/cpp/cpp_padding_optimizer.lo
CXX google/protobuf/compiler/cpp/cpp_primitive_field.lo
CXX google/protobuf/compiler/cpp/cpp_service.lo
CXX google/protobuf/compiler/cpp/cpp_string_field.lo
CXX google/protobuf/compiler/java/java_context.lo
CXX google/protobuf/compiler/java/java_enum.lo
CXX google/protobuf/compiler/java/java_enum_lite.lo
CXX google/protobuf/compiler/java/java_enum_field.lo
CXX google/protobuf/compiler/java/java_enum_field_lite.lo
CXX google/protobuf/compiler/java/java_extension.lo
CXX google/protobuf/compiler/java/java_extension_lite.lo
CXX google/protobuf/compiler/java/java_field.lo
CXX google/protobuf/compiler/java/java_file.lo
CXX google/protobuf/compiler/java/java_generator.lo
CXX google/protobuf/compiler/java/java_generator_factory.lo
CXX google/protobuf/compiler/java/java_helpers.lo
CXX google/protobuf/compiler/java/java_map_field.lo
CXX google/protobuf/compiler/java/java_map_field_lite.lo
CXX google/protobuf/compiler/java/java_message.lo
CXX google/protobuf/compiler/java/java_message_lite.lo
CXX google/protobuf/compiler/java/java_message_builder.lo
CXX google/protobuf/compiler/java/java_message_builder_lite.lo
CXX google/protobuf/compiler/java/java_message_field.lo
CXX google/protobuf/compiler/java/java_message_field_lite.lo
CXX google/protobuf/compiler/java/java_name_resolver.lo
CXX google/protobuf/compiler/java/java_primitive_field.lo
CXX google/protobuf/compiler/java/java_primitive_field_lite.lo
CXX google/protobuf/compiler/java/java_shared_code_generator.lo
CXX google/protobuf/compiler/java/java_service.lo
CXX google/protobuf/compiler/java/java_string_field.lo
CXX google/protobuf/compiler/java/java_string_field_lite.lo
CXX google/protobuf/compiler/java/java_doc_comment.lo
CXX google/protobuf/compiler/js/js_generator.lo
CXX google/protobuf/compiler/js/well_known_types_embed.lo
CXX google/protobuf/compiler/objectivec/objectivec_enum.lo
CXX google/protobuf/compiler/objectivec/objectivec_enum_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_extension.lo
CXX google/protobuf/compiler/objectivec/objectivec_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_file.lo
CXX google/protobuf/compiler/objectivec/objectivec_generator.lo
CXX google/protobuf/compiler/objectivec/objectivec_helpers.lo
CXX google/protobuf/compiler/objectivec/objectivec_map_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_message.lo
CXX google/protobuf/compiler/objectivec/objectivec_message_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_oneof.lo
CXX google/protobuf/compiler/objectivec/objectivec_primitive_field.lo
CXX google/protobuf/compiler/php/php_generator.lo
CXX google/protobuf/compiler/python/python_generator.lo
CXX google/protobuf/compiler/ruby/ruby_generator.lo
CXX google/protobuf/compiler/csharp/csharp_doc_comment.lo
CXX google/protobuf/compiler/csharp/csharp_enum.lo
CXX google/protobuf/compiler/csharp/csharp_enum_field.lo
CXX google/protobuf/compiler/csharp/csharp_field_base.lo
CXX google/protobuf/compiler/csharp/csharp_generator.lo
CXX google/protobuf/compiler/csharp/csharp_helpers.lo
CXX google/protobuf/compiler/csharp/csharp_map_field.lo
CXX google/protobuf/compiler/csharp/csharp_message.lo
CXX google/protobuf/compiler/csharp/csharp_message_field.lo
CXX google/protobuf/compiler/csharp/csharp_primitive_field.lo
CXX google/protobuf/compiler/csharp/csharp_reflection_class.lo
CXX google/protobuf/compiler/csharp/csharp_repeated_enum_field.lo
CXX google/protobuf/compiler/csharp/csharp_repeated_message_field.lo
CXX google/protobuf/compiler/csharp/csharp_repeated_primitive_field.lo
CXX google/protobuf/compiler/csharp/csharp_source_generator_base.lo
CXX google/protobuf/compiler/csharp/csharp_wrapper_field.lo
CXXLD libprotoc.la
ar: `u' modifier ignored since `D' is the default (see `U')
CXXLD protoc
CXXLD libprotobuf-lite.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/home/spo12/protobuf-3.11.4/src'
make[1]: Leaving directory '/home/spo12/protobuf-3.11.4'
spo12@CPI-SL64001:~/protobuf-3.11.4$ make check
Making check in .
make[1]: Entering directory '/home/spo12/protobuf-3.11.4'
make check-local
make[2]: Entering directory '/home/spo12/protobuf-3.11.4'
Making lib/libgmock.a lib/libgmock_main.a in gmock
make[3]: Entering directory '/home/spo12/protobuf-3.11.4/third_party/googletest/googletest'
depbase=`echo src/gtest-all.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -I./build-aux -I. -I./include -pthread -DGTEST_HAS_PTHREAD=1 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -MT src/gtest-all.lo -MD -MP -MF $depbase.Tpo -c -o src/gtest-all.lo src/gtest-all.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /usr/bin/g++ -DHAVE_CONFIG_H -I. -I./build-aux -I. -I./include -pthread -DGTEST_HAS_PTHREAD=1 -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -MT src/gtest-all.lo -MD -MP -MF src/.deps/gtest-all.Tpo -c src/gtest-all.cc -fPIC -DPIC -o src/.libs/gtest-all.o
In file included from /usr/include/c++/5/type_traits:35:0,
from ./include/gtest/internal/gtest-port.h:253,
from ./include/gtest/internal/gtest-internal.h:40,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
/usr/include/c++/5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support \
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:830:12: error: ‘std::get’ has not been declared
using std::get;
^
./include/gtest/internal/gtest-port.h:831:12: error: ‘std::make_tuple’ has not been declared
using std::make_tuple;
^
./include/gtest/internal/gtest-port.h:832:12: error: ‘std::tuple’ has not been declared
using std::tuple;
^
./include/gtest/internal/gtest-port.h:833:12: error: ‘std::tuple_element’ has not been declared
using std::tuple_element;
^
./include/gtest/internal/gtest-port.h:834:12: error: ‘std::tuple_size’ has not been declared
using std::tuple_size;
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:964:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(RE);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1007:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestLog);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1007:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestLog);
^
./include/gtest/internal/gtest-port.h: In function ‘void testing::internal::FlushInfoLog()’:
./include/gtest/internal/gtest-port.h:1017:37: error: ‘nullptr’ was not declared in this scope
inline void FlushInfoLog() { fflush(nullptr); }
^
./include/gtest/internal/gtest-port.h: In function ‘To testing::internal::DownCast_(From*)’:
./include/gtest/internal/gtest-port.h:1140:17: error: ‘nullptr’ was not declared in this scope
const To to = nullptr;
^
./include/gtest/internal/gtest-port.h:1146:21: error: ‘nullptr’ was not declared in this scope
GTEST_CHECK_(f == nullptr || dynamic_cast<To>(f) != nullptr);
^
./include/gtest/internal/gtest-port.h:1038:37: note: in definition of macro ‘GTEST_CHECK_’
if (::testing::internal::IsTrue(condition)) \
^
./include/gtest/internal/gtest-port.h: In function ‘void testing::internal::SleepMilliseconds(int)’:
./include/gtest/internal/gtest-port.h:1218:20: error: ‘nullptr’ was not declared in this scope
nanosleep(&time, nullptr);
^
./include/gtest/internal/gtest-port.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1267:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Notification);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1267:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Notification);
^
./include/gtest/internal/gtest-port.h: In constructor ‘testing::internal::Notification::Notification()’:
./include/gtest/internal/gtest-port.h:1236:60: error: ‘nullptr’ was not declared in this scope
GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_init(&mutex_, nullptr));
^
./include/gtest/internal/gtest-port.h:1050:32: note: in definition of macro ‘GTEST_CHECK_POSIX_SUCCESS_’
if (const int gtest_error = (posix_call)) \
^
./include/gtest/internal/gtest-port.h: In function ‘void* testing::internal::ThreadFuncWithCLinkage(void*)’:
./include/gtest/internal/gtest-port.h:1345:10: error: ‘nullptr’ was not declared in this scope
return nullptr;
^
./include/gtest/internal/gtest-port.h: At global scope:
./include/gtest/internal/gtest-port.h:1376:20: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~ThreadWithParam() override { Join(); }
^
./include/gtest/internal/gtest-port.h:1385:12: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void Run() override {
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1399:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ThreadWithParam);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1399:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ThreadWithParam);
^
./include/gtest/internal/gtest-port.h: In constructor ‘testing::internal::ThreadWithParam<T>::ThreadWithParam(void (*)(T), T, testing::internal::Notification*)’:
./include/gtest/internal/gtest-port.h:1374:34: error: ‘nullptr’ was not declared in this scope
pthread_create(&thread_, nullptr, &ThreadFuncWithCLinkage, base));
^
./include/gtest/internal/gtest-port.h:1050:32: note: in definition of macro ‘GTEST_CHECK_POSIX_SUCCESS_’
if (const int gtest_error = (posix_call)) \
^
./include/gtest/internal/gtest-port.h: In member function ‘void testing::internal::ThreadWithParam<T>::Join()’:
./include/gtest/internal/gtest-port.h:1380:56: error: ‘nullptr’ was not declared in this scope
GTEST_CHECK_POSIX_SUCCESS_(pthread_join(thread_, nullptr));
^
./include/gtest/internal/gtest-port.h:1050:32: note: in definition of macro ‘GTEST_CHECK_POSIX_SUCCESS_’
if (const int gtest_error = (posix_call)) \
^
./include/gtest/internal/gtest-port.h: In member function ‘void testing::internal::ThreadWithParam<T>::Run()’:
./include/gtest/internal/gtest-port.h:1386:30: error: ‘nullptr’ was not declared in this scope
if (thread_can_start_ != nullptr) thread_can_start_->WaitForNotification();
^
./include/gtest/internal/gtest-port.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1757:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Mutex);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1757:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Mutex);
^
./include/gtest/internal/gtest-port.h: In constructor ‘testing::internal::Mutex::Mutex()’:
./include/gtest/internal/gtest-port.h:1749:60: error: ‘nullptr’ was not declared in this scope
GTEST_CHECK_POSIX_SUCCESS_(pthread_mutex_init(&mutex_, nullptr));
^
./include/gtest/internal/gtest-port.h:1050:32: note: in definition of macro ‘GTEST_CHECK_POSIX_SUCCESS_’
if (const int gtest_error = (posix_call)) \
^
./include/gtest/internal/gtest-port.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1775:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestMutexLock);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1775:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestMutexLock);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1832:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ValueHolder);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1832:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ValueHolder);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1864:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ValueHolderFactory);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1864:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ValueHolderFactory);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1873:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultValueHolderFactory);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1873:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultValueHolderFactory);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1886:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(InstanceValueHolderFactory);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1886:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(InstanceValueHolderFactory);
^
./include/gtest/internal/gtest-port.h:1891:8: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
std::unique_ptr<ValueHolderFactory> default_factory_;
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-port.h:1893:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ThreadLocal);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-port.h:1893:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ThreadLocal);
^
./include/gtest/internal/gtest-port.h: In constructor ‘testing::internal::ThreadLocal<T>::ThreadLocal()’:
./include/gtest/internal/gtest-port.h:1802:28: error: class ‘testing::internal::ThreadLocal<T>’ does not have any field named ‘default_factory_’
: key_(CreateKey()), default_factory_(new DefaultValueHolderFactory()) {}
^
./include/gtest/internal/gtest-port.h: In constructor ‘testing::internal::ThreadLocal<T>::ThreadLocal(const T&)’:
./include/gtest/internal/gtest-port.h:1805:9: error: class ‘testing::internal::ThreadLocal<T>’ does not have any field named ‘default_factory_’
default_factory_(new InstanceValueHolderFactory(value)) {}
^
./include/gtest/internal/gtest-port.h: In member function ‘T* testing::internal::ThreadLocal<T>::GetOrCreateValue() const’:
./include/gtest/internal/gtest-port.h:1847:19: error: ‘nullptr’ was not declared in this scope
if (holder != nullptr) {
^
./include/gtest/internal/gtest-port.h:1851:37: error: ‘default_factory_’ was not declared in this scope
ValueHolder* const new_holder = default_factory_->MakeNewHolder();
^
./include/gtest/internal/gtest-port.h: At global scope:
./include/gtest/internal/gtest-port.h:2158:1: error: expected unqualified-id before ‘[’ token
[[noreturn]] inline void Abort() { abort(); }
^
In file included from ./include/gtest/internal/gtest-internal.h:64:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/gtest-message.h:196:14: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr< ::std::stringstream> ss_;
^
./include/gtest/gtest-message.h: In copy constructor ‘testing::Message::Message(const testing::Message&)’:
./include/gtest/gtest-message.h:101:33: error: class ‘testing::Message’ does not have any field named ‘ss_’
Message(const Message& msg) : ss_(new ::std::stringstream) { // NOLINT
^
./include/gtest/gtest-message.h:102:6: error: ‘ss_’ was not declared in this scope
*ss_ << msg.GetString();
^
./include/gtest/gtest-message.h: In constructor ‘testing::Message::Message(const char*)’:
./include/gtest/gtest-message.h:106:39: error: class ‘testing::Message’ does not have any field named ‘ss_’
explicit Message(const char* str) : ss_(new ::std::stringstream) {
^
./include/gtest/gtest-message.h:107:6: error: ‘ss_’ was not declared in this scope
*ss_ << str;
^
./include/gtest/gtest-message.h: In member function ‘testing::Message& testing::Message::operator<<(const T&)’:
./include/gtest/gtest-message.h:128:6: error: ‘ss_’ was not declared in this scope
*ss_ << val;
^
./include/gtest/gtest-message.h: In member function ‘testing::Message& testing::Message::operator<<(T* const&)’:
./include/gtest/gtest-message.h:147:20: error: ‘nullptr’ was not declared in this scope
if (pointer == nullptr) {
^
./include/gtest/gtest-message.h:148:8: error: ‘ss_’ was not declared in this scope
*ss_ << "(null)";
^
./include/gtest/gtest-message.h:150:8: error: ‘ss_’ was not declared in this scope
*ss_ << pointer;
^
./include/gtest/gtest-message.h: In member function ‘testing::Message& testing::Message::operator<<(testing::Message::BasicNarrowIoManip)’:
./include/gtest/gtest-message.h:162:6: error: ‘ss_’ was not declared in this scope
*ss_ << val;
^
In file included from ./include/gtest/internal/gtest-internal.h:67:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-type-util.h: In function ‘std::__cxx11::string testing::internal::GetTypeName()’:
./include/gtest/internal/gtest-type-util.h:91:52: error: ‘nullptr’ was not declared in this scope
char* const readable_name = __cxa_demangle(name, nullptr, nullptr, &status);
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h: At global scope:
./include/gtest/internal/gtest-internal.h:122:27: error: ‘enable_if’ in namespace ‘std’ does not name a template type
typename std::enable_if<!std::is_convertible<T, Sink>::value,
^
./include/gtest/internal/gtest-internal.h:122:36: error: expected ‘>’ before ‘<’ token
typename std::enable_if<!std::is_convertible<T, Sink>::value,
^
./include/gtest/internal/gtest-internal.h:131:1: error: expected unqualified-id before ‘using’
using TypeIsValidNullptrConstant = std::integral_constant<
^
./include/gtest/internal/gtest-internal.h:147:6: error: ‘true_type’ in namespace ‘std’ does not name a type
std::true_type IsNullLiteralHelper(Secret*, std::true_type);
^
./include/gtest/internal/gtest-internal.h:148:6: error: ‘false_type’ in namespace ‘std’ does not name a type
std::false_type IsNullLiteralHelper(IgnoredValue, std::false_type);
^
./include/gtest/internal/gtest-internal.h:149:6: error: ‘false_type’ in namespace ‘std’ does not name a type
std::false_type IsNullLiteralHelper(IgnoredValue, std::true_type);
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-internal.h:484:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestFactoryBase);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-internal.h:484:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestFactoryBase);
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h:492:20: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
Test* CreateTest() override { return new TestClass; }
^
./include/gtest/internal/gtest-internal.h:509:7: error: expected nested-name-specifier before ‘SetUpTestSuiteFunc’
using SetUpTestSuiteFunc = void (*)();
^
./include/gtest/internal/gtest-internal.h:510:7: error: expected nested-name-specifier before ‘TearDownTestSuiteFunc’
using TearDownTestSuiteFunc = void (*)();
^
./include/gtest/internal/gtest-internal.h:524:7: error: expected nested-name-specifier before ‘SetUpTearDownSuiteFuncType’
using SetUpTearDownSuiteFuncType = void (*)();
^
./include/gtest/internal/gtest-internal.h:526:8: error: ‘SetUpTearDownSuiteFuncType’ does not name a type
inline SetUpTearDownSuiteFuncType GetNotDefaultOrNull(
^
./include/gtest/internal/gtest-internal.h:538:9: error: expected nested-name-specifier before ‘Test’
using Test =
^
./include/gtest/internal/gtest-internal.h:541:10: error: ‘SetUpTearDownSuiteFuncType’ does not name a type
static SetUpTearDownSuiteFuncType GetSetUpCaseOrSuite() {
^
./include/gtest/internal/gtest-internal.h:554:10: error: ‘SetUpTearDownSuiteFuncType’ does not name a type
static SetUpTearDownSuiteFuncType GetTearDownCaseOrSuite() {
^
./include/gtest/internal/gtest-internal.h:589:30: error: ‘SetUpTestSuiteFunc’ has not been declared
TypeId fixture_class_id, SetUpTestSuiteFunc set_up_tc,
^
./include/gtest/internal/gtest-internal.h:590:5: error: ‘TearDownTestSuiteFunc’ has not been declared
TearDownTestSuiteFunc tear_down_tc, TestFactoryBase* factory);
^
./include/gtest/internal/gtest-internal.h: In member function ‘bool testing::internal::TypedTestSuitePState::AddTestName(const char*, int, const char*, const char*)’:
./include/gtest/internal/gtest-internal.h:618:7: error: ‘Abort’ is not a member of ‘testing::internal::posix’
posix::Abort();
^
./include/gtest/internal/gtest-internal.h: At global scope:
./include/gtest/internal/gtest-internal.h:650:7: error: expected nested-name-specifier before ‘TypedTestCasePState’
using TypedTestCasePState = TypedTestSuitePState;
^
./include/gtest/internal/gtest-internal.h: In function ‘const char* testing::internal::SkipComma(const char*)’:
./include/gtest/internal/gtest-internal.h:659:16: error: ‘nullptr’ was not declared in this scope
if (comma == nullptr) {
^
./include/gtest/internal/gtest-internal.h: In function ‘std::__cxx11::string testing::internal::GetPrefixUntilComma(const char*)’:
./include/gtest/internal/gtest-internal.h:670:19: error: ‘nullptr’ was not declared in this scope
return comma == nullptr ? str : std::string(str, comma);
^
./include/gtest/internal/gtest-internal.h: In static member function ‘static bool testing::internal::TypeParameterizedTest<Fixture, TestSel, Types>::Register(const char*, const testing::internal::CodeLocation&, const char*, const char*, int, const std::vector<std::__cxx11::basic_string<char> >&)’:
./include/gtest/internal/gtest-internal.h:739:9: error: ‘nullptr’ was not declared in this scope
nullptr, // No value parameter.
^
./include/gtest/internal/gtest-internal.h: In static member function ‘static bool testing::internal::TypeParameterizedTestSuite<Fixture, Tests, Types>::Register(const char*, testing::internal::CodeLocation, const testing::internal::TypedTestSuitePState*, const char*, const char*, const std::vector<std::__cxx11::basic_string<char> >&)’:
./include/gtest/internal/gtest-internal.h:789:7: error: ‘Abort’ is not a member of ‘testing::internal::posix’
posix::Abort();
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-internal.h:873:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Random);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-internal.h:873:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Random);
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h:929:3: error: ‘is_convertible’ is not a member of ‘std’
std::is_convertible<const T*, const ::ProtocolMessage*>::value ||
^
./include/gtest/internal/gtest-internal.h:929:3: error: ‘is_convertible’ is not a member of ‘std’
./include/gtest/internal/gtest-internal.h:929:57: error: template argument 1 is invalid
std::is_convertible<const T*, const ::ProtocolMessage*>::value ||
^
./include/gtest/internal/gtest-internal.h:929:58: error: expected ‘{’ before ‘::’ token
std::is_convertible<const T*, const ::ProtocolMessage*>::value ||
^
./include/gtest/internal/gtest-internal.h:929:66: error: expected initializer before ‘||’ token
std::is_convertible<const T*, const ::ProtocolMessage*>::value ||
^
./include/gtest/internal/gtest-internal.h:959:28: error: expected type-specifier before ‘decltype’
class Iterator = decltype(::std::declval<const C&>().begin()),
^
./include/gtest/internal/gtest-internal.h:959:28: error: expected ‘>’ before ‘decltype’
./include/gtest/internal/gtest-internal.h:964:44: error: default template arguments may not be used in function templates without -std=c++11 or -std=gnu++11
IsContainer IsContainerTest(int /* dummy */) {
^
./include/gtest/internal/gtest-internal.h:987:44: error: ‘nullptr’ was not declared in this scope
static const bool value = sizeof(test<T>(nullptr, nullptr)) == sizeof(int);
^
./include/gtest/internal/gtest-internal.h:987:53: error: ‘nullptr’ was not declared in this scope
static const bool value = sizeof(test<T>(nullptr, nullptr)) == sizeof(int);
^
./include/gtest/internal/gtest-internal.h:1006:9: error: expected nested-name-specifier before ‘value_type’
using value_type = decltype(*std::declval<typename C::const_iterator>());
^
./include/gtest/internal/gtest-internal.h:1007:9: error: expected nested-name-specifier before ‘type’
using type =
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-internal.h:1176:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(NativeArray);
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h:1180:21: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t... Is>
^
./include/gtest/internal/gtest-internal.h:1182:9: error: expected nested-name-specifier before ‘type’
using type = IndexSequence;
^
./include/gtest/internal/gtest-internal.h:1188:21: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t... I, size_t sizeofT>
^
./include/gtest/internal/gtest-internal.h:1190:9: error: expected nested-name-specifier before ‘type’
using type = IndexSequence<I..., (sizeofT + I)..., 2 * sizeofT>;
^
./include/gtest/internal/gtest-internal.h:1192:21: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t... I, size_t sizeofT>
^
./include/gtest/internal/gtest-internal.h:1194:9: error: expected nested-name-specifier before ‘type’
using type = IndexSequence<I..., (sizeofT + I)...>;
^
./include/gtest/internal/gtest-internal.h:1215:9: error: expected nested-name-specifier before ‘type’
using type = T;
^
./include/gtest/internal/gtest-internal.h:1220:41: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t N, typename I, typename... T>
^
./include/gtest/internal/gtest-internal.h:1223:31: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t N, size_t... I, typename... T>
^
./include/gtest/internal/gtest-internal.h:1223:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t N, size_t... I, typename... T>
^
./include/gtest/internal/gtest-internal.h:1227:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename... T>
^
./include/gtest/internal/gtest-internal.h:1233:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename... T, size_t I>
^
./include/gtest/internal/gtest-internal.h:1235:9: error: expected nested-name-specifier before ‘value_type’
using value_type =
^
./include/gtest/internal/gtest-internal.h:1238:25: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
FlatTupleElemBase() = default;
^
./include/gtest/internal/gtest-internal.h:1239:41: error: expected ‘)’ before ‘t’
explicit FlatTupleElemBase(value_type t) : value(std::move(t)) {}
^
./include/gtest/internal/gtest-internal.h:1240:3: error: ‘value_type’ does not name a type
value_type value;
^
./include/gtest/internal/gtest-internal.h:1246:21: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t... Idx, typename... T>
^
./include/gtest/internal/gtest-internal.h:1246:34: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <size_t... Idx, typename... T>
^
./include/gtest/internal/gtest-internal.h:1247:59: error: ‘>>’ should be ‘> >’ within a nested template argument list
struct FlatTupleBase<FlatTuple<T...>, IndexSequence<Idx...>>
^
./include/gtest/internal/gtest-internal.h:1249:9: error: expected nested-name-specifier before ‘Indices’
using Indices = IndexSequence<Idx...>;
^
./include/gtest/internal/gtest-internal.h:1250:21: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
FlatTupleBase() = default;
^
./include/gtest/internal/gtest-internal.h:1251:31: warning: variadic templates only available with -std=c++11 or -std=gnu++11
explicit FlatTupleBase(T... t)
^
./include/gtest/internal/gtest-internal.h: In constructor ‘testing::internal::FlatTupleBase<testing::internal::FlatTuple<T ...>, testing::internal::IndexSequence<I ...> >::FlatTupleBase(T ...)’:
./include/gtest/internal/gtest-internal.h:1252:49: error: ‘move’ is not a member of ‘std’
: FlatTupleElemBase<FlatTuple<T...>, Idx>(std::move(t))... {}
^
./include/gtest/internal/gtest-internal.h: At global scope:
./include/gtest/internal/gtest-internal.h:1264:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename... T>
^
./include/gtest/internal/gtest-internal.h:1267:62: warning: variadic templates only available with -std=c++11 or -std=gnu++11
typename MakeIndexSequence<sizeof...(T)>::type> {
^
./include/gtest/internal/gtest-internal.h:1268:9: error: expected nested-name-specifier before ‘Indices’
using Indices = typename FlatTuple::FlatTupleBase::Indices;
^
./include/gtest/internal/gtest-internal.h:1271:17: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
FlatTuple() = default;
^
./include/gtest/internal/gtest-internal.h:1272:27: warning: variadic templates only available with -std=c++11 or -std=gnu++11
explicit FlatTuple(T... t) : FlatTuple::FlatTupleBase(std::move(t)...) {}
^
./include/gtest/internal/gtest-internal.h:1275:34: error: ‘Indices’ was not declared in this scope
const typename ElemFromList<I, Indices, T...>::type& Get() const {
^
./include/gtest/internal/gtest-internal.h:1275:47: error: template argument 2 is invalid
const typename ElemFromList<I, Indices, T...>::type& Get() const {
^
./include/gtest/internal/gtest-internal.h:1280:28: error: ‘Indices’ was not declared in this scope
typename ElemFromList<I, Indices, T...>::type& Get() {
^
./include/gtest/internal/gtest-internal.h:1280:41: error: template argument 2 is invalid
typename ElemFromList<I, Indices, T...>::type& Get() {
^
./include/gtest/internal/gtest-internal.h: In constructor ‘testing::internal::FlatTuple<T>::FlatTuple(T ...)’:
./include/gtest/internal/gtest-internal.h:1272:57: error: ‘move’ is not a member of ‘std’
explicit FlatTuple(T... t) : FlatTuple::FlatTupleBase(std::move(t)...) {}
^
In file included from ./include/gtest/gtest-matchers.h:46:0,
from ./include/gtest/internal/gtest-death-test-internal.h:39,
from ./include/gtest/gtest-death-test.h:41,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/gtest-printers.h: In function ‘std::basic_ostream<_CharT, _Traits>& testing::internal2::operator<<(std::basic_ostream<_CharT, _Traits>&, const T&)’:
./include/gtest/gtest-printers.h:235:34: error: ‘is_convertible’ is not a member of ‘std’
: std::is_convertible<
^
./include/gtest/gtest-printers.h:236:68: error: template argument 2 is invalid
const T&, internal::BiggestInt>::value
^
./include/gtest/gtest-printers.h:237:38: error: qualified-id in declaration before ‘?’ token
? kConvertibleToInteger
^
./include/gtest/gtest-printers.h: In function ‘void testing::internal::DefaultPrintTo(testing::internal::WrapPrinterType<(testing::internal::DefaultPrinterType)1u>, T*, std::ostream*)’:
./include/gtest/gtest-printers.h:450:12: error: ‘nullptr’ was not declared in this scope
if (p == nullptr) {
^
./include/gtest/gtest-printers.h: In function ‘void testing::internal::DefaultPrintTo(testing::internal::WrapPrinterType<(testing::internal::DefaultPrinterType)2u>, T*, std::ostream*)’:
./include/gtest/gtest-printers.h:462:12: error: ‘nullptr’ was not declared in this scope
if (p == nullptr) {
^
./include/gtest/gtest-printers.h: In function ‘void testing::internal::PrintTo(const T&, std::ostream*)’:
./include/gtest/gtest-printers.h:517:14: error: ‘is_pointer’ is not a member of ‘std’
: !std::is_pointer<T>::value
^
./include/gtest/gtest-printers.h:513:7: error: parse error in template argument list
WrapPrinterType <
^
./include/gtest/gtest-printers.h:519:19: error: ‘is_function’ is not a member of ‘std’
: std::is_function<typename std::remove_pointer<T>::type>::value
^
./include/gtest/gtest-printers.h:519:50: error: ‘remove_pointer’ in namespace ‘std’ does not name a template type
: std::is_function<typename std::remove_pointer<T>::type>::value
^
./include/gtest/gtest-printers.h:519:64: error: expected ‘(’ before ‘<’ token
: std::is_function<typename std::remove_pointer<T>::type>::value
^
./include/gtest/gtest-printers.h:519:66: error: expected primary-expression before ‘>’ token
: std::is_function<typename std::remove_pointer<T>::type>::value
^
./include/gtest/gtest-printers.h:519:67: error: ‘::type’ has not been declared
: std::is_function<typename std::remove_pointer<T>::type>::value
^
./include/gtest/gtest-printers.h:519:74: error: ‘::value’ has not been declared
: std::is_function<typename std::remove_pointer<T>::type>::value
^
./include/gtest/gtest-printers.h:521:42: error: expected primary-expression before ‘)’ token
: kPrintPointer > (),
^
./include/gtest/gtest-printers.h: At global scope:
./include/gtest/gtest-printers.h:636:26: error: variable or field ‘PrintTo’ declared void
inline void PrintTo(std::nullptr_t, ::std::ostream* os) { *os << "(nullptr)"; }
^
./include/gtest/gtest-printers.h:636:21: error: ‘nullptr_t’ is not a member of ‘std’
inline void PrintTo(std::nullptr_t, ::std::ostream* os) { *os << "(nullptr)"; }
^
./include/gtest/gtest-printers.h:636:51: error: expected primary-expression before ‘*’ token
inline void PrintTo(std::nullptr_t, ::std::ostream* os) { *os << "(nullptr)"; }
^
./include/gtest/gtest-printers.h:636:53: error: ‘os’ was not declared in this scope
inline void PrintTo(std::nullptr_t, ::std::ostream* os) { *os << "(nullptr)"; }
^
./include/gtest/gtest-printers.h:639:19: error: variable or field ‘PrintTo’ declared void
void PrintTo(std::reference_wrapper<T> ref, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:639:14: error: ‘reference_wrapper’ is not a member of ‘std’
void PrintTo(std::reference_wrapper<T> ref, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:639:38: error: expected primary-expression before ‘>’ token
void PrintTo(std::reference_wrapper<T> ref, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:639:40: error: ‘ref’ was not declared in this scope
void PrintTo(std::reference_wrapper<T> ref, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:639:59: error: expected primary-expression before ‘*’ token
void PrintTo(std::reference_wrapper<T> ref, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:639:61: error: ‘os’ was not declared in this scope
void PrintTo(std::reference_wrapper<T> ref, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:646:34: error: ‘std::integral_constant’ has not been declared
void PrintTupleTo(const T&, std::integral_constant<size_t, 0>,
^
./include/gtest/gtest-printers.h:646:51: error: expected ‘,’ or ‘...’ before ‘<’ token
void PrintTupleTo(const T&, std::integral_constant<size_t, 0>,
^
./include/gtest/gtest-printers.h:650:36: error: ‘std::integral_constant’ has not been declared
void PrintTupleTo(const T& t, std::integral_constant<size_t, I>,
^
./include/gtest/gtest-printers.h:650:53: error: expected ‘,’ or ‘...’ before ‘<’ token
void PrintTupleTo(const T& t, std::integral_constant<size_t, I>,
^
./include/gtest/gtest-printers.h: In function ‘void testing::internal::PrintTupleTo(const T&, int)’:
./include/gtest/gtest-printers.h:652:19: error: ‘integral_constant’ is not a member of ‘std’
PrintTupleTo(t, std::integral_constant<size_t, I - 1>(), os);
^
./include/gtest/gtest-printers.h:652:48: error: expected primary-expression before ‘,’ token
PrintTupleTo(t, std::integral_constant<size_t, I - 1>(), os);
^
./include/gtest/gtest-printers.h:652:57: error: expected primary-expression before ‘)’ token
PrintTupleTo(t, std::integral_constant<size_t, I - 1>(), os);
^
./include/gtest/gtest-printers.h:652:60: error: ‘os’ was not declared in this scope
PrintTupleTo(t, std::integral_constant<size_t, I - 1>(), os);
^
./include/gtest/gtest-printers.h:658:34: error: ‘tuple_element’ in namespace ‘std’ does not name a template type
UniversalPrinter<typename std::tuple_element<I - 1, T>::type>::Print(
^
./include/gtest/gtest-printers.h:658:47: error: expected template-argument before ‘<’ token
UniversalPrinter<typename std::tuple_element<I - 1, T>::type>::Print(
^
./include/gtest/gtest-printers.h:658:47: error: expected ‘>’ before ‘<’ token
./include/gtest/gtest-printers.h:658:63: error: template argument 1 is invalid
UniversalPrinter<typename std::tuple_element<I - 1, T>::type>::Print(
^
./include/gtest/gtest-printers.h:659:7: error: ‘get’ is not a member of ‘std’
std::get<I - 1>(t), os);
^
./include/gtest/gtest-printers.h:659:29: error: expression list treated as compound expression in initializer [-fpermissive]
std::get<I - 1>(t), os);
^
./include/gtest/gtest-printers.h: At global scope:
./include/gtest/gtest-printers.h:662:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename... Types>
^
./include/gtest/gtest-printers.h:663:27: error: ‘tuple’ in namespace ‘std’ does not name a template type
void PrintTo(const ::std::tuple<Types...>& t, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h:663:32: error: expected ‘,’ or ‘...’ before ‘<’ token
void PrintTo(const ::std::tuple<Types...>& t, ::std::ostream* os) {
^
./include/gtest/gtest-printers.h: In function ‘void testing::internal::PrintTo(int)’:
./include/gtest/gtest-printers.h:664:4: error: ‘os’ was not declared in this scope
*os << "(";
^
./include/gtest/gtest-printers.h:665:16: error: ‘t’ was not declared in this scope
PrintTupleTo(t, std::integral_constant<size_t, sizeof...(Types)>(), os);
^
./include/gtest/gtest-printers.h:665:19: error: ‘integral_constant’ is not a member of ‘std’
PrintTupleTo(t, std::integral_constant<size_t, sizeof...(Types)>(), os);
^
./include/gtest/gtest-printers.h:665:48: error: expected primary-expression before ‘,’ token
PrintTupleTo(t, std::integral_constant<size_t, sizeof...(Types)>(), os);
^
./include/gtest/gtest-printers.h:665:56: warning: variadic templates only available with -std=c++11 or -std=gnu++11
PrintTupleTo(t, std::integral_constant<size_t, sizeof...(Types)>(), os);
^
./include/gtest/gtest-printers.h:665:68: error: expected primary-expression before ‘)’ token
PrintTupleTo(t, std::integral_constant<size_t, sizeof...(Types)>(), os);
^
./include/gtest/gtest-printers.h: In static member function ‘static void testing::internal::UniversalTersePrinter<const char*>::Print(const char*, std::ostream*)’:
./include/gtest/gtest-printers.h:841:16: error: ‘nullptr’ was not declared in this scope
if (str == nullptr) {
^
./include/gtest/gtest-printers.h: In static member function ‘static void testing::internal::UniversalTersePrinter<const wchar_t*>::Print(const wchar_t*, std::ostream*)’:
./include/gtest/gtest-printers.h:861:16: error: ‘nullptr’ was not declared in this scope
if (str == nullptr) {
^
./include/gtest/gtest-printers.h: At global scope:
./include/gtest/gtest-printers.h:900:51: error: ‘std::integral_constant’ has not been declared
void TersePrintPrefixToStrings(const Tuple&, std::integral_constant<size_t, 0>,
^
./include/gtest/gtest-printers.h:900:68: error: expected ‘,’ or ‘...’ before ‘<’ token
void TersePrintPrefixToStrings(const Tuple&, std::integral_constant<size_t, 0>,
^
./include/gtest/gtest-printers.h:904:37: error: ‘std::integral_constant’ has not been declared
std::integral_constant<size_t, I>,
^
./include/gtest/gtest-printers.h:904:54: error: expected ‘,’ or ‘...’ before ‘<’ token
std::integral_constant<size_t, I>,
^
./include/gtest/gtest-printers.h: In function ‘void testing::internal::TersePrintPrefixToStrings(const Tuple&, int ’:
./include/gtest/gtest-printers.h:906:32: error: ‘integral_constant’ is not a member of ‘std’
TersePrintPrefixToStrings(t, std::integral_constant<size_t, I - 1>(),
^
./include/gtest/gtest-printers.h:906:61: error: expected primary-expression before ‘,’ token
TersePrintPrefixToStrings(t, std::integral_constant<size_t, I - 1>(),
^
./include/gtest/gtest-printers.h:906:70: error: expected primary-expression before ‘)’ token
TersePrintPrefixToStrings(t, std::integral_constant<size_t, I - 1>(),
^
./include/gtest/gtest-printers.h:907:29: error: ‘strings’ was not declared in this scope
strings);
^
./include/gtest/gtest-printers.h:909:23: error: ‘get’ is not a member of ‘std’
UniversalTersePrint(std::get<I - 1>(t), &ss);
^
./include/gtest/gtest-printers.h: In function ‘testing::internal::Strings testing::internal::UniversalTersePrintTupleFieldsToStrings(const Tuple&)’:
./include/gtest/gtest-printers.h:920:14: error: ‘integral_constant’ is not a member of ‘std’
value, std::integral_constant<size_t, std::tuple_size<Tuple>::value>(),
^
./include/gtest/gtest-printers.h:920:43: error: expected primary-expression before ‘,’ token
value, std::integral_constant<size_t, std::tuple_size<Tuple>::value>(),
^
./include/gtest/gtest-printers.h:920:45: error: ‘tuple_size’ is not a member of ‘std’
value, std::integral_constant<size_t, std::tuple_size<Tuple>::value>(),
^
./include/gtest/gtest-printers.h:920:66: error: expected primary-expression before ‘>’ token
value, std::integral_constant<size_t, std::tuple_size<Tuple>::value>(),
^
./include/gtest/gtest-printers.h:920:67: error: ‘::value’ has not been declared
value, std::integral_constant<size_t, std::tuple_size<Tuple>::value>(),
^
./include/gtest/gtest-printers.h:920:76: error: expected primary-expression before ‘)’ token
value, std::integral_constant<size_t, std::tuple_size<Tuple>::value>(),
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-matchers.h💯3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(MatchResultListener);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-matchers.h💯3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(MatchResultListener);
^
In file included from ./include/gtest/internal/gtest-death-test-internal.h:39:0,
from ./include/gtest/gtest-death-test.h:41,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h: In member function ‘testing::MatchResultListener& testing::MatchResultListener::operator<<(const T&)’:
./include/gtest/gtest-matchers.h:84:20: error: ‘nullptr’ was not declared in this scope
if (stream_ != nullptr) *stream_ << x;
^
./include/gtest/gtest-matchers.h: In member function ‘bool testing::MatchResultListener::IsInterested() const’:
./include/gtest/gtest-matchers.h:95:49: error: ‘nullptr’ was not declared in this scope
bool IsInterested() const { return stream_ != nullptr; }
^
./include/gtest/gtest-matchers.h: At global scope:
./include/gtest/gtest-matchers.h:182:28: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~MatcherInterfaceAdapter() override { delete impl_; }
^
./include/gtest/gtest-matchers.h:184:39: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void DescribeTo(::std::ostream* os) const override { impl_->DescribeTo(os); }
^
./include/gtest/gtest-matchers.h:186:47: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void DescribeNegationTo(::std::ostream* os) const override {
^
./include/gtest/gtest-matchers.h:191:55: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
MatchResultListener* listener) const override {
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-matchers.h:198:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(MatcherInterfaceAdapter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-matchers.h:198:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(MatcherInterfaceAdapter);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-matchers.h:232:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DummyMatchResultListener);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-matchers.h:232:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DummyMatchResultListener);
^
In file included from ./include/gtest/internal/gtest-death-test-internal.h:39:0,
from ./include/gtest/gtest-death-test.h:41,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h: In constructor ‘testing::internal::DummyMatchResultListener::DummyMatchResultListener()’:
./include/gtest/gtest-matchers.h:229:52: error: ‘nullptr’ was not declared in this scope
DummyMatchResultListener() : MatchResultListener(nullptr) {}
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-matchers.h:244:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(StreamMatchResultListener);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-matchers.h:244:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(StreamMatchResultListener);
^
In file included from ./include/gtest/internal/gtest-death-test-internal.h:39:0,
from ./include/gtest/gtest-death-test.h:41,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h:299:37: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
MatcherBase(const MatcherBase&) = default;
^
./include/gtest/gtest-matchers.h:300:48: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
MatcherBase& operator=(const MatcherBase&) = default;
^
./include/gtest/gtest-matchers.h:301:26: error: expected ‘,’ or ‘...’ before ‘&&’ token
MatcherBase(MatcherBase&&) = default;
^
./include/gtest/gtest-matchers.h:301:32: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
MatcherBase(MatcherBase&&) = default;
^
./include/gtest/gtest-matchers.h:301:32: error: invalid constructor; you probably meant ‘testing::internal::MatcherBase<T> (const testing::internal::MatcherBase<T>&)’
./include/gtest/gtest-matchers.h:302:37: error: expected ‘,’ or ‘...’ before ‘&&’ token
MatcherBase& operator=(MatcherBase&&) = default;
^
./include/gtest/gtest-matchers.h:302:43: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
MatcherBase& operator=(MatcherBase&&) = default;
^
./include/gtest/gtest-matchers.h:307:8: error: ‘shared_ptr’ in namespace ‘std’ does not name a template type
std::shared_ptr<const MatcherInterface<const T&>> impl_;
^
./include/gtest/gtest-matchers.h:296:59: error: ‘nullptr’ was not declared in this scope
!internal::IsSame<U, const U&>::value>::type* = nullptr)
^
./include/gtest/gtest-matchers.h: In member function ‘bool testing::internal::MatcherBase<T>::MatchAndExplain(const T&, testing::MatchResultListener*) const’:
./include/gtest/gtest-matchers.h:256:12: error: ‘impl_’ was not declared in this scope
return impl_->MatchAndExplain(x, listener);
^
./include/gtest/gtest-matchers.h: In member function ‘void testing::internal::MatcherBase<T>::DescribeTo(std::ostream*) const’:
./include/gtest/gtest-matchers.h:266:47: error: ‘impl_’ was not declared in this scope
void DescribeTo(::std::ostream* os) const { impl_->DescribeTo(os); }
^
./include/gtest/gtest-matchers.h: In member function ‘void testing::internal::MatcherBase<T>::DescribeNegationTo(std::ostream*) const’:
./include/gtest/gtest-matchers.h:270:5: error: ‘impl_’ was not declared in this scope
impl_->DescribeNegationTo(os);
^
./include/gtest/gtest-matchers.h: In member function ‘const testing::MatcherDescriberInterface* testing::internal::MatcherBase<T>::GetDescriber() const’:
./include/gtest/gtest-matchers.h:283:12: error: ‘impl_’ was not declared in this scope
return impl_.get();
^
./include/gtest/gtest-matchers.h: In constructor ‘testing::internal::MatcherBase<T>::MatcherBase(const testing::MatcherInterface<const T&>*)’:
./include/gtest/gtest-matchers.h:290:66: error: class ‘testing::internal::MatcherBase<T>’ does not have any field named ‘impl_’
explicit MatcherBase(const MatcherInterface<const T&>* impl) : impl_(impl) {}
^
./include/gtest/gtest-matchers.h: In constructor ‘testing::internal::MatcherBase<T>::MatcherBase(const testing::MatcherInterface<U>*, typename testing::internal::EnableIf<(! testing::internal::IsSame<U, const U&>::value)>::type*)’:
./include/gtest/gtest-matchers.h:297:9: error: class ‘testing::internal::MatcherBase<T>’ does not have any field named ‘impl_’
: impl_(new internal::MatcherInterfaceAdapter<U>(impl)) {}
^
./include/gtest/gtest-matchers.h: At global scope:
./include/gtest/gtest-matchers.h:331:72: error: ‘nullptr’ was not declared in this scope
!internal::IsSame<U, const U&>::value>::type* = nullptr)
^
./include/gtest/gtest-matchers.h: In instantiation of ‘class testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&>’:
./include/gtest/gtest-matchers.h:344:24: required from here
./include/gtest/gtest-matchers.h:302:16: error: defaulted declaration ‘testing::internal::MatcherBase<T>& testing::internal::MatcherBase<T>::operator=(testing::internal::MatcherBase<T>) [with T = const std::__cxx11::basic_string<char>&; testing::internal::MatcherBase<T> = testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&> ’
MatcherBase& operator=(MatcherBase&&) = default;
^
./include/gtest/gtest-matchers.h:302:16: error: does not match expected signature ‘testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&>& testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&>::operator=(testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&>&)’
./include/gtest/gtest-matchers.h: In instantiation of ‘class testing::internal::MatcherBase<std::__cxx11::basic_string<char> >’:
./include/gtest/gtest-matchers.h:367:24: required from here
./include/gtest/gtest-matchers.h:302:16: error: defaulted declaration ‘testing::internal::MatcherBase<T>& testing::internal::MatcherBase<T>::operator=(testing::internal::MatcherBase<T>) [with T = std::__cxx11::basic_string<char>; testing::internal::MatcherBase<T> = testing::internal::MatcherBase<std::__cxx11::basic_string<char> >]’
./include/gtest/gtest-matchers.h:302:16: error: does not match expected signature ‘testing::internal::MatcherBase<std::__cxx11::basic_string<char> >& testing::internal::MatcherBase<std::__cxx11::basic_string<char> >::operator=(testing::internal::MatcherBase<std::__cxx11::basic_string<char> >&)’
./include/gtest/gtest-matchers.h: In constructor ‘testing::Matcher<std::__cxx11::basic_string<char> >::Matcher(const testing::MatcherInterface<std::__cxx11::basic_string<char> >*)’:
./include/gtest/gtest-matchers.h:374:48: error: call to ‘testing::internal::MatcherBase<T>::MatcherBase(const testing::MatcherInterface<U>*, typename testing::internal::EnableIf<(! testing::internal::IsSame<U, const U&>::value)>::type*) [with U = std::__cxx11::basic_string<char>; T = std::__cxx11::basic_string<char>; typename testing::internal::EnableIf<(! testing::internal::IsSame<U, const U&>::value)>::type = void]’ uses the default argument for parameter 2, which is not yet defined
: internal::MatcherBase<std::string>(impl) {}
^
./include/gtest/gtest-matchers.h: At global scope:
./include/gtest/gtest-matchers.h:607:63: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
MatchResultListener* /* listener */) const override {
^
./include/gtest/gtest-matchers.h:610:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void DescribeTo(::std::ostream* os) const override {
^
./include/gtest/gtest-matchers.h:614:49: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void DescribeNegationTo(::std::ostream* os) const override {
^
./include/gtest/gtest-matchers.h:723:14: error: ‘shared_ptr’ in namespace ‘std’ does not name a template type
const std::shared_ptr<const RE> regex_;
^
./include/gtest/gtest-matchers.h: In constructor ‘testing::internal::MatchesRegexMatcher::MatchesRegexMatcher(const testing::internal::RE*, bool)’:
./include/gtest/gtest-matchers.h:680:9: error: class ‘testing::internal::MatchesRegexMatcher’ does not have any field named ‘regex_’
: regex_(regex), full_match_(full_match) {}
^
./include/gtest/gtest-matchers.h: In member function ‘bool testing::internal::MatchesRegexMatcher::MatchAndExplain(CharType*, testing::MatchResultListener*) const’:
./include/gtest/gtest-matchers.h:696:17: error: ‘nullptr’ was not declared in this scope
return s != nullptr && MatchAndExplain(std::string(s), listener);
^
./include/gtest/gtest-matchers.h: In member function ‘bool testing::internal::MatchesRegexMatcher::MatchAndExplain(const MatcheeStringType&, testing::MatchResultListener*) const’:
./include/gtest/gtest-matchers.h:707:45: error: ‘regex_’ was not declared in this scope
return full_match_ ? RE::FullMatch(s2, *regex_)
^
./include/gtest/gtest-matchers.h: In member function ‘void testing::internal::MatchesRegexMatcher::DescribeTo(std::ostream*) const’:
./include/gtest/gtest-matchers.h:713:42: error: ‘regex_’ was not declared in this scope
UniversalPrinter<std::string>::Print(regex_->pattern(), os);
^
./include/gtest/gtest-matchers.h: In member function ‘void testing::internal::MatchesRegexMatcher::DescribeNegationTo(std::ostream*) const’:
./include/gtest/gtest-matchers.h:719:42: error: ‘regex_’ was not declared in this scope
UniversalPrinter<std::string>::Print(regex_->pattern(), os);
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-death-test-internal.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-death-test-internal.h:95:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ReturnSentinel);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-death-test-internal.h:95:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ReturnSentinel);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-death-test-internal.h:140:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DeathTest);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-death-test-internal.h:140:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DeathTest);
^
In file included from ./include/gtest/gtest-death-test.h:41:0,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-death-test-internal.h:158:59: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
const char* file, int line, DeathTest** test) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-death-test-internal.h:297:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(InternalRunDeathTestFlag);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-death-test-internal.h:297:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(InternalRunDeathTestFlag);
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:157:8: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
std::unique_ptr<ParamIteratorInterface<T> > impl_;
^
./include/gtest/internal/gtest-param-util.h: In copy constructor ‘testing::internal::ParamIterator<T>::ParamIterator(const testing::internal::ParamIterator<T>&)’:
./include/gtest/internal/gtest-param-util.h:127:47: error: class ‘testing::internal::ParamIterator<T>’ does not have any field named ‘impl_’
ParamIterator(const ParamIterator& other) : impl_(other.impl_->Clone()) {}
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParamIterator<T>& testing::internal::ParamIterator<T>::operator=(const testing::internal::ParamIterator<T>&)’:
./include/gtest/internal/gtest-param-util.h:130:7: error: ‘impl_’ was not declared in this scope
impl_.reset(other.impl_->Clone());
^
./include/gtest/internal/gtest-param-util.h: In member function ‘const T& testing::internal::ParamIterator<T>::operator*() const’:
./include/gtest/internal/gtest-param-util.h:134:40: error: ‘impl_’ was not declared in this scope
const T& operator*() const { return *impl_->Current(); }
^
./include/gtest/internal/gtest-param-util.h: In member function ‘const T* testing::internal::ParamIterator<T>::operator->() const’:
./include/gtest/internal/gtest-param-util.h:135:40: error: ‘impl_’ was not declared in this scope
const T* operator->() const { return impl_->Current(); }
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParamIterator<T>& testing::internal::ParamIterator<T>::operator++()’:
./include/gtest/internal/gtest-param-util.h:138:5: error: ‘impl_’ was not declared in this scope
impl_->Advance();
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParamIterator<T> testing::internal::ParamIterator<T>::operator++(int)’:
./include/gtest/internal/gtest-param-util.h:143:40: error: ‘impl_’ was not declared in this scope
ParamIteratorInterface<T>* clone = impl_->Clone();
^
./include/gtest/internal/gtest-param-util.h: In member function ‘bool testing::internal::ParamIterator<T>::operator==(const testing::internal::ParamIterator<T>&) const’:
./include/gtest/internal/gtest-param-util.h:148:12: error: ‘impl_’ was not declared in this scope
return impl_.get() == other.impl_.get() || impl_->Equals(*other.impl_);
^
./include/gtest/internal/gtest-param-util.h: In constructor ‘testing::internal::ParamIterator<T>::ParamIterator(testing::internal::ParamIteratorInterface<T>*)’:
./include/gtest/internal/gtest-param-util.h:156:61: error: class ‘testing::internal::ParamIterator<T>’ does not have any field named ‘impl_’
explicit ParamIterator(ParamIteratorInterface<T>* impl) : impl_(impl) {}
^
./include/gtest/internal/gtest-param-util.h: At global scope:
./include/gtest/internal/gtest-param-util.h:196:8: error: ‘shared_ptr’ in namespace ‘std’ does not name a template type
std::shared_ptr<const ParamGeneratorInterface<T> > impl_;
^
./include/gtest/internal/gtest-param-util.h: In constructor ‘testing::internal::ParamGenerator< <template-parameter-1-1> >::ParamGenerator(testing::internal::ParamGeneratorInterface<T>*)’:
./include/gtest/internal/gtest-param-util.h:184:63: error: class ‘testing::internal::ParamGenerator< <template-parameter-1-1> >’ does not have any field named ‘impl_’
explicit ParamGenerator(ParamGeneratorInterface<T>* impl) : impl_(impl) {}
^
./include/gtest/internal/gtest-param-util.h: In copy constructor ‘testing::internal::ParamGenerator< <template-parameter-1-1> >::ParamGenerator(const testing::internal::ParamGenerator< <template-parameter-1-1> >&)’:
./include/gtest/internal/gtest-param-util.h:185:49: error: class ‘testing::internal::ParamGenerator< <template-parameter-1-1> >’ does not have any field named ‘impl_’
ParamGenerator(const ParamGenerator& other) : impl_(other.impl_) {}
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParamGenerator< <template-parameter-1-1> >& testing::internal::ParamGenerator< <template-parameter-1-1> >::operator=(const testing::internal::ParamGenerator< <template-parameter-1-1> >&)’:
./include/gtest/internal/gtest-param-util.h:188:5: error: ‘impl_’ was not declared in this scope
impl_ = other.impl_;
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParamGenerator< <template-parameter-1-1> >::iterator testing::internal::ParamGenerator< <template-parameter-1-1> >::begin() const’:
./include/gtest/internal/gtest-param-util.h:192:44: error: ‘impl_’ was not declared in this scope
iterator begin() const { return iterator(impl_->Begin()); }
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParamGenerator< <template-parameter-1-1> >::iterator testing::internal::ParamGenerator< <template-parameter-1-1> >::end() const’:
./include/gtest/internal/gtest-param-util.h:193:42: error: ‘impl_’ was not declared in this scope
iterator end() const { return iterator(impl_->End()); }
^
./include/gtest/internal/gtest-param-util.h: At global scope:
./include/gtest/internal/gtest-param-util.h:209:19: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~RangeGenerator() override {}
^
./include/gtest/internal/gtest-param-util.h:211:38: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
ParamIteratorInterface<T>* Begin() const override {
^
./include/gtest/internal/gtest-param-util.h:214:36: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
ParamIteratorInterface<T>* End() const override {
^
./include/gtest/internal/gtest-param-util.h:224:15: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~Iterator() override {}
^
./include/gtest/internal/gtest-param-util.h:226:55: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
const ParamGeneratorInterface<T>* BaseGenerator() const override {
^
./include/gtest/internal/gtest-param-util.h:229:18: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void Advance() override {
^
./include/gtest/internal/gtest-param-util.h:233:40: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
ParamIteratorInterface<T>* Clone() const override {
^
./include/gtest/internal/gtest-param-util.h:236:24: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
const T* Current() const override { return &value_; }
^
./include/gtest/internal/gtest-param-util.h:237:57: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
bool Equals(const ParamIteratorInterface<T>& other) const override {
^
./include/gtest/internal/gtest-param-util.h:294:35: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~ValuesInIteratorRangeGenerator() override {}
^
./include/gtest/internal/gtest-param-util.h:296:38: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
ParamIteratorInterface<T>* Begin() const override {
^
./include/gtest/internal/gtest-param-util.h:299:36: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
ParamIteratorInterface<T>* End() const override {
^
./include/gtest/internal/gtest-param-util.h:311:15: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~Iterator() override {}
^
./include/gtest/internal/gtest-param-util.h:313:55: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
const ParamGeneratorInterface<T>* BaseGenerator() const override {
^
./include/gtest/internal/gtest-param-util.h:316:18: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void Advance() override {
^
./include/gtest/internal/gtest-param-util.h:320:40: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
ParamIteratorInterface<T>* Clone() const override {
^
./include/gtest/internal/gtest-param-util.h:330:24: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
const T* Current() const override {
^
./include/gtest/internal/gtest-param-util.h:334:57: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
bool Equals(const ParamIteratorInterface<T>& other) const override {
^
./include/gtest/internal/gtest-param-util.h:359:18: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
mutable std::unique_ptr<const T> value_;
^
./include/gtest/internal/gtest-param-util.h: In member function ‘void testing::internal::ValuesInIteratorRangeGenerator<T>::Iterator::Advance()’:
./include/gtest/internal/gtest-param-util.h:318:7: error: ‘value_’ was not declared in this scope
value_.reset();
^
./include/gtest/internal/gtest-param-util.h: In member function ‘const T* testing::internal::ValuesInIteratorRangeGenerator<T>::Iterator::Current() const’:
./include/gtest/internal/gtest-param-util.h:331:11: error: ‘value_’ was not declared in this scope
if (value_.get() == nullptr) value_.reset(new T(*iterator_));
^
./include/gtest/internal/gtest-param-util.h:331:27: error: ‘nullptr’ was not declared in this scope
if (value_.get() == nullptr) value_.reset(new T(*iterator_));
^
./include/gtest/internal/gtest-param-util.h:332:14: error: ‘value_’ was not declared in this scope
return value_.get();
^
./include/gtest/internal/gtest-param-util.h: At global scope:
./include/gtest/internal/gtest-param-util.h:409:20: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
Test* CreateTest() override {
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-param-util.h:417:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestFactory);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-param-util.h:417:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestFactory);
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:444:9: error: expected nested-name-specifier before ‘ParamType’
using ParamType = typename TestSuite::ParamType;
^
./include/gtest/internal/gtest-param-util.h:448:20: error: expected ‘;’ at end of member declaration
TestFactoryBase* CreateTestFactory(ParamType parameter) override {
^
./include/gtest/internal/gtest-param-util.h:448:48: error: expected ‘)’ before ‘parameter’
TestFactoryBase* CreateTestFactory(ParamType parameter) override {
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-param-util.h:453:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestMetaFactory);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-param-util.h:453:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestMetaFactory);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-param-util.h:484:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestSuiteInfoBase);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-param-util.h:484:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestSuiteInfoBase);
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:500:9: error: expected nested-name-specifier before ‘ParamType’
using ParamType = typename TestSuite::ParamType;
^
./include/gtest/internal/gtest-param-util.h:502:26: error: ‘ParamType’ was not declared in this scope
typedef ParamGenerator<ParamType>(GeneratorCreationFunc)();
^
./include/gtest/internal/gtest-param-util.h:502:35: error: template argument 1 is invalid
typedef ParamGenerator<ParamType>(GeneratorCreationFunc)();
^
./include/gtest/internal/gtest-param-util.h:503:37: error: ‘ParamType’ was not declared in this scope
typedef typename ParamNameGenFunc<ParamType>::Type ParamNameGeneratorFunc;
^
./include/gtest/internal/gtest-param-util.h:503:46: error: template argument 1 is invalid
typedef typename ParamNameGenFunc<ParamType>::Type ParamNameGeneratorFunc;
^
./include/gtest/internal/gtest-param-util.h:510:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
const std::string& GetTestSuiteName() const override {
^
./include/gtest/internal/gtest-param-util.h:514:31: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
TypeId GetTestSuiteTypeId() const override { return GetTypeId<TestSuite>(); }
^
./include/gtest/internal/gtest-param-util.h:522:43: error: ‘ParamType’ was not declared in this scope
TestMetaFactoryBase<ParamType>* meta_factory) {
^
./include/gtest/internal/gtest-param-util.h:522:52: error: template argument 1 is invalid
TestMetaFactoryBase<ParamType>* meta_factory) {
^
./include/gtest/internal/gtest-param-util.h:541:22: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void RegisterTests() override {
^
./include/gtest/internal/gtest-param-util.h:599:34: error: ‘ParamType’ was not declared in this scope
TestMetaFactoryBase<ParamType>* a_test_meta_factory)
^
./include/gtest/internal/gtest-param-util.h:599:43: error: template argument 1 is invalid
TestMetaFactoryBase<ParamType>* a_test_meta_factory)
^
./include/gtest/internal/gtest-param-util.h:606:16: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr<TestMetaFactoryBase<ParamType> > test_meta_factory;
^
./include/gtest/internal/gtest-param-util.h:608:9: error: expected nested-name-specifier before ‘TestInfoContainer’
using TestInfoContainer = ::std::vector<std::shared_ptr<TestInfo> >;
^
./include/gtest/internal/gtest-param-util.h:648:3: error: ‘TestInfoContainer’ does not name a type
TestInfoContainer tests_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-param-util.h:651:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestSuiteInfo);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-param-util.h:651:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestSuiteInfo);
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h: In member function ‘void testing::internal::ParameterizedTestSuiteInfo<TestSuite>::AddTestPattern(const char*, const char*, int*)’:
./include/gtest/internal/gtest-param-util.h:523:5: error: ‘tests_’ was not declared in this scope
tests_.push_back(std::shared_ptr<TestInfo>(
^
./include/gtest/internal/gtest-param-util.h:523:22: error: ‘shared_ptr’ is not a member of ‘std’
tests_.push_back(std::shared_ptr<TestInfo>(
^
./include/gtest/internal/gtest-param-util.h:523:46: error: expected primary-expression before ‘>’ token
tests_.push_back(std::shared_ptr<TestInfo>(
^
./include/gtest/internal/gtest-param-util.h: In member function ‘void testing::internal::ParameterizedTestSuiteInfo<TestSuite>::RegisterTests()’:
./include/gtest/internal/gtest-param-util.h:542:36: error: expected ‘;’ before ‘::’ token
for (typename TestInfoContainer::iterator test_it = tests_.begin();
^
./include/gtest/internal/gtest-param-util.h:542:36: error: ‘::iterator’ has not been declared
./include/gtest/internal/gtest-param-util.h:542:36: note: suggested alternatives:
In file included from /usr/include/c++/5/bits/stl_algobase.h:65:0,
from /usr/include/c++/5/memory:62,
from ./include/gtest/gtest.h:56,
from src/gtest-all.cc:38:
/usr/include/c++/5/bits/stl_iterator_base_types.h:118:12: note: ‘std::iterator’
struct iterator
^
/usr/include/c++/5/bits/stl_iterator_base_types.h:118:12: note: ‘std::iterator’
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:542:47: error: expected ‘;’ before ‘test_it’
for (typename TestInfoContainer::iterator test_it = tests_.begin();
^
./include/gtest/internal/gtest-param-util.h:542:47: error: ‘test_it’ was not declared in this scope
./include/gtest/internal/gtest-param-util.h:542:57: error: ‘tests_’ was not declared in this scope
for (typename TestInfoContainer::iterator test_it = tests_.begin();
^
./include/gtest/internal/gtest-param-util.h:542:71: error: expected ‘)’ before ‘;’ token
for (typename TestInfoContainer::iterator test_it = tests_.begin();
^
./include/gtest/internal/gtest-param-util.h:543:10: error: ‘test_it’ was not declared in this scope
test_it != tests_.end(); ++test_it) {
^
./include/gtest/internal/gtest-param-util.h:543:21: error: ‘tests_’ was not declared in this scope
test_it != tests_.end(); ++test_it) {
^
./include/gtest/internal/gtest-param-util.h: In constructor ‘testing::internal::ParameterizedTestSuiteInfo<TestSuite>::TestInfo::TestInfo(const char*, const char*, int*)’:
./include/gtest/internal/gtest-param-util.h:602:11: error: class ‘testing::internal::ParameterizedTestSuiteInfo<TestSuite>::TestInfo’ does not have any field named ‘test_meta_factory’
test_meta_factory(a_test_meta_factory) {}
^
./include/gtest/internal/gtest-param-util.h: At global scope:
./include/gtest/internal/gtest-param-util.h:657:1: error: expected unqualified-id before ‘using’
using ParameterizedTestCaseInfo = ParameterizedTestSuiteInfo<TestCase>;
^
./include/gtest/internal/gtest-param-util.h:714:3: error: ‘ParameterizedTestCaseInfo’ does not name a type
ParameterizedTestCaseInfo<TestCase>* GetTestCasePatternHolder(
^
./include/gtest/internal/gtest-param-util.h:722:9: error: expected nested-name-specifier before ‘TestSuiteInfoContainer’
using TestSuiteInfoContainer = ::std::vector<ParameterizedTestSuiteInfoBase*>;
^
./include/gtest/internal/gtest-param-util.h:724:3: error: ‘TestSuiteInfoContainer’ does not name a type
TestSuiteInfoContainer test_suite_infos_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/internal/gtest-param-util.h:726:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestSuiteRegistry);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/internal/gtest-param-util.h:726:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ParameterizedTestSuiteRegistry);
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h: In destructor ‘testing::internal::ParameterizedTestSuiteRegistry::~ParameterizedTestSuiteRegistry()’:
./include/gtest/internal/gtest-param-util.h:670:16: error: ISO C++ forbids declaration of ‘test_suite_info’ with no type [-fpermissive]
for (auto& test_suite_info : test_suite_infos_) {
^
./include/gtest/internal/gtest-param-util.h:670:34: warning: range-based ‘for’ loops only available with -std=c++11 or -std=gnu++11
for (auto& test_suite_info : test_suite_infos_) {
^
./include/gtest/internal/gtest-param-util.h:670:34: error: ‘test_suite_infos_’ was not declared in this scope
./include/gtest/internal/gtest-param-util.h:671:14: error: type ‘int’ argument given to ‘delete’, expected pointer
delete test_suite_info;
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ParameterizedTestSuiteInfo<TestSuite>* testing::internal::ParameterizedTestSuiteRegistry::GetTestSuitePatternHolder(const char*, testing::internal::CodeLocation)’:
./include/gtest/internal/gtest-param-util.h:680:62: error: ‘nullptr’ was not declared in this scope
ParameterizedTestSuiteInfo<TestSuite>* typed_test_info = nullptr;
^
./include/gtest/internal/gtest-param-util.h:681:16: error: ISO C++ forbids declaration of ‘test_suite_info’ with no type [-fpermissive]
for (auto& test_suite_info : test_suite_infos_) {
^
./include/gtest/internal/gtest-param-util.h:681:34: warning: range-based ‘for’ loops only available with -std=c++11 or -std=gnu++11
for (auto& test_suite_info : test_suite_infos_) {
^
./include/gtest/internal/gtest-param-util.h:681:34: error: ‘test_suite_infos_’ was not declared in this scope
./include/gtest/internal/gtest-param-util.h:682:26: error: base operand of ‘->’ is not a pointer
if (test_suite_info->GetTestSuiteName() == test_suite_name) {
^
./include/gtest/internal/gtest-param-util.h:683:28: error: base operand of ‘->’ is not a pointer
if (test_suite_info->GetTestSuiteTypeId() != GetTypeId<TestSuite>()) {
^
./include/gtest/internal/gtest-param-util.h:688:11: error: ‘Abort’ is not a member of ‘testing::internal::posix’
posix::Abort();
^
./include/gtest/internal/gtest-param-util.h: In member function ‘void testing::internal::ParameterizedTestSuiteRegistry::RegisterTests()’:
./include/gtest/internal/gtest-param-util.h:707:16: error: ISO C++ forbids declaration of ‘test_suite_info’ with no type [-fpermissive]
for (auto& test_suite_info : test_suite_infos_) {
^
./include/gtest/internal/gtest-param-util.h:707:34: warning: range-based ‘for’ loops only available with -std=c++11 or -std=gnu++11
for (auto& test_suite_info : test_suite_infos_) {
^
./include/gtest/internal/gtest-param-util.h:707:34: error: ‘test_suite_infos_’ was not declared in this scope
./include/gtest/internal/gtest-param-util.h:708:22: error: base operand of ‘->’ is not a pointer
test_suite_info->RegisterTests();
^
./include/gtest/internal/gtest-param-util.h: At global scope:
./include/gtest/internal/gtest-param-util.h:740:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename... Ts>
^
./include/gtest/internal/gtest-param-util.h:743:20: warning: variadic templates only available with -std=c++11 or -std=gnu++11
ValueArray(Ts... v) : v_{std::move(v)...} {}
^
./include/gtest/internal/gtest-param-util.h:751:35: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename T, size_t... I>
^
./include/gtest/internal/gtest-param-util.h: In constructor ‘testing::internal::ValueArray<Ts>::ValueArray(Ts ...)’:
./include/gtest/internal/gtest-param-util.h:743:27: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
ValueArray(Ts... v) : v_{std::move(v)...} {}
^
./include/gtest/internal/gtest-param-util.h:743:28: error: ‘move’ is not a member of ‘std’
ValueArray(Ts... v) : v_{std::move(v)...} {}
^
./include/gtest/internal/gtest-param-util.h: In member function ‘testing::internal::ValueArray<Ts>::operator testing::internal::ParamGenerator<T>() const’:
./include/gtest/internal/gtest-param-util.h:747:59: warning: variadic templates only available with -std=c++11 or -std=gnu++11
return ValuesIn(MakeVector<T>(MakeIndexSequence<sizeof...(Ts)>()));
^
./include/gtest/internal/gtest-param-util.h: In member function ‘std::vector<T> testing::internal::ValueArray<Ts>::MakeVector(testing::internal::IndexSequence<I ...>) const’:
./include/gtest/internal/gtest-param-util.h:753:26: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
return std::vector<T>{static_cast<T>(v_.template Get<I>())...};
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h: At global scope:
./include/gtest/internal/gtest-param-util-generated.h:67:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2> > {
^
./include/gtest/internal/gtest-param-util-generated.h:67:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:67:58: error: wrong number of template arguments (2, should be 1)
: public ParamGeneratorInterface< ::std::tuple<T1, T2> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:67:60: error: expected ‘{’ before ‘>’ token
: public ParamGeneratorInterface< ::std::tuple<T1, T2> > {
^
./include/gtest/internal/gtest-param-util-generated.h:67:60: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:182:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3> > {
^
./include/gtest/internal/gtest-param-util-generated.h:182:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:182:62: error: wrong number of template arguments (3, should be 1)
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:182:64: error: expected ‘{’ before ‘>’ token
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3> > {
^
./include/gtest/internal/gtest-param-util-generated.h:182:64: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:314:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4> > {
^
./include/gtest/internal/gtest-param-util-generated.h:314:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:314:66: error: wrong number of template arguments (4, should be 1)
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:314:68: error: expected ‘{’ before ‘>’ token
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4> > {
^
./include/gtest/internal/gtest-param-util-generated.h:314:68: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:465:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5> > {
^
./include/gtest/internal/gtest-param-util-generated.h:465:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:465:70: error: wrong number of template arguments (5, should be 1)
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:465:72: error: expected ‘{’ before ‘>’ token
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5> > {
^
./include/gtest/internal/gtest-param-util-generated.h:465:72: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:633:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6> > {
^
./include/gtest/internal/gtest-param-util-generated.h:633:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:633:74: error: wrong number of template arguments (6, should be 1)
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:633:76: error: expected ‘{’ before ‘>’ token
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6> > {
^
./include/gtest/internal/gtest-param-util-generated.h:633:76: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:818:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6,
^
./include/gtest/internal/gtest-param-util-generated.h:818:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:819:11: error: wrong number of template arguments (7, should be 1)
T7> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:819:13: error: expected ‘{’ before ‘>’ token
T7> > {
^
./include/gtest/internal/gtest-param-util-generated.h:819:13: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:1021:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6, T7,
^
./include/gtest/internal/gtest-param-util-generated.h:1021:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1022:11: error: wrong number of template arguments (8, should be 1)
T8> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1022:13: error: expected ‘{’ before ‘>’ token
T8> > {
^
./include/gtest/internal/gtest-param-util-generated.h:1022:13: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:1243:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6, T7,
^
./include/gtest/internal/gtest-param-util-generated.h:1243:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1244:15: error: wrong number of template arguments (9, should be 1)
T8, T9> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1244:17: error: expected ‘{’ before ‘>’ token
T8, T9> > {
^
./include/gtest/internal/gtest-param-util-generated.h:1244:17: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:1482:39: error: ‘tuple’ is not a member of ‘std’
: public ParamGeneratorInterface< ::std::tuple<T1, T2, T3, T4, T5, T6, T7,
^
./include/gtest/internal/gtest-param-util-generated.h:1482:39: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1483:20: error: wrong number of template arguments (10, should be 1)
T8, T9, T10> > {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:84:27: note: provided for ‘template<class> class testing::internal::ParamGeneratorInterface’
template <typename> class ParamGeneratorInterface;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1483:22: error: expected ‘{’ before ‘>’ token
T8, T9, T10> > {
^
./include/gtest/internal/gtest-param-util-generated.h:1483:22: error: expected unqualified-id before ‘>’ token
./include/gtest/internal/gtest-param-util-generated.h:1747:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1747:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1747:47: error: wrong number of template arguments (2, should be 1)
operator ParamGenerator< ::std::tuple<T1, T2> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1747:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1769:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1769:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1769:51: error: wrong number of template arguments (3, should be 1)
operator ParamGenerator< ::std::tuple<T1, T2, T3> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1769:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1794:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1794:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1794:55: error: wrong number of template arguments (4, should be 1)
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1794:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1821:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1821:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1821:59: error: wrong number of template arguments (5, should be 1)
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1821:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1852:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1852:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1852:63: error: wrong number of template arguments (6, should be 1)
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1852:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1885:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1885:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1885:67: error: wrong number of template arguments (7, should be 1)
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1885:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7> >() const {
^
./include/gtest/internal/gtest-param-util-generated.h:1922:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7,
^
./include/gtest/internal/gtest-param-util-generated.h:1922:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1923:9: error: wrong number of template arguments (8, should be 1)
T8> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1922:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7,
^
./include/gtest/internal/gtest-param-util-generated.h:1963:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7, T8,
^
./include/gtest/internal/gtest-param-util-generated.h:1963:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:1964:9: error: wrong number of template arguments (9, should be 1)
T9> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:1963:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7, T8,
^
./include/gtest/internal/gtest-param-util-generated.h:2006:28: error: ‘tuple’ is not a member of ‘std’
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7, T8, T9,
^
./include/gtest/internal/gtest-param-util-generated.h:2006:28: error: ‘tuple’ is not a member of ‘std’
./include/gtest/internal/gtest-param-util-generated.h:2007:10: error: wrong number of template arguments (10, should be 1)
T10> >() const {
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h:85:27: note: provided for ‘template<class> class testing::internal::ParamGenerator’
template <typename> class ParamGenerator;
^
In file included from ./include/gtest/gtest-param-test.h:185:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util-generated.h:2006:3: error: ‘<expression error>’ does not name a type
operator ParamGenerator< ::std::tuple<T1, T2, T3, T4, T5, T6, T7, T8, T9,
^
In file included from ./include/gtest/gtest.h:65:0,
from src/gtest-all.cc:38:
./include/gtest/gtest-param-test.h:339:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <typename... T>
^
./include/gtest/gtest-param-test.h:340:40: warning: variadic templates only available with -std=c++11 or -std=gnu++11
internal::ValueArray<T...> Values(T... v) {
^
./include/gtest/gtest-param-test.h: In function ‘testing::internal::ValueArray<T ...> testing::Values(T ...)’:
./include/gtest/gtest-param-test.h:341:37: error: ‘move’ is not a member of ‘std’
return internal::ValueArray<T...>(std::move(v)...);
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h: In instantiation of ‘struct testing::internal::MakeIndexSequence<1ul>’:
./include/gtest/internal/gtest-internal.h:1200:8: required from ‘struct testing::internal::MakeIndexSequence<2ul ’
./include/gtest/internal/gtest-internal.h:1265:7: required from ‘class testing::internal::FlatTuple<bool, bool>’
./include/gtest/internal/gtest-param-util.h:756:20: required from ‘class testing::internal::ValueArray<bool, bool>’
./include/gtest/gtest-param-test.h:365:28: required from here
./include/gtest/internal/gtest-internal.h:1200:8: error: no type named ‘type’ in ‘struct testing::internal::MakeIndexSequence<0ul>’
struct MakeIndexSequence
^
./include/gtest/internal/gtest-internal.h: In instantiation of ‘struct testing::internal::MakeIndexSequence<2ul>’:
./include/gtest/internal/gtest-internal.h:1265:7: required from ‘class testing::internal::FlatTuple<bool, bool>’
./include/gtest/internal/gtest-param-util.h:756:20: required from ‘class testing::internal::ValueArray<bool, bool>’
./include/gtest/gtest-param-test.h:365:28: required from here
./include/gtest/internal/gtest-internal.h:1200:8: error: no type named ‘type’ in ‘struct testing::internal::MakeIndexSequence<1ul>’
./include/gtest/internal/gtest-internal.h: In instantiation of ‘class testing::internal::FlatTuple<bool, bool>’:
./include/gtest/internal/gtest-param-util.h:756:20: required from ‘class testing::internal::ValueArray<bool, bool>’
./include/gtest/gtest-param-test.h:365:28: required from here
./include/gtest/internal/gtest-internal.h:1265:7: error: no type named ‘type’ in ‘struct testing::internal::MakeIndexSequence<2ul>’
class FlatTuple
^
In file included from ./include/gtest/gtest.h:68:0,
from src/gtest-all.cc:38:
./include/gtest/gtest-test-part.h: In constructor ‘testing::TestPartResult::TestPartResult(testing::TestPartResult::Type, const char*, int, const char*)’:
./include/gtest/gtest-test-part.h:66:35: error: ‘nullptr’ was not declared in this scope
file_name_(a_file_name == nullptr ? "" : a_file_name),
^
./include/gtest/gtest-test-part.h: In member function ‘const char* testing::TestPartResult::file_name() const’:
./include/gtest/gtest-test-part.h:77:33: error: ‘nullptr’ was not declared in this scope
return file_name_.empty() ? nullptr : file_name_.c_str();
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/gtest-test-part.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-test-part.h:145:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestPartResultArray);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-test-part.h:145:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestPartResultArray);
^
In file included from ./include/gtest/gtest.h:68:0,
from src/gtest-all.cc:38:
./include/gtest/gtest-test-part.h:168:29: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~HasNewFatalFailureHelper() override;
^
./include/gtest/gtest-test-part.h:169:57: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void ReportTestPartResult(const TestPartResult& result) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-test-part.h:175:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(HasNewFatalFailureHelper);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-test-part.h:175:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(HasNewFatalFailureHelper);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:204:7: error: expected nested-name-specifier before ‘TestCase’
using TestCase = TestSuite;
^
./include/gtest/gtest.h:309:12: error: ‘is_convertible’ is not a member of ‘std’
!std::is_convertible<T, AssertionResult>::value>::type*
^
./include/gtest/gtest.h:309:50: error: wrong number of template arguments (2, should be 1)
!std::is_convertible<T, AssertionResult>::value>::type*
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h:1026:23: note: provided for ‘template<bool <anonymous> > struct testing::internal::EnableIf’
template<bool> struct EnableIf;
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:309:12: error: ‘is_convertible’ is not a member of ‘std’
!std::is_convertible<T, AssertionResult>::value>::type*
^
./include/gtest/gtest.h:309:50: error: wrong number of template arguments (2, should be 1)
!std::is_convertible<T, AssertionResult>::value>::type*
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h:1026:23: note: provided for ‘template<bool <anonymous> > struct testing::internal::EnableIf’
template<bool> struct EnableIf;
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:308:26: error: invalid use of template-name ‘testing::internal::EnableIf’ without an argument list
typename internal::EnableIf<
^
./include/gtest/gtest.h:308:34: error: expected ‘,’ or ‘...’ before ‘<’ token
typename internal::EnableIf<
^
./include/gtest/gtest.h:370:8: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
std::unique_ptr< ::std::string> message_;
^
./include/gtest/gtest.h: In member function ‘const char* testing::AssertionResult::message() const’:
./include/gtest/gtest.h:335:12: error: ‘message_’ was not declared in this scope
return message_.get() != nullptr ? message_->c_str() : "";
^
./include/gtest/gtest.h:335:30: error: ‘nullptr’ was not declared in this scope
return message_.get() != nullptr ? message_->c_str() : "";
^
./include/gtest/gtest.h: In member function ‘void testing::AssertionResult::AppendMessage(const testing::Message&)’:
./include/gtest/gtest.h:357:9: error: ‘message_’ was not declared in this scope
if (message_.get() == nullptr) message_.reset(new ::std::string);
^
./include/gtest/gtest.h:357:27: error: ‘nullptr’ was not declared in this scope
if (message_.get() == nullptr) message_.reset(new ::std::string);
^
./include/gtest/gtest.h:358:5: error: ‘message_’ was not declared in this scope
message_->append(a_message.GetString().c_str());
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h: At global scope:
./include/gtest/gtest.h:503:14: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr<GTEST_FLAG_SAVER_> gtest_flag_saver_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:525:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Test);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:525:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(Test);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h: In member function ‘virtual testing::Test::Setup_should_be_spelled_SetUp* testing::Test::Setup()’:
./include/gtest/gtest.h:522:59: error: ‘nullptr’ was not declared in this scope
virtual Setup_should_be_spelled_SetUp* Setup() { return nullptr; }
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/gtest.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:681:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestResult);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:681:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestResult);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:774:52: error: ‘testing::internal::SetUpTestSuiteFunc’ has not been declared
internal::TypeId fixture_class_id, internal::SetUpTestSuiteFunc set_up_tc,
^
./include/gtest/gtest.h:775:17: error: ‘testing::internal::TearDownTestSuiteFunc’ has not been declared
internal::TearDownTestSuiteFunc tear_down_tc,
^
./include/gtest/gtest.h:806:14: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr<const ::std::string> type_param_;
^
./include/gtest/gtest.h:809:14: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr<const ::std::string> value_param_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:824:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestInfo);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:824:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestInfo);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h: In member function ‘const char* testing::TestInfo::type_param() const’:
./include/gtest/gtest.h:715:9: error: ‘type_param_’ was not declared in this scope
if (type_param_.get() != nullptr) return type_param_->c_str();
^
./include/gtest/gtest.h:715:30: error: ‘nullptr’ was not declared in this scope
if (type_param_.get() != nullptr) return type_param_->c_str();
^
./include/gtest/gtest.h:716:12: error: ‘nullptr’ was not declared in this scope
return nullptr;
^
./include/gtest/gtest.h: In member function ‘const char* testing::TestInfo::value_param() const’:
./include/gtest/gtest.h:722:9: error: ‘value_param_’ was not declared in this scope
if (value_param_.get() != nullptr) return value_param_->c_str();
^
./include/gtest/gtest.h:722:31: error: ‘nullptr’ was not declared in this scope
if (value_param_.get() != nullptr) return value_param_->c_str();
^
./include/gtest/gtest.h:723:12: error: ‘nullptr’ was not declared in this scope
return nullptr;
^
./include/gtest/gtest.h: At global scope:
./include/gtest/gtest.h:845:23: error: ‘testing::internal::SetUpTestSuiteFunc’ has not been declared
internal::SetUpTestSuiteFunc set_up_tc,
^
./include/gtest/gtest.h:846:23: error: ‘testing::internal::TearDownTestSuiteFunc’ has not been declared
internal::TearDownTestSuiteFunc tear_down_tc);
^
./include/gtest/gtest.h:1001:14: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr<const ::std::string> type_param_;
^
./include/gtest/gtest.h:1010:13: error: ‘SetUpTestSuiteFunc’ in namespace ‘testing::internal’ does not name a type
internal::SetUpTestSuiteFunc set_up_tc_;
^
./include/gtest/gtest.h:1012:13: error: ‘TearDownTestSuiteFunc’ in namespace ‘testing::internal’ does not name a type
internal::TearDownTestSuiteFunc tear_down_tc_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:1022:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestSuite);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:1022:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestSuite);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h: In member function ‘const char* testing::TestSuite::type_param() const’:
./include/gtest/gtest.h:857:9: error: ‘type_param_’ was not declared in this scope
if (type_param_.get() != nullptr) return type_param_->c_str();
^
./include/gtest/gtest.h:857:30: error: ‘nullptr’ was not declared in this scope
if (type_param_.get() != nullptr) return type_param_->c_str();
^
./include/gtest/gtest.h:858:12: error: ‘nullptr’ was not declared in this scope
return nullptr;
^
./include/gtest/gtest.h: In member function ‘void testing::TestSuite::RunSetUpTestSuite()’:
./include/gtest/gtest.h:942:9: error: ‘set_up_tc_’ was not declared in this scope
if (set_up_tc_ != nullptr) {
^
./include/gtest/gtest.h:942:23: error: ‘nullptr’ was not declared in this scope
if (set_up_tc_ != nullptr) {
^
./include/gtest/gtest.h: In member function ‘void testing::TestSuite::RunTearDownTestSuite()’:
./include/gtest/gtest.h:950:9: error: ‘tear_down_tc_’ was not declared in this scope
if (tear_down_tc_ != nullptr) {
^
./include/gtest/gtest.h:950:26: error: ‘nullptr’ was not declared in this scope
if (tear_down_tc_ != nullptr) {
^
./include/gtest/gtest.h: In member function ‘virtual testing::Environment::Setup_should_be_spelled_SetUp* testing::Environment::Setup()’:
./include/gtest/gtest.h:1053:59: error: ‘nullptr’ was not declared in this scope
virtual Setup_should_be_spelled_SetUp* Setup() { return nullptr; }
^
./include/gtest/gtest.h: At global scope:
./include/gtest/gtest.h:1094:38: error: ‘TestCase’ does not name a type
virtual void OnTestCaseStart(const TestCase& /*test_case*/) {}
^
./include/gtest/gtest.h:1113:36: error: ‘TestCase’ does not name a type
virtual void OnTestCaseEnd(const TestCase& /*test_case*/) {}
^
./include/gtest/gtest.h:1137:56: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramStart(const UnitTest& /*unit_test*/) override {}
^
./include/gtest/gtest.h:1139:46: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
int /*iteration*/) override {}
^
./include/gtest/gtest.h:1140:62: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsSetUpStart(const UnitTest& /*unit_test*/) override {}
^
./include/gtest/gtest.h:1141:60: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsSetUpEnd(const UnitTest& /*unit_test*/) override {}
^
./include/gtest/gtest.h:1142:56: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestSuiteStart(const TestSuite& /*test_suite*/) override {}
^
./include/gtest/gtest.h:1145:30: error: ‘TestCase’ does not name a type
void OnTestCaseStart(const TestCase& /*test_case*/) override {}
^
./include/gtest/gtest.h:1145:53: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseStart(const TestCase& /*test_case*/) override {}
^
./include/gtest/gtest.h:1148:49: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestStart(const TestInfo& /*test_info*/) override {}
^
./include/gtest/gtest.h:1149:67: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestPartResult(const TestPartResult& /*test_part_result*/) override {}
^
./include/gtest/gtest.h:1150:47: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestEnd(const TestInfo& /*test_info*/) override {}
^
./include/gtest/gtest.h:1151:54: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestSuiteEnd(const TestSuite& /*test_suite*/) override {}
^
./include/gtest/gtest.h:1153:28: error: ‘TestCase’ does not name a type
void OnTestCaseEnd(const TestCase& /*test_case*/) override {}
^
./include/gtest/gtest.h:1153:51: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseEnd(const TestCase& /*test_case*/) override {}
^
./include/gtest/gtest.h:1156:65: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsTearDownStart(const UnitTest& /*unit_test*/) override {}
^
./include/gtest/gtest.h:1157:63: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsTearDownEnd(const UnitTest& /*unit_test*/) override {}
^
./include/gtest/gtest.h:1159:44: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
int /*iteration*/) override {}
^
./include/gtest/gtest.h:1160:54: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramEnd(const UnitTest& /*unit_test*/) override {}
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:1238:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestEventListeners);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:1238:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestEventListeners);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:1276:9: error: ‘TestCase’ does not name a type
const TestCase* current_test_case() const GTEST_LOCK_EXCLUDED_(mutex_);
^
./include/gtest/gtest.h:1359:9: error: ‘TestCase’ does not name a type
const TestCase* GetTestCase(int i) const;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:1447:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(UnitTest);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:1447:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(UnitTest);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:1583:26: error: ‘is_pointer’ is not a member of ‘std’
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:44: error: template argument 1 is invalid
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:16: error: expected nested-name-specifier before ‘EnableIf’
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:26: error: ‘is_pointer’ is not a member of ‘std’
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:44: error: template argument 1 is invalid
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:26: error: ‘is_pointer’ is not a member of ‘std’
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:44: error: template argument 1 is invalid
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:26: error: ‘is_pointer’ is not a member of ‘std’
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:44: error: template argument 1 is invalid
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h:1583:24: error: expected ‘,’ or ‘...’ before ‘<’ token
typename EnableIf<!std::is_pointer<T2>::value>::type* = nullptr) {
^
./include/gtest/gtest.h: In static member function ‘static testing::AssertionResult testing::internal::EqHelper<true>::Compare(const char*, const char*, testing::internal::Secret*, T*)’:
./include/gtest/gtest.h:1602:72: error: ‘nullptr’ was not declared in this scope
return CmpHelperEQ(lhs_expression, rhs_expression, static_cast<T*>(nullptr),
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/gtest.h: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:1824:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(AssertHelperData);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:1824:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(AssertHelperData);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:1829:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(AssertHelper);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:1829:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(AssertHelper);
^
./include/gtest/gtest.h: In static member function ‘static const ParamType& testing::WithParamInterface<T>::GetParam()’:
./include/gtest/gtest.h:1883:32: error: ‘nullptr’ was not declared in this scope
GTEST_CHECK_(parameter_ != nullptr)
^
./include/gtest/internal/gtest-port.h:1038:37: note: in definition of macro ‘GTEST_CHECK_’
if (::testing::internal::IsTrue(condition)) \
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h: At global scope:
./include/gtest/gtest.h:1904:46: error: ‘nullptr’ was not declared in this scope
const T* WithParamInterface<T>::parameter_ = nullptr;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest.h:2276:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedTrace);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest.h:2276:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedTrace);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:2467:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
template <int&... ExplicitParameterBarrier, typename Factory>
^
./include/gtest/gtest.h: In function ‘testing::TestInfo* testing::RegisterTest(const char*, const char*, const char*, const char*, const char*, int, Factory)’:
./include/gtest/gtest.h:2471:9: error: expected nested-name-specifier before ‘TestT’
using TestT = typename std::remove_pointer<decltype(factory())>::type;
^
./include/gtest/gtest.h:2476:22: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
Test* CreateTest() override { return factory_(); }
^
./include/gtest/gtest.h: In constructor ‘testing::RegisterTest(const char*, const char*, const char*, const char*, const char*, int, Factory)::FactoryImpl::FactoryImpl(Factory)’:
./include/gtest/gtest.h:2475:48: error: ‘move’ is not a member of ‘std’
explicit FactoryImpl(Factory f) : factory_(std::move(f)) {}
^
./include/gtest/gtest.h: In function ‘testing::TestInfo* testing::RegisterTest(const char*, const char*, const char*, const char*, const char*, int, Factory)’:
./include/gtest/gtest.h:2484:63: error: ‘TestT’ was not declared in this scope
internal::CodeLocation(file, line), internal::GetTypeId<TestT>(),
^
./include/gtest/gtest.h:2485:39: error: type/value mismatch at argument 1 in template parameter list for ‘template<class T> struct testing::internal::SuiteApiResolver’
internal::SuiteApiResolver<TestT>::GetSetUpCaseOrSuite(),
^
./include/gtest/gtest.h:2485:39: note: expected a type, got ‘TestT’
./include/gtest/gtest.h:2486:39: error: type/value mismatch at argument 1 in template parameter list for ‘template<class T> struct testing::internal::SuiteApiResolver’
internal::SuiteApiResolver<TestT>::GetTearDownCaseOrSuite(),
^
./include/gtest/gtest.h:2486:39: note: expected a type, got ‘TestT’
./include/gtest/gtest.h:2487:22: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
new FactoryImpl{std::move(factory)});
^
./include/gtest/gtest.h:2487:23: error: ‘move’ is not a member of ‘std’
new FactoryImpl{std::move(factory)});
^
In file included from ./src/gtest.cc:35:0,
from src/gtest-all.cc:41:
./include/gtest/gtest-spi.h: At global scope:
./include/gtest/gtest-spi.h:75:37: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~ScopedFakeTestPartResultReporter() override;
^
./include/gtest/gtest-spi.h:82:57: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void ReportTestPartResult(const TestPartResult& result) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-spi.h:91:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedFakeTestPartResultReporter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-spi.h:91:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedFakeTestPartResultReporter);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./include/gtest/gtest-spi.h:112:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(SingleFailureChecker);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./include/gtest/gtest-spi.h:112:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(SingleFailureChecker);
^
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:438:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(OsStackTraceGetterInterface);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:438:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(OsStackTraceGetterInterface);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h:446:62: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
std::string CurrentStackTrace(int max_depth, int skip_count) override;
^
./src/gtest-internal-inl.h:447:25: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void UponLeavingGTest() override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:460:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(OsStackTraceGetter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:460:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(OsStackTraceGetter);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h:478:57: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void ReportTestPartResult(const TestPartResult& result) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:483:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultGlobalTestPartResultReporter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:483:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultGlobalTestPartResultReporter);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h:494:57: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void ReportTestPartResult(const TestPartResult& result) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:499:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultPerThreadTestPartResultReporter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:499:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(DefaultPerThreadTestPartResultReporter);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h:594:9: error: ‘TestCase’ does not name a type
const TestCase* GetTestCase(int i) const { return GetTestSuite(i); }
^
./src/gtest-internal-inl.h:649:37: error: ‘testing::internal::SetUpTestSuiteFunc’ has not been declared
internal::SetUpTestSuiteFunc set_up_tc,
^
./src/gtest-internal-inl.h:650:37: error: ‘testing::internal::TearDownTestSuiteFunc’ has not been declared
internal::TearDownTestSuiteFunc tear_down_tc);
^
./src/gtest-internal-inl.h:654:3: error: ‘TestCase’ does not name a type
TestCase* GetTestCase(const char* test_case_name, const char* type_param,
^
./src/gtest-internal-inl.h:668:30: error: ‘testing::internal::SetUpTestSuiteFunc’ has not been declared
void AddTestInfo(internal::SetUpTestSuiteFunc set_up_tc,
^
./src/gtest-internal-inl.h:669:30: error: ‘testing::internal::TearDownTestSuiteFunc’ has not been declared
internal::TearDownTestSuiteFunc tear_down_tc,
^
./src/gtest-internal-inl.h:929:8: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
std::unique_ptr<InternalRunDeathTestFlag> internal_run_death_test_flag_;
^
./src/gtest-internal-inl.h:930:8: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
std::unique_ptr<internal::DeathTestFactory> death_test_factory_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:940:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(UnitTestImpl);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:940:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(UnitTestImpl);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h: In member function ‘const testing::TestSuite* testing::internal::UnitTestImpl::GetTestSuite(int) const’:
./src/gtest-internal-inl.h:589:24: error: ‘nullptr’ was not declared in this scope
return index < 0 ? nullptr : test_suites_[i];
^
./src/gtest-internal-inl.h: In member function ‘testing::TestSuite* testing::internal::UnitTestImpl::GetMutableSuiteCase(int)’:
./src/gtest-internal-inl.h:601:24: error: ‘nullptr’ was not declared in this scope
return index < 0 ? nullptr : test_suites_[index];
^
./src/gtest-internal-inl.h: In member function ‘void testing::internal::UnitTestImpl::InitDeathTestSubprocessControlInfo()’:
./src/gtest-internal-inl.h:771:5: error: ‘internal_run_death_test_flag_’ was not declared in this scope
internal_run_death_test_flag_.reset(ParseInternalRunDeathTestFlag());
^
./src/gtest-internal-inl.h: In member function ‘const testing::internal::InternalRunDeathTestFlag* testing::internal::UnitTestImpl::internal_run_death_test_flag() const’:
./src/gtest-internal-inl.h:778:12: error: ‘internal_run_death_test_flag_’ was not declared in this scope
return internal_run_death_test_flag_.get();
^
./src/gtest-internal-inl.h: In member function ‘testing::internal::DeathTestFactory* testing::internal::UnitTestImpl::death_test_factory()’:
./src/gtest-internal-inl.h:783:12: error: ‘death_test_factory_’ was not declared in this scope
return death_test_factory_.get();
^
./src/gtest-internal-inl.h: At global scope:
./src/gtest-internal-inl.h:1076:19: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~SocketWriter() override {
^
./src/gtest-internal-inl.h:1082:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void Send(const std::string& message) override {
^
./src/gtest-internal-inl.h:1099:26: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void CloseConnection() override {
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:1111:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(SocketWriter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:1111:5: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(SocketWriter);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h:1125:58: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramStart(const UnitTest& /* unit_test */) override {
^
./src/gtest-internal-inl.h:1129:50: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramEnd(const UnitTest& unit_test) override {
^
./src/gtest-internal-inl.h:1139:42: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
int iteration) override {
^
./src/gtest-internal-inl.h:1145:46: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
int /* iteration */) override {
^
./src/gtest-internal-inl.h:1153:30: error: ‘TestCase’ does not name a type
void OnTestCaseStart(const TestCase& test_case) override {
^
./src/gtest-internal-inl.h:1153:49: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseStart(const TestCase& test_case) override {
^
./src/gtest-internal-inl.h:1159:28: error: ‘TestCase’ does not name a type
void OnTestCaseEnd(const TestCase& test_case) override {
^
./src/gtest-internal-inl.h:1159:47: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseEnd(const TestCase& test_case) override {
^
./src/gtest-internal-inl.h:1165:45: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestStart(const TestInfo& test_info) override {
^
./src/gtest-internal-inl.h:1169:43: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestEnd(const TestInfo& test_info) override {
^
./src/gtest-internal-inl.h:1176:63: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestPartResult(const TestPartResult& test_part_result) override {
^
./src/gtest-internal-inl.h:1194:14: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
const std::unique_ptr<AbstractSocketWriter> socket_writer_;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-internal-inl.h:1196:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(StreamingListener);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-internal-inl.h:1196:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(StreamingListener);
^
In file included from ./src/gtest.cc:122:0,
from src/gtest-all.cc:41:
./src/gtest-internal-inl.h: In constructor ‘testing::internal::StreamingListener::StreamingListener(const string&, const string&)’:
./src/gtest-internal-inl.h:1118:9: error: class ‘testing::internal::StreamingListener’ does not have any field named ‘socket_writer_’
: socket_writer_(new SocketWriter(host, port)) {
^
./src/gtest-internal-inl.h: In constructor ‘testing::internal::StreamingListener::StreamingListener(testing::internal::StreamingListener::AbstractSocketWriter*)’:
./src/gtest-internal-inl.h:1123:9: error: class ‘testing::internal::StreamingListener’ does not have any field named ‘socket_writer_’
: socket_writer_(socket_writer) { Start(); }
^
./src/gtest-internal-inl.h: In member function ‘virtual void testing::internal::StreamingListener::OnTestProgramEnd(const testing::UnitTest&)’:
./src/gtest-internal-inl.h:1135:5: error: ‘socket_writer_’ was not declared in this scope
socket_writer_->CloseConnection();
^
./src/gtest-internal-inl.h: In member function ‘virtual void testing::internal::StreamingListener::OnTestCaseStart(const int&)’:
./src/gtest-internal-inl.h:1154:65: error: request for member ‘name’ in ‘test_case’, which is of non-class type ‘const int’
SendLn(std::string("event=TestCaseStart&name=") + test_case.name());
^
./src/gtest-internal-inl.h: In member function ‘virtual void testing::internal::StreamingListener::OnTestCaseEnd(const int&)’:
./src/gtest-internal-inl.h:1160:63: error: request for member ‘Passed’ in ‘test_case’, which is of non-class type const int’
SendLn("event=TestCaseEnd&passed=" + FormatBool(test_case.Passed()) +
^
./src/gtest-internal-inl.h:1161:60: error: request for member ‘elapsed_time’ in ‘test_case’, which is of non-class type ‘const int’
"&elapsed_time=" + StreamableToString(test_case.elapsed_time()) +
^
./src/gtest-internal-inl.h: In member function ‘virtual void testing::internal::StreamingListener::OnTestPartResult(const testing::TestPartResult&)’:
./src/gtest-internal-inl.h:1178:22: error: ‘nullptr’ was not declared in this scope
if (file_name == nullptr) file_name = "";
^
./src/gtest-internal-inl.h: In member function ‘void testing::internal::StreamingListener::SendLn(const string&)’:
./src/gtest-internal-inl.h:1186:45: error: ‘socket_writer_’ was not declared in this scope
void SendLn(const std::string& message) { socket_writer_->SendLn(message); }
^
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc: In function ‘FILE* testing::internal::OpenFileForWriting(const string&)’:
./src/gtest.cc:186:19: error: ‘nullptr’ was not declared in this scope
FILE* fileout = nullptr;
^
./src/gtest.cc: In function ‘const char* testing::GetDefaultFilter()’:
./src/gtest.cc:206:31: error: ‘nullptr’ was not declared in this scope
if (testbridge_test_only != nullptr) {
^
./src/gtest.cc: In static member function ‘static std::__cxx11::string testing::internal::UnitTestOptions::GetOutputFormat()’:
./src/gtest.cc:447:20: error: ‘nullptr’ was not declared in this scope
return (colon == nullptr)
^
./src/gtest.cc: In static member function ‘static std::__cxx11::string testing::internal::UnitTestOptions::GetAbsolutePathToOutputFile()’:
./src/gtest.cc:462:16: error: ‘nullptr’ was not declared in this scope
if (colon == nullptr)
^
./src/gtest.cc: In static member function ‘static bool testing::internal::UnitTestOptions::MatchesFilter(const string&, const char*)’:
./src/gtest.cc:518:24: error: ‘nullptr’ was not declared in this scope
if (cur_pattern == nullptr) {
^
./src/gtest.cc: In static member function ‘static bool testing::internal::UnitTestOptions::FilterMatchesTest(const string&, const string&)’:
./src/gtest.cc:539:15: error: ‘nullptr’ was not declared in this scope
if (dash == nullptr) {
^
./src/gtest.cc: In function ‘testing::AssertionResult testing::internal::HasOneFailure(const char*, const char*, const char*, const testing::TestPartResultArray&, testing::TestPartResult::Type, const string&)’:
./src/gtest.cc:684:46: error: ‘nullptr’ was not declared in this scope
if (strstr(r.message(), substr.c_str()) == nullptr) {
^
./src/gtest.cc: In function ‘testing::internal::TimeInMillis testing::internal::GetTimeInMillis()’:
./src/gtest.cc:867:22: error: ‘nullptr’ was not declared in this scope
gettimeofday(&now, nullptr);
^
./src/gtest.cc: In static member function ‘static bool testing::internal::String::CStringEquals(const char*, const char*)’:
./src/gtest.cc:918:14: error: ‘nullptr’ was not declared in this scope
if (lhs == nullptr) return rhs == nullptr;
^
./src/gtest.cc:920:14: error: ‘nullptr’ was not declared in this scope
if (rhs == nullptr) return false;
^
./src/gtest.cc: In constructor ‘testing::Message::Message()’:
./src/gtest.cc:969:22: error: class ‘testing::Message’ does not have any field named ‘ss_’
Message::Message() : ss_(new ::std::stringstream) {
^
./src/gtest.cc:972:4: error: ‘ss_’ was not declared in this scope
*ss_ << std::setprecision(std::numeric_limits<double>::digits10 + 2);
^
./src/gtest.cc: In member function ‘std::__cxx11::string testing::Message::GetString() const’:
./src/gtest.cc:1005:41: error: ‘ss_’ was not declared in this scope
return internal::StringStreamToString(ss_.get());
^
./src/gtest.cc: In copy constructor ‘testing::AssertionResult::AssertionResult(const testing::AssertionResult&)’:
./src/gtest.cc:1012:7: error: class ‘testing::AssertionResult’ does not have any field named ‘message_’
message_(other.message_.get() != nullptr
^
./src/gtest.cc:1012:22: error: ‘const class testing::AssertionResult’ has no member named ‘message_’
message_(other.message_.get() != nullptr
^
./src/gtest.cc:1012:40: error: ‘nullptr’ was not declared in this scope
message_(other.message_.get() != nullptr
^
./src/gtest.cc:1013:47: error: ‘const class testing::AssertionResult’ has no member named ‘message_’
? new ::std::string(*other.message_)
^
./src/gtest.cc: In member function ‘void testing::AssertionResult::swap(testing::AssertionResult&)’:
./src/gtest.cc:1020:8: error: ‘message_’ was not declared in this scope
swap(message_, other.message_);
^
./src/gtest.cc:1020:24: error: ‘class testing::AssertionResult’ has no member named ‘message_’
swap(message_, other.message_);
^
./src/gtest.cc: In member function ‘testing::AssertionResult testing::AssertionResult::operator!() const’:
./src/gtest.cc:1025:37: error: no matching function for call to ‘testing::AssertionResult::AssertionResult(bool)’
AssertionResult negation(!success_);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:306:12: note: candidate: template<class T> testing::AssertionResult::AssertionResult(const T&, int)
explicit AssertionResult(
^
./include/gtest/gtest.h:306:12: note: template argument deduction/substitution failed:
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:1025:37: note: candidate expects 2 arguments, 1 provided
AssertionResult negation(!success_);
^
./src/gtest.cc:1010:1: note: candidate: testing::AssertionResult::AssertionResult(const testing::AssertionResult&)
AssertionResult::AssertionResult(const AssertionResult& other)
^
./src/gtest.cc:1010:1: note: no known conversion for argument 1 from ‘bool’ to ‘const testing::AssertionResult&’
./src/gtest.cc:1026:7: error: ‘message_’ was not declared in this scope
if (message_.get() != nullptr) negation << *message_;
^
./src/gtest.cc:1026:25: error: ‘nullptr’ was not declared in this scope
if (message_.get() != nullptr) negation << *message_;
^
./src/gtest.cc: In function ‘testing::AssertionResult testing::AssertionSuccess()’:
./src/gtest.cc:1032:30: error: no matching function for call to ‘testing::AssertionResult::AssertionResult(bool)’
return AssertionResult(true);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:306:12: note: candidate: template<class T> testing::AssertionResult::AssertionResult(const T&, int)
explicit AssertionResult(
^
./include/gtest/gtest.h:306:12: note: template argument deduction/substitution failed:
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:1032:30: note: candidate expects 2 arguments, 1 provided
return AssertionResult(true);
^
./src/gtest.cc:1010:1: note: candidate: testing::AssertionResult::AssertionResult(const testing::AssertionResult&)
AssertionResult::AssertionResult(const AssertionResult& other)
^
./src/gtest.cc:1010:1: note: no known conversion for argument 1 from ‘bool’ to ‘const testing::AssertionResult&’
./src/gtest.cc: In function ‘testing::AssertionResult testing::AssertionFailure()’:
./src/gtest.cc:1037:31: error: no matching function for call to ‘testing::AssertionResult::AssertionResult(bool)’
return AssertionResult(false);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:306:12: note: candidate: template<class T> testing::AssertionResult::AssertionResult(const T&, int)
explicit AssertionResult(
^
./include/gtest/gtest.h:306:12: note: template argument deduction/substitution failed:
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:1037:31: note: candidate expects 2 arguments, 1 provided
return AssertionResult(false);
^
./src/gtest.cc:1010:1: note: candidate: testing::AssertionResult::AssertionResult(const testing::AssertionResult&)
AssertionResult::AssertionResult(const AssertionResult& other)
^
./src/gtest.cc:1010:1: note: no known conversion for argument 1 from ‘bool’ to ‘const testing::AssertionResult&’
./src/gtest.cc: In function ‘bool testing::{anonymous}::IsSubstringPred(const char*, const char*)’:
./src/gtest.cc:1578:17: error: ‘nullptr’ was not declared in this scope
if (needle == nullptr || haystack == nullptr) return needle == haystack;
^
./src/gtest.cc:1580:38: error: ‘nullptr’ was not declared in this scope
return strstr(haystack, needle) != nullptr;
^
./src/gtest.cc: In function ‘bool testing::{anonymous}::IsSubstringPred(const wchar_t*, const wchar_t*)’:
./src/gtest.cc:1584:17: error: ‘nullptr’ was not declared in this scope
if (needle == nullptr || haystack == nullptr) return needle == haystack;
^
./src/gtest.cc:1586:38: error: ‘nullptr’ was not declared in this scope
return wcsstr(haystack, needle) != nullptr;
^
./src/gtest.cc: In static member function ‘static std::__cxx11::string testing::internal::String::ShowWideCString(const wchar_t*)’:
./src/gtest.cc:1867:21: error: ‘nullptr’ was not declared in this scope
if (wide_c_str == nullptr) return "(null)";
^
./src/gtest.cc: In static member function ‘static bool testing::internal::String::WideCStringEquals(const wchar_t*, const wchar_t*)’:
./src/gtest.cc:1879:14: error: ‘nullptr’ was not declared in this scope
if (lhs == nullptr) return rhs == nullptr;
^
./src/gtest.cc:1881:14: error: ‘nullptr’ was not declared in this scope
if (rhs == nullptr) return false;
^
./src/gtest.cc: In static member function ‘static bool testing::internal::String::CaseInsensitiveCStringEquals(const char*, const char*)’:
./src/gtest.cc:1924:14: error: ‘nullptr’ was not declared in this scope
if (lhs == nullptr) return rhs == nullptr;
^
./src/gtest.cc:1925:14: error: ‘nullptr’ was not declared in this scope
if (rhs == nullptr) return false;
^
./src/gtest.cc: In static member function ‘static bool testing::internal::String::CaseInsensitiveWideCStringEquals(const wchar_t*, const wchar_t*)’:
./src/gtest.cc:1943:14: error: ‘nullptr’ was not declared in this scope
if (lhs == nullptr) return rhs == nullptr;
^
./src/gtest.cc:1945:14: error: ‘nullptr’ was not declared in this scope
if (rhs == nullptr) return false;
^
./src/gtest.cc: In member function ‘const testing::TestPartResult& testing::TestResult::GetTestPartResult(int) const’:
./src/gtest.cc:2047:5: error: ‘Abort’ is not a member of ‘testing::internal::posix’
internal::posix::Abort();
^
./src/gtest.cc: In member function ‘const testing::TestProperty& testing::TestResult::GetTestProperty(int) const’:
./src/gtest.cc:2056:5: error: ‘Abort’ is not a member of ‘testing::internal::posix’
internal::posix::Abort();
^
./src/gtest.cc: In constructor ‘testing::Test::Test()’:
./src/gtest.cc:2237:7: error: class ‘testing::Test’ does not have any field named ‘gtest_flag_saver_’
: gtest_flag_saver_(new GTEST_FLAG_SAVER_) {
^
./src/gtest.cc: In function ‘void testing::internal::ReportFailureInUnknownLocation(testing::TestPartResult::Type, const string&)’:
./src/gtest.cc:2278:7: error: ‘nullptr’ was not declared in this scope
nullptr, // No info about the source file where the exception occurred.
^
./src/gtest.cc: In function ‘std::__cxx11::string testing::internal::FormatCxxExceptionMessage(const char*, const char*)’:
./src/gtest.cc:2377:22: error: ‘nullptr’ was not declared in this scope
if (description != nullptr) {
^
./src/gtest.cc: In function ‘Result testing::internal::HandleExceptionsInMethodIfSupported(T*, Result (T::*)(), const char*)’:
./src/gtest.cc:2475:37: error: ‘nullptr’ was not declared in this scope
FormatCxxExceptionMessage(nullptr, location));
^
./src/gtest.cc: In constructor ‘testing::TestInfo::TestInfo(const string&, const string&, const char*, const char*, testing::internal::CodeLocation, testing::internal::TypeId, testing::internal::TestFactoryBase*)’:
./src/gtest.cc:2539:7: error: class ‘testing::TestInfo’ does not have any field named ‘type_param_’
type_param_(a_type_param ? new std::string(a_type_param) : nullptr),
^
./src/gtest.cc:2539:66: error: ‘nullptr’ was not declared in this scope
type_param_(a_type_param ? new std::string(a_type_param) : nullptr),
^
./src/gtest.cc:2540:7: error: class ‘testing::TestInfo’ does not have any field named ‘value_param_’
value_param_(a_value_param ? new std::string(a_value_param) : nullptr),
^
./src/gtest.cc: At global scope:
./src/gtest.cc:2575:30: error: ‘SetUpTestSuiteFunc’ has not been declared
TypeId fixture_class_id, SetUpTestSuiteFunc set_up_tc,
^
./src/gtest.cc:2576:5: error: ‘TearDownTestSuiteFunc’ has not been declared
TearDownTestSuiteFunc tear_down_tc, TestFactoryBase* factory) {
^
./src/gtest.cc: In member function ‘void testing::TestInfo::Run()’:
./src/gtest.cc:2690:31: error: ‘nullptr’ was not declared in this scope
impl->set_current_test_info(nullptr);
^
./src/gtest.cc: At global scope:
./src/gtest.cc:2745:32: error: ‘testing::internal::SetUpTestSuiteFunc’ has not been declared
internal::SetUpTestSuiteFunc set_up_tc,
^
./src/gtest.cc:2746:32: error: ‘testing::internal::TearDownTestSuiteFunc’ has not been declared
internal::TearDownTestSuiteFunc tear_down_tc)
^
./src/gtest.cc: In constructor ‘testing::TestSuite::TestSuite(const char*, const char*, int, int)’:
./src/gtest.cc:2748:7: error: class ‘testing::TestSuite’ does not have any field named ‘type_param_’
type_param_(a_type_param ? new std::string(a_type_param) : nullptr),
^
./src/gtest.cc:2748:66: error: ‘nullptr’ was not declared in this scope
type_param_(a_type_param ? new std::string(a_type_param) : nullptr),
^
./src/gtest.cc:2749:7: error: class ‘testing::TestSuite’ does not have any field named ‘set_up_tc_’
set_up_tc_(set_up_tc),
^
./src/gtest.cc:2750:7: error: class ‘testing::TestSuite’ does not have any field named ‘tear_down_tc_’
tear_down_tc_(tear_down_tc),
^
./src/gtest.cc: In member function ‘const testing::TestInfo* testing::TestSuite::GetTestInfo(int) const’:
./src/gtest.cc:2764:22: error: ‘nullptr’ was not declared in this scope
return index < 0 ? nullptr : test_info_list_[index];
^
./src/gtest.cc: In member function ‘testing::TestInfo* testing::TestSuite::GetMutableTestInfo(int)’:
./src/gtest.cc:2771:22: error: ‘nullptr’ was not declared in this scope
return index < 0 ? nullptr : test_info_list_[index];
^
./src/gtest.cc: In member function ‘void testing::TestSuite::Run()’:
./src/gtest.cc:2794:34: error: no matching function for call to ‘testing::TestEventListener::OnTestCaseStart(testing::TestSuite&)’
repeater->OnTestCaseStart(*this);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:1094:16: note: candidate: virtual void testing::TestEventListener::OnTestCaseStart(const int&)
virtual void OnTestCaseStart(const TestCase& /*test_case*/) {}
^
./include/gtest/gtest.h:1094:16: note: no known conversion for argument 1 from ‘testing::TestSuite’ to ‘const int&’
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:2815:32: error: no matching function for call to ‘testing::TestEventListener::OnTestCaseEnd(testing::TestSuite&)’
repeater->OnTestCaseEnd(*this);
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:1113:16: note: candidate: virtual void testing::TestEventListener::OnTestCaseEnd(const int&)
virtual void OnTestCaseEnd(const TestCase& /*test_case*/) {}
^
./include/gtest/gtest.h:1113:16: note: no known conversion for argument 1 from ‘testing::TestSuite’ to ‘const int&’
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:2818:32: error: ‘nullptr’ was not declared in this scope
impl->set_current_test_suite(nullptr);
^
./src/gtest.cc: In function ‘const char* testing::internal::GetAnsiColorCode(testing::internal::GTestColor)’:
./src/gtest.cc:2970:14: error: ‘nullptr’ was not declared in this scope
return nullptr;
^
./src/gtest.cc: In function ‘void testing::internal::PrintFullTestCommentIfPresent(const testing::TestInfo&)’:
./src/gtest.cc:3074:21: error: ‘nullptr’ was not declared in this scope
if (type_param != nullptr || value_param != nullptr) {
^
./src/gtest.cc: At global scope:
./src/gtest.cc:3097:56: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramStart(const UnitTest& /*unit_test*/) override {}
^
./src/gtest.cc:3098:69: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestIterationStart(const UnitTest& unit_test, int iteration) override;
^
./src/gtest.cc:3099:58: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsSetUpStart(const UnitTest& unit_test) override;
^
./src/gtest.cc:3100:60: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsSetUpEnd(const UnitTest& /*unit_test*/) override {}
^
./src/gtest.cc:3101:51: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseStart(const TestSuite& test_suite) override;
^
./src/gtest.cc:3102:45: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestStart(const TestInfo& test_info) override;
^
./src/gtest.cc:3103:53: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestPartResult(const TestPartResult& result) override;
^
./src/gtest.cc:3104:43: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestEnd(const TestInfo& test_info) override;
^
./src/gtest.cc:3105:49: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseEnd(const TestSuite& test_suite) override;
^
./src/gtest.cc:3106:61: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsTearDownStart(const UnitTest& unit_test) override;
^
./src/gtest.cc:3107:63: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsTearDownEnd(const UnitTest& /*unit_test*/) override {}
^
./src/gtest.cc:3108:67: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestIterationEnd(const UnitTest& unit_test, int iteration) override;
^
./src/gtest.cc:3109:54: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramEnd(const UnitTest& /*unit_test*/) override {}
^
./src/gtest.cc:3101:8: error: ‘void testing::internal::PrettyUnitTestResultPrinter::OnTestCaseStart(const testing::TestSuite&)’ marked ‘override’, but does not override
void OnTestCaseStart(const TestSuite& test_suite) override;
^
./src/gtest.cc:3105:8: error: ‘void testing::internal::PrettyUnitTestResultPrinter::OnTestCaseEnd(const testing::TestSuite&)’ marked ‘override’, but does not override
void OnTestCaseEnd(const TestSuite& test_suite) override;
^
./src/gtest.cc: In member function ‘void testing::internal::PrettyUnitTestResultPrinter::OnTestCaseStart(const testing::TestSuite&)’:
./src/gtest.cc:3164:34: error: ‘nullptr’ was not declared in this scope
if (test_suite.type_param() == nullptr) {
^
./src/gtest.cc: At global scope:
./src/gtest.cc:3337:22: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~TestEventRepeater() override;
^
./src/gtest.cc:3346:52: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramStart(const UnitTest& unit_test) override;
^
./src/gtest.cc:3347:69: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestIterationStart(const UnitTest& unit_test, int iteration) override;
^
./src/gtest.cc:3348:58: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsSetUpStart(const UnitTest& unit_test) override;
^
./src/gtest.cc:3349:56: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsSetUpEnd(const UnitTest& unit_test) override;
^
./src/gtest.cc:3352:50: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseStart(const TestSuite& parameter) override;
^
./src/gtest.cc:3354:51: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestSuiteStart(const TestSuite& parameter) override;
^
./src/gtest.cc:3355:45: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestStart(const TestInfo& test_info) override;
^
./src/gtest.cc:3356:53: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestPartResult(const TestPartResult& result) override;
^
./src/gtest.cc:3357:43: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestEnd(const TestInfo& test_info) override;
^
./src/gtest.cc:3360:48: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestCaseEnd(const TestSuite& parameter) override;
^
./src/gtest.cc:3362:49: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestSuiteEnd(const TestSuite& parameter) override;
^
./src/gtest.cc:3363:61: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsTearDownStart(const UnitTest& unit_test) override;
^
./src/gtest.cc:3364:59: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnEnvironmentsTearDownEnd(const UnitTest& unit_test) override;
^
./src/gtest.cc:3365:67: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestIterationEnd(const UnitTest& unit_test, int iteration) override;
^
./src/gtest.cc:3366:50: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestProgramEnd(const UnitTest& unit_test) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest.cc:3375:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestEventRepeater);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest.cc:3375:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(TestEventRepeater);
^
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:3352:8: error: ‘void testing::internal::TestEventRepeater::OnTestCaseStart(const testing::TestSuite&)’ marked ‘override’, but does not override
void OnTestCaseStart(const TestSuite& parameter) override;
^
./src/gtest.cc:3360:8: error: ‘void testing::internal::TestEventRepeater::OnTestCaseEnd(const testing::TestSuite&)’ marked ‘override’, but does not override
void OnTestCaseEnd(const TestSuite& parameter) override;
^
./src/gtest.cc: In member function ‘testing::TestEventListener* testing::internal::TestEventRepeater::Release(testing::TestEventListener*)’:
./src/gtest.cc:3394:10: error: ‘nullptr’ was not declared in this scope
return nullptr;
^
./src/gtest.cc: In member function ‘void testing::internal::TestEventRepeater::OnTestCaseStart(const testing::TestSuite&)’:
./src/gtest.cc:3403:36: error: no matching function for call to ‘testing::TestEventListener::OnTestCaseStart(const testing::TestSuite&)’
listeners_[i]->Name(parameter); \
^
./src/gtest.cc:3422:1: note: in expansion of macro ‘GTEST_REPEATER_METHOD_’
GTEST_REPEATER_METHOD_(OnTestCaseStart, TestSuite)
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:1094:16: note: candidate: virtual void testing::TestEventListener::OnTestCaseStart(const int&)
virtual void OnTestCaseStart(const TestCase& /*test_case*/) {}
^
./include/gtest/gtest.h:1094:16: note: no known conversion for argument 1 from ‘const testing::TestSuite’ to ‘const int&’
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc: In member function ‘void testing::internal::TestEventRepeater::OnTestCaseEnd(const testing::TestSuite&)’:
./src/gtest.cc:3413:36: error: no matching function for call to ‘testing::TestEventListener::OnTestCaseEnd(const testing::TestSuite&)’
listeners_[i]->Name(parameter); \
^
./src/gtest.cc:3433:1: note: in expansion of macro ‘GTEST_REVERSE_REPEATER_METHOD_’
GTEST_REVERSE_REPEATER_METHOD_(OnTestCaseEnd, TestSuite)
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:1113:16: note: candidate: virtual void testing::TestEventListener::OnTestCaseEnd(const int&)
virtual void OnTestCaseEnd(const TestCase& /*test_case*/) {}
^
./include/gtest/gtest.h:1113:16: note: no known conversion for argument 1 from ‘const testing::TestSuite’ to ‘const int&’
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc: At global scope:
./src/gtest.cc:3466:67: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestIterationEnd(const UnitTest& unit_test, int iteration) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest.cc:3541:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(XmlUnitTestResultPrinter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest.cc:3541:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(XmlUnitTestResultPrinter);
^
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc: In function ‘bool testing::internal::PortableLocaltime(time_t, tm*)’:
./src/gtest.cc:3673:40: error: ‘nullptr’ was not declared in this scope
return localtime_r(&seconds, out) != nullptr;
^
./src/gtest.cc: In static member function ‘static void testing::internal::XmlUnitTestResultPrinter::OutputXmlCDataSection(std::ostream*, const char*)’:
./src/gtest.cc:3699:25: error: ‘nullptr’ was not declared in this scope
if (next_segment != nullptr) {
^
./src/gtest.cc: In static member function ‘static void testing::internal::XmlUnitTestResultPrinter::OutputXmlTestInfo(std::ostream*, const char*, const testing::TestInfo&)’:
./src/gtest.cc:3742:34: error: ‘nullptr’ was not declared in this scope
if (test_info.value_param() != nullptr) {
^
./src/gtest.cc:3746:33: error: ‘nullptr’ was not declared in this scope
if (test_info.type_param() != nullptr) {
^
./src/gtest.cc: In static member function ‘static void testing::internal::XmlUnitTestResultPrinter::PrintXmlTestsList(std::ostream*, const std::vector<testing::TestSuite*>&)’:
./src/gtest.cc:3869:13: error: ‘test_suite’ does not name a type
for (auto test_suite : test_suites) {
^
./src/gtest.cc:3872:3: error: expected ‘;’ before ‘OutputXmlAttribute’
OutputXmlAttribute(stream, kTestsuites, "tests",
^
./src/gtest.cc:3872:21: error: could not convert ‘testing::internal::XmlUnitTestResultPrinter::OutputXmlAttribute(stream, kTestsuites, std::__cxx11::basic_string<char>(((const char*)"tests"), std::allocator<char>()), testing::internal::StreamableToString(const T&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]())’ from ‘void’ to ‘bool’
OutputXmlAttribute(stream, kTestsuites, "tests",
^
./src/gtest.cc:3874:62: error: expected ‘)’ before ‘;’ token
OutputXmlAttribute(stream, kTestsuites, "name", "AllTests");
^
./src/gtest.cc:3877:13: error: ‘test_suite’ does not name a type
for (auto test_suite : test_suites) {
^
./src/gtest.cc:3880:3: error: expected ‘;’ before ‘*’ token
*stream << "</" << kTestsuites << ">\n";
^
./src/gtest.cc:3881:1: error: expected primary-expression before ‘}’ token
}
^
./src/gtest.cc:3881:1: error: expected ‘)’ before ‘}’ token
./src/gtest.cc:3881:1: error: expected primary-expression before ‘}’ token
./src/gtest.cc: At global scope:
./src/gtest.cc:3923:67: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void OnTestIterationEnd(const UnitTest& unit_test, int iteration) override;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest.cc:3969:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(JsonUnitTestResultPrinter);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest.cc:3969:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(JsonUnitTestResultPrinter);
^
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc: In static member function ‘static void testing::internal::JsonUnitTestResultPrinter::OutputJsonTestInfo(std::ostream*, const char*, const testing::TestInfo&)’:
./src/gtest.cc:4109:34: error: ‘nullptr’ was not declared in this scope
if (test_info.value_param() != nullptr) {
^
./src/gtest.cc:4113:33: error: ‘nullptr’ was not declared in this scope
if (test_info.type_param() != nullptr) {
^
./src/gtest.cc: In static member function ‘static void testing::internal::JsonUnitTestResultPrinter::PrintJsonTestList(std::ostream*, const std::vector<testing::TestSuite*>&)’:
./src/gtest.cc:4249:13: error: ‘test_suite’ does not name a type
for (auto test_suite : test_suites) {
^
./src/gtest.cc:4252:3: error: expected ‘;’ before ‘OutputJsonKey’
OutputJsonKey(stream, kTestsuites, "tests", total_tests, kIndent);
^
./src/gtest.cc:4252:16: error: could not convert ‘testing::internal::JsonUnitTestResultPrinter::OutputJsonKey(stream, kTestsuites, std::__cxx11::basic_string<char>(((const char*)"tests"), std::allocator<char>()), total_tests, kIndent, 1)’ from ‘void’ to ‘bool’
OutputJsonKey(stream, kTestsuites, "tests", total_tests, kIndent);
^
./src/gtest.cc:4254:66: error: expected ‘)’ before ‘;’ token
OutputJsonKey(stream, kTestsuites, "name", "AllTests", kIndent);
^
./src/gtest.cc: In member function ‘void testing::internal::StreamingListener::SocketWriter::MakeConnection()’:
./src/gtest.cc:4317:24: error: ‘nullptr’ was not declared in this scope
addrinfo* servinfo = nullptr;
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./src/gtest.cc: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest.cc:4452:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedPrematureExitFile);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest.cc:4452:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(ScopedPrematureExitFile);
^
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc: In constructor ‘testing::TestEventListeners::TestEventListeners()’:
./src/gtest.cc:4461:31: error: ‘nullptr’ was not declared in this scope
default_result_printer_(nullptr),
^
./src/gtest.cc: In member function ‘testing::TestEventListener* testing::TestEventListeners::Release(testing::TestEventListener*)’:
./src/gtest.cc:4479:31: error: ‘nullptr’ was not declared in this scope
default_result_printer_ = nullptr;
^
./src/gtest.cc:4481:30: error: ‘nullptr’ was not declared in this scope
default_xml_generator_ = nullptr;
^
./src/gtest.cc: In member function ‘void testing::TestEventListeners::SetDefaultResultPrinter(testing::TestEventListener*)’:
./src/gtest.cc:4500:21: error: ‘nullptr’ was not declared in this scope
if (listener != nullptr) Append(listener);
^
./src/gtest.cc: In member function ‘void testing::TestEventListeners::SetDefaultXmlGenerator(testing::TestEventListener*)’:
./src/gtest.cc:4515:21: error: ‘nullptr’ was not declared in this scope
if (listener != nullptr) Append(listener);
^
./src/gtest.cc: At global scope:
./src/gtest.cc:4649:7: error: ‘TestCase’ does not name a type
const TestCase* UnitTest::GetTestCase(int i) const {
^
./src/gtest.cc: In member function ‘testing::Environment* testing::UnitTest::AddEnvironment(testing::Environment*)’:
./src/gtest.cc:4683:14: error: ‘nullptr’ was not declared in this scope
if (env == nullptr) {
^
./src/gtest.cc: In member function ‘void testing::UnitTest::AddTestPartResult(testing::TestPartResult::Type, const char*, int, const string&, const string&)’:
./src/gtest.cc:4716:33: error: ‘nullptr’ was not declared in this scope
if (os_stack_trace.c_str() != nullptr && !os_stack_trace.empty()) {
^
./src/gtest.cc: In member function ‘int testing::UnitTest::Run()’:
./src/gtest.cc:4803:13: error: ‘nullptr’ was not declared in this scope
? nullptr
^
./src/gtest.cc: At global scope:
./src/gtest.cc:4865:7: error: ‘TestCase’ does not name a type
const TestCase* UnitTest::current_test_case() const
^
./src/gtest.cc: In constructor ‘testing::internal::UnitTestImpl::UnitTestImpl(testing::UnitTest*)’:
./src/gtest.cc:4929:27: error: ‘nullptr’ was not declared in this scope
current_test_suite_(nullptr),
^
./src/gtest.cc:4939:7: error: class ‘testing::internal::UnitTestImpl’ does not have any field named ‘death_test_factory_’
death_test_factory_(new DefaultDeathTestFactory),
^
./src/gtest.cc: In member function ‘void testing::internal::UnitTestImpl::RecordProperty(const testing::TestProperty&)’:
./src/gtest.cc:4965:29: error: ‘nullptr’ was not declared in this scope
if (current_test_info_ != nullptr) {
^
./src/gtest.cc: In member function ‘void testing::internal::UnitTestImpl::SuppressTestEventsIfInSubprocess()’:
./src/gtest.cc:4982:7: error: ‘internal_run_death_test_flag_’ was not declared in this scope
if (internal_run_death_test_flag_.get() != nullptr)
^
./src/gtest.cc:4982:46: error: ‘nullptr’ was not declared in this scope
if (internal_run_death_test_flag_.get() != nullptr)
^
./src/gtest.cc: In member function ‘bool testing::internal::TestSuiteNameIs::operator()(const testing::TestSuite*) const’:
./src/gtest.cc:5079:26: error: ‘nullptr’ was not declared in this scope
return test_suite != nullptr &&
^
./src/gtest.cc: At global scope:
./src/gtest.cc:5101:15: error: ‘testing::internal::SetUpTestSuiteFunc’ has not been declared
internal::SetUpTestSuiteFunc set_up_tc,
^
./src/gtest.cc:5102:15: error: ‘testing::internal::TearDownTestSuiteFunc’ has not been declared
internal::TearDownTestSuiteFunc tear_down_tc) {
^
./src/gtest.cc: In member function ‘testing::TestSuite* testing::internal::UnitTestImpl::GetTestSuite(const char*, const char*, int, int)’:
./src/gtest.cc:5104:14: error: ‘test_suite’ does not name a type
const auto test_suite =
^
./src/gtest.cc:5108:7: error: ‘test_suite’ was not declared in this scope
if (test_suite != test_suites_.rend()) return *test_suite;
^
./src/gtest.cc:5111:15: error: ISO C++ forbids declaration of ‘new_test_suite’ with no type [-fpermissive]
auto* const new_test_suite =
^
./src/gtest.cc:5112:73: error: cannot convert ‘testing::TestSuite*’ to ‘int* const’ in initialization
new TestSuite(test_suite_name, type_param, set_up_tc, tear_down_tc);
^
./src/gtest.cc:5123:39: error: no matching function for call to ‘std::vector<testing::TestSuite*>::insert(__gnu_cxx::__normal_iterator<testing::TestSuite**, std::vector<testing::TestSuite*> >, int* const&)’
new_test_suite);
^
In file included from /usr/include/c++/5/vector:69:0,
from ./include/gtest/gtest.h:58,
from src/gtest-all.cc:38:
/usr/include/c++/5/bits/vector.tcc:107:5: note: candidate: std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, const value_type&) [with _Tp = testing::TestSuite*; _Alloc = std::allocator<testing::TestSuite*>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<testing::TestSuite**, std::vector<testing::TestSuite*> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = testing::TestSuite**; std::vector<_Tp, _Alloc>::value_type = testing::TestSuite*]
vector<_Tp, _Alloc>::
^
/usr/include/c++/5/bits/vector.tcc:107:5: note: no known conversion for argument 2 from ‘int* const’ to ‘testing::TestSuite* const&’
In file included from /usr/include/c++/5/vector:64:0,
from ./include/gtest/gtest.h:58,
from src/gtest-all.cc:38:
/usr/include/c++/5/bits/stl_vector.h:1072:7: note: candidate: void std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = testing::TestSuite*; _Alloc = std::allocator<testing::TestSuite*>; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<testing::TestSuite**, std::vector<testing::TestSuite*> >; typename std::_Vector_base<_Tp, _Alloc>::pointer = testing::TestSuite**; std::vector<_Tp, _Alloc>::size_type = long unsigned int; std::vector<_Tp, _Alloc>::value_type = testing::TestSuite*]
insert(iterator __position, size_type __n, const value_type& __x)
^
/usr/include/c++/5/bits/stl_vector.h:1072:7: note: candidate expects 3 arguments, 2 provided
/usr/include/c++/5/bits/stl_vector.h:1120:9: note: candidate: template<class _InputIterator> void std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, _InputIterator, _InputIterator) [with _InputIterator = _InputIterator; _Tp = testing::TestSuite*; _Alloc = std::allocator<testing::TestSuite*>]
insert(iterator __position, _InputIterator __first,
^
/usr/include/c++/5/bits/stl_vector.h:1120:9: note: template argument deduction/substitution failed:
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:5123:39: note: candidate expects 3 arguments, 2 provided
new_test_suite);
^
./src/gtest.cc:5126:42: error: no matching function for call to ‘std::vector<testing::TestSuite*>::push_back(int* const&)’
test_suites_.push_back(new_test_suite);
^
In file included from /usr/include/c++/5/vector:64:0,
from ./include/gtest/gtest.h:58,
from src/gtest-all.cc:38:
/usr/include/c++/5/bits/stl_vector.h:913:7: note: candidate: void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = testing::TestSuite*; _Alloc = std::allocator<testing::TestSuite*>; std::vector<_Tp, _Alloc>::value_type = testing::TestSuite*]
push_back(const value_type& __x)
^
/usr/include/c++/5/bits/stl_vector.h:913:7: note: no known conversion for argument 1 from ‘int* const’ to ‘testing::TestSuite* const&’
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:5130:10: error: cannot convert ‘int* const’ to ‘testing::TestSuite*’ in return
return new_test_suite;
^
./src/gtest.cc: In member function ‘bool testing::internal::UnitTestImpl::RunAllTests()’:
./src/gtest.cc:5170:8: error: ‘internal_run_death_test_flag_’ was not declared in this scope
(internal_run_death_test_flag_.get() != nullptr);
^
./src/gtest.cc:5170:47: error: ‘nullptr’ was not declared in this scope
(internal_run_death_test_flag_.get() != nullptr);
^
./src/gtest.cc: In function ‘void testing::internal::WriteToShardStatusFileIfNeeded()’:
./src/gtest.cc:5301:26: error: ‘nullptr’ was not declared in this scope
if (test_shard_file != nullptr) {
^
./src/gtest.cc: In function ‘testing::internal::Int32 testing::internal::Int32FromEnvOrDie(const char*, testing::internal::Int32)’:
./src/gtest.cc:5368:18: error: ‘nullptr’ was not declared in this scope
if (str_val == nullptr) {
^
./src/gtest.cc: In member function ‘int testing::internal::UnitTestImpl::FilterTests(testing::internal::UnitTestImpl::ReactionToSharding)’:
./src/gtest.cc:5407:14: error: ISO C++ forbids declaration of ‘test_suite’ with no type [-fpermissive]
for (auto* test_suite : test_suites_) {
^
./src/gtest.cc:5407:27: warning: range-based ‘for’ loops only available with -std=c++11 or -std=gnu++11
for (auto* test_suite : test_suites_) {
^
./src/gtest.cc:5408:54: error: request for member ‘name’ in ‘* test_suite’, which is of non-class type ‘int’
const std::string& test_suite_name = test_suite->name();
^
./src/gtest.cc:5409:17: error: request for member ‘set_should_run’ in ‘* test_suite’, which is of non-class type ‘int’
test_suite->set_should_run(false);
^
./src/gtest.cc:5411:40: error: request for member ‘test_info_list’ in ‘* test_suite’, which is of non-class type ‘int’
for (size_t j = 0; j < test_suite->test_info_list().size(); j++) {
^
./src/gtest.cc:5412:47: error: request for member ‘test_info_list’ in ‘* test_suite’, which is of non-class type ‘int’
TestInfo* const test_info = test_suite->test_info_list()[j];
^
./src/gtest.cc:5440:19: error: request for member ‘set_should_run’ in ‘* test_suite’, which is of non-class type ‘int’
test_suite->set_should_run(test_suite->should_run() || is_selected);
^
./src/gtest.cc:5440:46: error: request for member ‘should_run’ in ‘* test_suite’, which is of non-class type ‘int’
test_suite->set_should_run(test_suite->should_run() || is_selected);
^
./src/gtest.cc: In function ‘void testing::internal::PrintOnOneLine(const char*, int)’:
./src/gtest.cc:5451:14: error: ‘nullptr’ was not declared in this scope
if (str != nullptr) {
^
./src/gtest.cc: In member function ‘void testing::internal::UnitTestImpl::ListTestsMatchingFilter()’:
./src/gtest.cc:5473:14: error: ISO C++ forbids declaration of ‘test_suite’ with no type [-fpermissive]
for (auto* test_suite : test_suites_) {
^
./src/gtest.cc:5473:27: warning: range-based ‘for’ loops only available with -std=c++11 or -std=gnu++11
for (auto* test_suite : test_suites_) {
^
./src/gtest.cc:5476:40: error: request for member ‘test_info_list’ in ‘* test_suite’, which is of non-class type ‘int’
for (size_t j = 0; j < test_suite->test_info_list().size(); j++) {
^
./src/gtest.cc:5477:53: error: request for member ‘test_info_list’ in ‘* test_suite’, which is of non-class type ‘int’
const TestInfo* const test_info = test_suite->test_info_list()[j];
^
./src/gtest.cc:5481:37: error: request for member ‘name’ in ‘* test_suite’, which is of non-class type ‘int’
printf("%s.", test_suite->name());
^
./src/gtest.cc:5482:27: error: request for member ‘type_param’ in ‘* test_suite’, which is of non-class type ‘int’
if (test_suite->type_param() != nullptr) {
^
./src/gtest.cc:5482:43: error: ‘nullptr’ was not declared in this scope
if (test_suite->type_param() != nullptr) {
^
./src/gtest.cc:5486:40: error: request for member ‘type_param’ in ‘* test_suite’, which is of non-class type ‘int’
PrintOnOneLine(test_suite->type_param(), kMaxParamLength);
^
./src/gtest.cc:5491:41: error: ‘nullptr’ was not declared in this scope
if (test_info->value_param() != nullptr) {
^
./src/gtest.cc: In member function ‘testing::internal::OsStackTraceGetterInterface* testing::internal::UnitTestImpl::os_stack_trace_getter()’:
./src/gtest.cc:5538:33: error: ‘nullptr’ was not declared in this scope
if (os_stack_trace_getter_ == nullptr) {
^
./src/gtest.cc: In member function ‘testing::TestResult* testing::internal::UnitTestImpl::current_test_result()’:
./src/gtest.cc:5551:29: error: ‘nullptr’ was not declared in this scope
if (current_test_info_ != nullptr) {
^
./src/gtest.cc:5554:30: error: ‘nullptr’ was not declared in this scope
if (current_test_suite_ != nullptr) {
^
./src/gtest.cc: In member function ‘void testing::internal::UnitTestImpl::ShuffleTests()’:
./src/gtest.cc:5571:14: error: ISO C++ forbids declaration of ‘test_suite’ with no type [-fpermissive]
for (auto& test_suite : test_suites_) {
^
./src/gtest.cc:5571:27: warning: range-based ‘for’ loops only available with -std=c++11 or -std=gnu++11
for (auto& test_suite : test_suites_) {
^
./src/gtest.cc:5572:15: error: base operand of ‘->’ is not a pointer
test_suite->ShuffleTests(random());
^
./src/gtest.cc: In function ‘const char* testing::internal::ParseFlagValue(const char*, const char*, bool)’:
./src/gtest.cc:5641:14: error: ‘nullptr’ was not declared in this scope
if (str == nullptr || flag == nullptr) return nullptr;
^
./src/gtest.cc:5646:61: error: ‘nullptr’ was not declared in this scope
if (strncmp(str, flag_str.c_str(), flag_len) != 0) return nullptr;
^
./src/gtest.cc:5659:34: error: ‘nullptr’ was not declared in this scope
if (flag_end[0] != '=') return nullptr;
^
./src/gtest.cc: In function ‘bool testing::internal::ParseBoolFlag(const char*, const char*, bool*)’:
./src/gtest.cc:5680:20: error: ‘nullptr’ was not declared in this scope
if (value_str == nullptr) return false;
^
./src/gtest.cc: In function ‘bool testing::internal::ParseInt32Flag(const char*, const char*, testing::internal::Int32*)’:
./src/gtest.cc:5697:20: error: ‘nullptr’ was not declared in this scope
if (value_str == nullptr) return false;
^
./src/gtest.cc: In function ‘bool testing::internal::ParseStringFlag(const char*, const char*, String*)’:
./src/gtest.cc:5715:20: error: ‘nullptr’ was not declared in this scope
if (value_str == nullptr) return false;
^
./src/gtest.cc: In function ‘void testing::internal::PrintColorEncoded(const char*)’:
./src/gtest.cc:5755:14: error: ‘nullptr’ was not declared in this scope
if (p == nullptr) {
^
./src/gtest.cc: In function ‘void testing::InitGoogleTest()’:
./src/gtest.cc:6028:14: error: ‘arg0’ does not name a type
const auto arg0 = "dummy";
^
./src/gtest.cc:6029:35: error: ‘arg0’ was not declared in this scope
char* argv0 = const_cast<char*>(arg0);
^
In file included from src/gtest-all.cc:42:0:
./src/gtest-death-test.cc: In function ‘void testing::internal::DeathTestAbort(const string&)’:
./src/gtest-death-test.cc:290:15: error: ‘nullptr’ was not declared in this scope
if (flag != nullptr) {
^
./src/gtest-death-test.cc:299:5: error: ‘Abort’ is not a member of ‘testing::internal::posix’
posix::Abort();
^
./src/gtest-death-test.cc: In constructor ‘testing::internal::DeathTest::DeathTest()’:
./src/gtest-death-test.cc:370:15: error: ‘nullptr’ was not declared in this scope
if (info == nullptr) {
^
./src/gtest-death-test.cc: In static member function ‘static bool testing::internal::DeathTest::Create(const char*, testing::Matcher<const std::__cxx11::basic_string<char>&>, const char*, int, testing::internal::DeathTest**)’:
./src/gtest-death-test.cc:382:18: error: ‘move’ is not a member of ‘std’
statement, std::move(matcher), file, line, test);
^
./src/gtest-death-test.cc: At global scope:
./src/gtest-death-test.cc:408:18: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
~DeathTestImpl() override { GTEST_DEATH_TEST_CHECK_(read_fd_ == -1); }
^
./src/gtest-death-test.cc:410:32: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
void Abort(AbortReason reason) override;
^
./src/gtest-death-test.cc:411:29: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
bool Passed(bool status_ok) override;
^
./src/gtest-death-test.cc: In constructor ‘testing::internal::DeathTestImpl::DeathTestImpl(const char*, testing::Matcher<const std::__cxx11::basic_string<char>&>)’:
./src/gtest-death-test.cc:400:18: error: ‘move’ is not a member of ‘std’
matcher_(std::move(matcher)),
^
./src/gtest-death-test.cc: At global scope:
./src/gtest-death-test.cc:1066:12: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
int Wait() override;
^
./src/gtest-death-test.cc: In constructor ‘testing::internal::ForkingDeathTest::ForkingDeathTest(const char*, testing::Matcher<const std::__cxx11::basic_string<char>&>)’:
./src/gtest-death-test.cc:1079:34: error: ‘move’ is not a member of ‘std’
: DeathTestImpl(a_statement, std::move(matcher)), child_pid_(-1) {}
^
./src/gtest-death-test.cc: At global scope:
./src/gtest-death-test.cc:1102:23: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
TestRole AssumeRole() override;
^
./src/gtest-death-test.cc: In constructor ‘testing::internal::NoExecDeathTest::NoExecDeathTest(const char*, testing::Matcher<const std::__cxx11::basic_string<char>&>)’:
./src/gtest-death-test.cc:1101:39: error: ‘move’ is not a member of ‘std’
: ForkingDeathTest(a_statement, std::move(matcher)) {}
^
./src/gtest-death-test.cc: At global scope:
./src/gtest-death-test.cc:1160:23: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11
TestRole AssumeRole() override;
^
./src/gtest-death-test.cc: In constructor ‘testing::internal::ExecDeathTest::ExecDeathTest(const char*, testing::Matcher<const std::__cxx11::basic_string<char>&>, const char*, int)’:
./src/gtest-death-test.cc:1157:39: error: ‘move’ is not a member of ‘std’
: ForkingDeathTest(a_statement, std::move(matcher)),
^
./src/gtest-death-test.cc: In constructor ‘testing::internal::Arguments::Arguments()’:
./src/gtest-death-test.cc:1181:33: error: ‘nullptr’ was not declared in this scope
Arguments() { args_.push_back(nullptr); }
^
./src/gtest-death-test.cc: In function ‘pid_t testing::internal::ExecDeathTestSpawnChild(char* const*, int)’:
./src/gtest-death-test.cc:1353:30: error: ‘nullptr’ was not declared in this scope
void* const stack = mmap(nullptr, stack_size, PROT_READ | PROT_WRITE,
^
./src/gtest-death-test.cc:1385:49: error: ‘nullptr’ was not declared in this scope
sigaction(SIGPROF, &saved_sigprof_action, nullptr));
^
./src/gtest-death-test.cc:326:23: note: in definition of macro ‘GTEST_DEATH_TEST_CHECK_SYSCALL_’
gtest_retval = (expression); \
^
./src/gtest-death-test.cc: In member function ‘virtual testing::internal::DeathTest::TestRole testing::internal::ExecDeathTest::AssumeRole()’:
./src/gtest-death-test.cc:1403:15: error: ‘nullptr’ was not declared in this scope
if (flag != nullptr) {
^
./src/gtest-death-test.cc: In member function ‘virtual bool testing::internal::DefaultDeathTestFactory::Create(const char*, testing::Matcher<const std::__cxx11::basic_string<char>&>, const char*, int, testing::internal::DeathTest**)’:
./src/gtest-death-test.cc:1459:15: error: ‘nullptr’ was not declared in this scope
if (flag != nullptr) {
^
./src/gtest-death-test.cc:1492:42: error: ‘move’ is not a member of ‘std’
*test = new ExecDeathTest(statement, std::move(matcher), file, line);
^
./src/gtest-death-test.cc:1494:44: error: ‘move’ is not a member of ‘std’
*test = new NoExecDeathTest(statement, std::move(matcher));
^
./src/gtest-death-test.cc: In function ‘testing::internal::InternalRunDeathTestFlag* testing::internal::ParseInternalRunDeathTestFlag()’:
./src/gtest-death-test.cc:1579:57: error: ‘nullptr’ was not declared in this scope
if (GTEST_FLAG(internal_run_death_test) == "") return nullptr;
^
In file included from src/gtest-all.cc:43:0:
./src/gtest-filepath.cc: In static member function ‘static testing::internal::FilePath testing::internal::FilePath::GetCurrentDir()’:
./src/gtest-filepath.cc:111:29: error: ‘nullptr’ was not declared in this scope
return FilePath(result == nullptr ? "" : cwd);
^
./src/gtest-filepath.cc: In member function ‘void testing::internal::FilePath::Normalize()’:
./src/gtest-filepath.cc:348:28: error: ‘nullptr’ was not declared in this scope
if (pathname_.c_str() == nullptr) {
^
In file included from ./include/gtest/internal/gtest-death-test-internal.h:39:0,
from ./include/gtest/gtest-death-test.h:41,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h: In member function ‘testing::Matcher<const std::__cxx11::basic_string<char>&>& testing::Matcher<const std::__cxx11::basic_string<char>&>::operator=(const testing::Matcher<const std::__cxx11::basic_string<char>&>&)’:
./include/gtest/gtest-matchers.h:343:18: error: call of overloaded ‘operator=(const testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&>&)’ is ambiguous
class GTEST_API_ Matcher<const std::string&>
^
./include/gtest/gtest-matchers.h:300:16: note: candidate: testing::internal::MatcherBase<T>& testing::internal::MatcherBase<T>::operator=(const testing::internal::MatcherBase<T>&) [with T = const std::__cxx11::basic_string<char>&]
MatcherBase& operator=(const MatcherBase&) = default;
^
./include/gtest/gtest-matchers.h:302:16: note: candidate: testing::internal::MatcherBase<T>& testing::internal::MatcherBase<T>::operator=(testing::internal::MatcherBase<T>) [with T = const std::__cxx11::basic_string<char>&; testing::internal::MatcherBase<T> = testing::internal::MatcherBase<const std::__cxx11::basic_string<char>&>]
MatcherBase& operator=(MatcherBase&&) = default;
^
In file included from src/gtest-all.cc:44:0:
./src/gtest-matchers.cc: In constructor ‘testing::Matcher<const std::__cxx11::basic_string<char>&>::Matcher(const string&)’:
./src/gtest-matchers.cc:45:68: note: synthesized method ‘testing::Matcher<const std::__cxx11::basic_string<char>&>& testing::Matcher<const std::__cxx11::basic_string<char>&>::operator=(const testing::Matcher<const std::__cxx11::basic_string<char>&>&)’ first required here
Matcher<const std::string&>::Matcher(const std::string& s) { *this = Eq(s); }
^
In file included from ./include/gtest/internal/gtest-death-test-internal.h:39:0,
from ./include/gtest/gtest-death-test.h:41,
from ./include/gtest/gtest.h:62,
from src/gtest-all.cc:38:
./include/gtest/gtest-matchers.h: In member function ‘testing::Matcher<std::__cxx11::basic_string<char> >& testing::Matcher<std::__cxx11::basic_string<char> >::operator=(const testing::Matcher<std::__cxx11::basic_string<char> >&)’:
./include/gtest/gtest-matchers.h:366:18: error: call of overloaded ‘operator=(const testing::internal::MatcherBase<std::__cxx11::basic_string<char> >&)’ is ambiguous
class GTEST_API_ Matcher<std::string>
^
./include/gtest/gtest-matchers.h:300:16: note: candidate: testing::internal::MatcherBase<T>& testing::internal::MatcherBase<T>::operator=(const testing::internal::MatcherBase<T>&) [with T = std::__cxx11::basic_string<char>]
MatcherBase& operator=(const MatcherBase&) = default;
^
./include/gtest/gtest-matchers.h:302:16: note: candidate: testing::internal::MatcherBase<T>& testing::internal::MatcherBase<T>::operator=(testing::internal::MatcherBase<T>) [with T = std::__cxx11::basic_string<char>; testing::internal::MatcherBase<T> = testing::internal::MatcherBase<std::__cxx11::basic_string<char> >]
MatcherBase& operator=(MatcherBase&&) = default;
^
In file included from src/gtest-all.cc:44:0:
./src/gtest-matchers.cc: In constructor ‘testing::Matcher<std::__cxx11::basic_string<char> >::Matcher(const string&)’:
./src/gtest-matchers.cc:63:61: note: synthesized method ‘testing::Matcher<std::__cxx11::basic_string<char> >& testing::Matcher<std::__cxx11::basic_string<char> >::operator=(const testing::Matcher<std::__cxx11::basic_string<char> >&)’ first required here
Matcher<std::string>::Matcher(const std::string& s) { *this = Eq(s); }
^
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./src/gtest-port.cc: In member function ‘void testing::internal::RE::Init(const char*)’:
./include/gtest/internal/gtest-internal.h:1378:44: error: no matching function for call to ‘testing::AssertionResult::AssertionResult(bool&)’
::testing::AssertionResult(expression)) \
^
./include/gtest/gtest.h:1990:3: note: in expansion of macro ‘GTEST_TEST_BOOLEAN_’
GTEST_TEST_BOOLEAN_(condition, #condition, false, true, \
^
./src/gtest-port.cc:673:3: note: in expansion of macro ‘EXPECT_TRUE’
EXPECT_TRUE(is_valid_)
^
In file included from src/gtest-all.cc:38:0:
./include/gtest/gtest.h:306:12: note: candidate: template<class T> testing::AssertionResult::AssertionResult(const T&, int)
explicit AssertionResult(
^
./include/gtest/gtest.h:306:12: note: template argument deduction/substitution failed:
In file included from ./include/gtest/gtest.h:60:0,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-internal.h:1378:44: note: candidate expects 2 arguments, 1 provided
::testing::AssertionResult(expression)) \
^
./include/gtest/gtest.h:1990:3: note: in expansion of macro ‘GTEST_TEST_BOOLEAN_’
GTEST_TEST_BOOLEAN_(condition, #condition, false, true, \
^
./src/gtest-port.cc:673:3: note: in expansion of macro ‘EXPECT_TRUE’
EXPECT_TRUE(is_valid_)
^
In file included from src/gtest-all.cc:41:0:
./src/gtest.cc:1010:1: note: candidate: testing::AssertionResult::AssertionResult(const testing::AssertionResult&)
AssertionResult::AssertionResult(const AssertionResult& other)
^
./src/gtest.cc:1010:1: note: no known conversion for argument 1 from ‘bool’ to ‘const testing::AssertionResult&’
In file included from src/gtest-all.cc:45:0:
./src/gtest-port.cc: In function ‘std::__cxx11::string testing::internal::FormatFileLocation(const char*, int)’:
./src/gtest-port.cc:934:39: error: ‘nullptr’ was not declared in this scope
const std::string file_name(file == nullptr ? kUnknownFile : file);
^
./src/gtest-port.cc: In function ‘std::__cxx11::string testing::internal::FormatCompilerIndependentFileLocation(const char*, int)’:
./src/gtest-port.cc:953:39: error: ‘nullptr’ was not declared in this scope
const std::string file_name(file == nullptr ? kUnknownFile : file);
^
./src/gtest-port.cc: In destructor ‘testing::internal::GTestLog::~GTestLog()’:
./src/gtest-port.cc:976:5: error: ‘Abort’ is not a member of ‘testing::internal::posix’
posix::Abort();
^
In file included from ./include/gtest/internal/gtest-internal.h:40:0,
from ./include/gtest/gtest.h:60,
from src/gtest-all.cc:38:
./src/gtest-port.cc: At global scope:
./include/gtest/internal/gtest-port.h:694:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
type(type const &) = delete; \
^
./src/gtest-port.cc:1063:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(CapturedStream);
^
./include/gtest/internal/gtest-port.h:689:34: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11
void operator=(type const &) = delete
^
./include/gtest/internal/gtest-port.h:695:3: note: in expansion of macro ‘GTEST_DISALLOW_ASSIGN_’
GTEST_DISALLOW_ASSIGN_(type)
^
./src/gtest-port.cc:1063:3: note: in expansion of macro ‘GTEST_DISALLOW_COPY_AND_ASSIGN_’
GTEST_DISALLOW_COPY_AND_ASSIGN_(CapturedStream);
^
In file included from src/gtest-all.cc:45:0:
./src/gtest-port.cc: In constructor ‘testing::internal::CapturedStream::CapturedStream(int)’:
./src/gtest-port.cc:1033:12: error: ‘nullptr’ was not declared in this scope
fflush(nullptr);
^
./src/gtest-port.cc: In member function ‘std::__cxx11::string testing::internal::CapturedStream::GetCapturedString()’:
./src/gtest-port.cc:1045:14: error: ‘nullptr’ was not declared in this scope
fflush(nullptr);
^
./src/gtest-port.cc: At global scope:
./src/gtest-port.cc:1068:44: error: ‘nullptr’ was not declared in this scope
static CapturedStream* g_captured_stderr = nullptr;
^
./src/gtest-port.cc:1069:44: error: ‘nullptr’ was not declared in this scope
static CapturedStream* g_captured_stdout = nullptr;
^
./src/gtest-port.cc: In function ‘void testing::internal::CaptureStream(int, const char*, testing::internal::CapturedStream**)’:
./src/gtest-port.cc:1074:18: error: ‘nullptr’ was not declared in this scope
if (*stream != nullptr) {
^
./src/gtest-port.cc: In function ‘std::__cxx11::string testing::internal::GetCapturedStream(testing::internal::CapturedStream**)’:
./src/gtest-port.cc:1086:22: error: ‘nullptr’ was not declared in this scope
*captured_stream = nullptr;
^
./src/gtest-port.cc: At global scope:
./src/gtest-port.cc:1146:5: error: ‘nullptr’ was not declared in this scope
nullptr; // Owned.
^
./src/gtest-port.cc: In function ‘std::vector<std::__cxx11::basic_string<char> > testing::internal::GetInjectableArgvs()’:
./src/gtest-port.cc:1149:32: error: ‘nullptr’ was not declared in this scope
if (g_injected_test_argvs != nullptr) {
^
./src/gtest-port.cc: In function ‘void testing::internal::ClearInjectableArgvs()’:
./src/gtest-port.cc:1174:27: error: ‘nullptr’ was not declared in this scope
g_injected_test_argvs = nullptr;
^
./src/gtest-port.cc: In function ‘bool testing::internal::ParseInt32(const testing::Message&, const char*, testing::internal::Int32*)’:
./src/gtest-port.cc:1207:15: error: ‘nullptr’ was not declared in this scope
char* end = nullptr;
^
./src/gtest-port.cc: In function ‘bool testing::internal::BoolFromGTestEnv(const char*, bool)’:
./src/gtest-port.cc:1253:26: error: ‘nullptr’ was not declared in this scope
return string_value == nullptr ? default_value
^
./src/gtest-port.cc: In function ‘testing::internal::Int32 testing::internal::Int32FromGTestEnv(const char*, testing::internal::Int32)’:
./src/gtest-port.cc:1267:23: error: ‘nullptr’ was not declared in this scope
if (string_value == nullptr) {
^
./src/gtest-port.cc: In function ‘std::__cxx11::string testing::internal::OutputFlagAlsoCheckEnvVar()’:
./src/gtest-port.cc:1296:7: error: ‘nullptr’ was not declared in this scope
if (nullptr != xml_output_file_env) {
^
./src/gtest-port.cc: In function ‘const char* testing::internal::StringFromGTestEnv(const char*, const char*)’:
./src/gtest-port.cc:1310:19: error: ‘nullptr’ was not declared in this scope
return value == nullptr ? default_value : value;
^
In file included from src/gtest-all.cc:46:0:
./src/gtest-printers.cc: In function ‘void testing::internal::PrintTo(const char*, std::ostream*)’:
./src/gtest-printers.cc:329:12: error: ‘nullptr’ was not declared in this scope
if (s == nullptr) {
^
./src/gtest-printers.cc: In function ‘void testing::internal::PrintTo(const wchar_t*, std::ostream*)’:
./src/gtest-printers.cc:346:12: error: ‘nullptr’ was not declared in this scope
if (s == nullptr) {
^
In file included from src/gtest-all.cc:47:0:
./src/gtest-test-part.cc: In static member function ‘static std::__cxx11::string testing::TestPartResult::ExtractSummary(const char*)’:
./src/gtest-test-part.cc:44:25: error: ‘nullptr’ was not declared in this scope
return stack_trace == nullptr ? message : std::string(message, stack_trace);
^
./src/gtest-test-part.cc: In member function ‘const testing::TestPartResult& testing::TestPartResultArray::GetTestPartResult(int) const’:
./src/gtest-test-part.cc:70:5: error: ‘Abort’ is not a member of ‘testing::internal::posix’
internal::posix::Abort();
^
In file included from src/gtest-all.cc:48:0:
./src/gtest-typed-test.cc: In function ‘std::vector<std::__cxx11::basic_string<char> > testing::internal::SplitIntoTestNames(const char*)’:
./src/gtest-typed-test.cc:51:17: error: ‘nullptr’ was not declared in this scope
for (; src != nullptr; src = SkipComma(src)) {
^
./src/gtest-typed-test.cc: In member function ‘const char* testing::internal::TypedTestSuitePState::VerifyRegisteredTestNames(const char*, int, const char*)’:
./src/gtest-typed-test.cc:109:5: error: ‘Abort’ is not a member of ‘testing::internal::posix’
posix::Abort();
^
In file included from ./include/gtest/gtest-param-test.h:184:0,
from ./include/gtest/gtest.h:65,
from src/gtest-all.cc:38:
./include/gtest/internal/gtest-param-util.h: In instantiation of ‘testing::internal::ValueArray<Ts>::operator testing::internal::ParamGenerator<T>() const [with T = bool; Ts = {bool, bool}]’:
./include/gtest/gtest-param-test.h:365:28: required from here
./include/gtest/internal/gtest-param-util.h:747:34: error: no matching function for call to ‘testing::internal::ValueArray<bool, bool>::MakeVector(testing::internal::MakeIndexSequence<2ul>) const’
return ValuesIn(MakeVector<T>(MakeIndexSequence<sizeof...(Ts)>()));
^
./include/gtest/internal/gtest-param-util.h:752:18: note: candidate: template<class T, long unsigned int ...I> std::vector<T> testing::internal::ValueArray<Ts>::MakeVector(testing::internal::IndexSequence<I ...>) const [with T = T; long unsigned int ...I = {I ...}; Ts = {bool, bool}]
std::vector<T> MakeVector(IndexSequence<I...>) const {
^
./include/gtest/internal/gtest-param-util.h:752:18: note: template argument deduction/substitution failed:
./include/gtest/internal/gtest-param-util.h:747:34: note: ‘testing::internal::MakeIndexSequence<2ul>’ is not derived from ‘testing::internal::IndexSequence<I ...>’
return ValuesIn(MakeVector<T>(MakeIndexSequence<sizeof...(Ts)>()));
^
Makefile:1209: recipe for target 'src/gtest-all.lo' failed
make[3]: *** [src/gtest-all.lo] Error 1
make[3]: Leaving directory '/home/spo12/protobuf-3.11.4/third_party/googletest/googletest'
Makefile:2170: recipe for target 'check-local' failed
make[2]: *** [check-local] Error 2
make[2]: Leaving directory '/home/spo12/protobuf-3.11.4'
Makefile:2032: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/spo12/protobuf-3.11.4'
Makefile:1741: recipe for target 'check-recursive' failed
make: *** [check-recursive] Error 1
spo12@CPI-SL64001:~/protobuf-3.11.4$ sudo make install
[sudo] password for spo12:
Making install in .
make[1]: Entering directory '/home/spo12/protobuf-3.11.4'
make[2]: Entering directory '/home/spo12/protobuf-3.11.4'
make[2]: Nothing to be done for 'install-exec-am'.
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/lib/pkgconfig'
/usr/bin/miniconda3/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/usr/local/lib/pkgconfig'
make[2]: Leaving directory '/home/spo12/protobuf-3.11.4'
make[1]: Leaving directory '/home/spo12/protobuf-3.11.4'
Making install in src
make[1]: Entering directory '/home/spo12/protobuf-3.11.4/src'
make[2]: Entering directory '/home/spo12/protobuf-3.11.4/src'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/lib'
/bin/bash ../libtool --mode=install /usr/bin/miniconda3/bin/install -c libprotobuf-lite.la libprotobuf.la libprotoc.la '/usr/local/lib'
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotobuf-lite.so.22.0.4 /usr/local/lib/libprotobuf-lite.so.22.0.4
libtool: install: (cd /usr/local/lib && { ln -s -f libprotobuf-lite.so.22.0.4 libprotobuf-lite.so.22 || { rm -f libprotobuf-lite.so.22 && ln -s libprotobuf-lite.so.22.0.4 libprotobuf-lite.so.22; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libprotobuf-lite.so.22.0.4 libprotobuf-lite.so || { rm -f libprotobuf-lite.so && ln -s libprotobuf-lite.so.22.0.4 libprotobuf-lite.so; }; })
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotobuf-lite.lai /usr/local/lib/libprotobuf-lite.la
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotobuf.so.22.0.4 /usr/local/lib/libprotobuf.so.22.0.4
libtool: install: (cd /usr/local/lib && { ln -s -f libprotobuf.so.22.0.4 libprotobuf.so.22 || { rm -f libprotobuf.so.22 && ln -s libprotobuf.so.22.0.4 libprotobuf.so.22; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libprotobuf.so.22.0.4 libprotobuf.so || { rm -f libprotobuf.so && ln -s libprotobuf.so.22.0.4 libprotobuf.so; }; })
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotobuf.lai /usr/local/lib/libprotobuf.la
libtool: warning: relinking 'libprotoc.la'
libtool: install: (cd /home/spo12/protobuf-3.11.4/src; /bin/bash "/home/spo12/protobuf-3.11.4/libtool" --silent --tag CXX --mode=relink /usr/bin/g++ -std=c++11 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -version-info 22:4:0 -export-dynamic -no-undefined -Wl,--version-script=./libprotoc.map -o libprotoc.la -rpath /usr/local/lib google/protobuf/compiler/code_generator.lo google/protobuf/compiler/command_line_interface.lo google/protobuf/compiler/plugin.lo google/protobuf/compiler/plugin.pb.lo google/protobuf/compiler/subprocess.lo google/protobuf/compiler/zip_writer.lo google/protobuf/compiler/cpp/cpp_enum.lo google/protobuf/compiler/cpp/cpp_enum_field.lo google/protobuf/compiler/cpp/cpp_extension.lo google/protobuf/compiler/cpp/cpp_field.lo google/protobuf/compiler/cpp/cpp_file.lo google/protobuf/compiler/cpp/cpp_generator.lo google/protobuf/compiler/cpp/cpp_helpers.lo google/protobuf/compiler/cpp/cpp_map_field.lo google/protobuf/compiler/cpp/cpp_message.lo google/protobuf/compiler/cpp/cpp_message_field.lo google/protobuf/compiler/cpp/cpp_padding_optimizer.lo google/protobuf/compiler/cpp/cpp_primitive_field.lo google/protobuf/compiler/cpp/cpp_service.lo google/protobuf/compiler/cpp/cpp_string_field.lo google/protobuf/compiler/java/java_context.lo google/protobuf/compiler/java/java_enum.lo google/protobuf/compiler/java/java_enum_lite.lo google/protobuf/compiler/java/java_enum_field.lo google/protobuf/compiler/java/java_enum_field_lite.lo google/protobuf/compiler/java/java_extension.lo google/protobuf/compiler/java/java_extension_lite.lo google/protobuf/compiler/java/java_field.lo google/protobuf/compiler/java/java_file.lo google/protobuf/compiler/java/java_generator.lo google/protobuf/compiler/java/java_generator_factory.lo google/protobuf/compiler/java/java_helpers.lo google/protobuf/compiler/java/java_map_field.lo google/protobuf/compiler/java/java_map_field_lite.lo google/protobuf/compiler/java/java_message.lo google/protobuf/compiler/java/java_message_lite.lo google/protobuf/compiler/java/java_message_builder.lo google/protobuf/compiler/java/java_message_builder_lite.lo google/protobuf/compiler/java/java_message_field.lo google/protobuf/compiler/java/java_message_field_lite.lo google/protobuf/compiler/java/java_name_resolver.lo google/protobuf/compiler/java/java_primitive_field.lo google/protobuf/compiler/java/java_primitive_field_lite.lo google/protobuf/compiler/java/java_shared_code_generator.lo google/protobuf/compiler/java/java_service.lo google/protobuf/compiler/java/java_string_field.lo google/protobuf/compiler/java/java_string_field_lite.lo google/protobuf/compiler/java/java_doc_comment.lo google/protobuf/compiler/js/js_generator.lo google/protobuf/compiler/js/well_known_types_embed.lo google/protobuf/compiler/objectivec/objectivec_enum.lo google/protobuf/compiler/objectivec/objectivec_enum_field.lo google/protobuf/compiler/objectivec/objectivec_extension.lo google/protobuf/compiler/objectivec/objectivec_field.lo google/protobuf/compiler/objectivec/objectivec_file.lo google/protobuf/compiler/objectivec/objectivec_generator.lo google/protobuf/compiler/objectivec/objectivec_helpers.lo google/protobuf/compiler/objectivec/objectivec_map_field.lo google/protobuf/compiler/objectivec/objectivec_message.lo google/protobuf/compiler/objectivec/objectivec_message_field.lo google/protobuf/compiler/objectivec/objectivec_oneof.lo google/protobuf/compiler/objectivec/objectivec_primitive_field.lo google/protobuf/compiler/php/php_generator.lo google/protobuf/compiler/python/python_generator.lo google/protobuf/compiler/ruby/ruby_generator.lo google/protobuf/compiler/csharp/csharp_doc_comment.lo google/protobuf/compiler/csharp/csharp_enum.lo google/protobuf/compiler/csharp/csharp_enum_field.lo google/protobuf/compiler/csharp/csharp_field_base.lo google/protobuf/compiler/csharp/csharp_generator.lo google/protobuf/compiler/csharp/csharp_helpers.lo google/protobuf/compiler/csharp/csharp_map_field.lo google/protobuf/compiler/csharp/csharp_message.lo google/protobuf/compiler/csharp/csharp_message_field.lo google/protobuf/compiler/csharp/csharp_primitive_field.lo google/protobuf/compiler/csharp/csharp_reflection_class.lo google/protobuf/compiler/csharp/csharp_repeated_enum_field.lo google/protobuf/compiler/csharp/csharp_repeated_message_field.lo google/protobuf/compiler/csharp/csharp_repeated_primitive_field.lo google/protobuf/compiler/csharp/csharp_source_generator_base.lo google/protobuf/compiler/csharp/csharp_wrapper_field.lo libprotobuf.la -lz )
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotoc.so.22.0.4T /usr/local/lib/libprotoc.so.22.0.4
libtool: install: (cd /usr/local/lib && { ln -s -f libprotoc.so.22.0.4 libprotoc.so.22 || { rm -f libprotoc.so.22 && ln -s libprotoc.so.22.0.4 libprotoc.so.22; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libprotoc.so.22.0.4 libprotoc.so || { rm -f libprotoc.so && ln -s libprotoc.so.22.0.4 libprotoc.so; }; })
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotoc.lai /usr/local/lib/libprotoc.la
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotobuf-lite.a /usr/local/lib/libprotobuf-lite.a
libtool: install: chmod 644 /usr/local/lib/libprotobuf-lite.a
libtool: install: ranlib /usr/local/lib/libprotobuf-lite.a
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotobuf.a /usr/local/lib/libprotobuf.a
libtool: install: chmod 644 /usr/local/lib/libprotobuf.a
libtool: install: ranlib /usr/local/lib/libprotobuf.a
libtool: install: /usr/bin/miniconda3/bin/install -c .libs/libprotoc.a /usr/local/lib/libprotoc.a
libtool: install: chmod 644 /usr/local/lib/libprotoc.a
libtool: install: ranlib /usr/local/lib/libprotoc.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the 'LD_RUN_PATH' environment variable
during linking
- use the '-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to '/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/bin'
/bin/bash ../libtool --mode=install /usr/bin/miniconda3/bin/install -c protoc '/usr/local/bin'
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/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/descriptor.proto google/protobuf/any.proto google/protobuf/api.proto google/protobuf/duration.proto google/protobuf/empty.proto google/protobuf/field_mask.proto google/protobuf/source_context.proto google/protobuf/struct.proto google/protobuf/timestamp.proto google/protobuf/type.proto google/protobuf/wrappers.proto '/usr/local/include/google/protobuf'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/plugin.proto '/usr/local/include/google/protobuf/compiler'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/any.pb.h google/protobuf/api.pb.h google/protobuf/any.h google/protobuf/arena.h google/protobuf/arena_impl.h google/protobuf/arenastring.h google/protobuf/descriptor_database.h google/protobuf/descriptor.h google/protobuf/descriptor.pb.h google/protobuf/duration.pb.h google/protobuf/dynamic_message.h google/protobuf/empty.pb.h google/protobuf/extension_set.h google/protobuf/extension_set_inl.h google/protobuf/field_mask.pb.h google/protobuf/generated_enum_reflection.h google/protobuf/generated_enum_util.h google/protobuf/generated_message_reflection.h google/protobuf/generated_message_table_driven.h google/protobuf/generated_message_util.h google/protobuf/has_bits.h google/protobuf/implicit_weak_message.h google/protobuf/inlined_string_field.h google/protobuf/map_entry.h google/protobuf/map_entry_lite.h google/protobuf/map_field.h google/protobuf/map_field_inl.h google/protobuf/map_field_lite.h google/protobuf/map.h google/protobuf/map_type_handler.h google/protobuf/message.h google/protobuf/message_lite.h google/protobuf/metadata.h google/protobuf/metadata_lite.h google/protobuf/parse_context.h google/protobuf/port.h google/protobuf/port_def.inc google/protobuf/port_undef.inc google/protobuf/reflection.h google/protobuf/reflection_ops.h '/usr/local/include/google/protobuf'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/java'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/java/java_generator.h google/protobuf/compiler/java/java_names.h '/usr/local/include/google/protobuf/compiler/java'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/cpp'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/cpp/cpp_generator.h '/usr/local/include/google/protobuf/compiler/cpp'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/python'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/python/python_generator.h '/usr/local/include/google/protobuf/compiler/python'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/js'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/js/js_generator.h google/protobuf/compiler/js/well_known_types_embed.h '/usr/local/include/google/protobuf/compiler/js'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/repeated_field.h google/protobuf/service.h google/protobuf/source_context.pb.h google/protobuf/struct.pb.h google/protobuf/text_format.h google/protobuf/timestamp.pb.h google/protobuf/type.pb.h google/protobuf/unknown_field_set.h google/protobuf/wire_format.h google/protobuf/wire_format_lite.h google/protobuf/wrappers.pb.h '/usr/local/include/google/protobuf'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/stubs'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/stubs/callback.h google/protobuf/stubs/bytestream.h google/protobuf/stubs/casts.h google/protobuf/stubs/common.h google/protobuf/stubs/fastmem.h google/protobuf/stubs/hash.h google/protobuf/stubs/logging.h google/protobuf/stubs/macros.h google/protobuf/stubs/map_util.h google/protobuf/stubs/mutex.h google/protobuf/stubs/once.h google/protobuf/stubs/platform_macros.h google/protobuf/stubs/port.h google/protobuf/stubs/status.h google/protobuf/stubs/stl_util.h google/protobuf/stubs/stringpiece.h google/protobuf/stubs/strutil.h google/protobuf/stubs/template_util.h '/usr/local/include/google/protobuf/stubs'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/util'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/util/type_resolver.h google/protobuf/util/delimited_message_util.h google/protobuf/util/field_comparator.h google/protobuf/util/field_mask_util.h google/protobuf/util/json_util.h google/protobuf/util/time_util.h google/protobuf/util/type_resolver_util.h google/protobuf/util/message_differencer.h '/usr/local/include/google/protobuf/util'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/php'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/php/php_generator.h '/usr/local/include/google/protobuf/compiler/php'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/code_generator.h google/protobuf/compiler/command_line_interface.h google/protobuf/compiler/importer.h google/protobuf/compiler/parser.h google/protobuf/compiler/plugin.h google/protobuf/compiler/plugin.pb.h '/usr/local/include/google/protobuf/compiler'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/ruby'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/ruby/ruby_generator.h '/usr/local/include/google/protobuf/compiler/ruby'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/io'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/io/io_win32.h google/protobuf/io/coded_stream.h google/protobuf/io/gzip_stream.h google/protobuf/io/printer.h google/protobuf/io/strtod.h google/protobuf/io/tokenizer.h google/protobuf/io/zero_copy_stream.h google/protobuf/io/zero_copy_stream_impl.h google/protobuf/io/zero_copy_stream_impl_lite.h '/usr/local/include/google/protobuf/io'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/csharp'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/csharp/csharp_generator.h google/protobuf/compiler/csharp/csharp_names.h '/usr/local/include/google/protobuf/compiler/csharp'
/usr/bin/miniconda3/bin/mkdir -p '/usr/local/include/google/protobuf/compiler/objectivec'
/usr/bin/miniconda3/bin/install -c -m 644 google/protobuf/compiler/objectivec/objectivec_generator.h google/protobuf/compiler/objectivec/objectivec_helpers.h '/usr/local/include/google/protobuf/compiler/objectivec'
make[2]: Leaving directory '/home/spo12/protobuf-3.11.4/src'
make[1]: Leaving directory '/home/spo12/protobuf-3.11.4/src'
Unfortunately, make check resulted in a lot of errors, but it seems that sudo make install still worked.
protoc --version
libprotoc 3.11.4
Great! Now let’s see what happens.
cd /data3/genome_graphs/vg-rotella/
. ./source_me.sh && make
-> click here for the make output <-
rm -f /data3/genome_graphs/vg-rotella/include/vg.pb.h /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h
rm -Rf /data3/genome_graphs/vg-rotella/include/vg/io/
. ./source_me.sh && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/data3/genome_graphs/vg-rotella/lib/pkgconfig: cmake -DCMAKE_PREFIX_PATH=/data3/genome_graphs/vg-rotella -DCMAKE_LIBRARY_PATH=/data3/genome_graphs/vg-rotella/lib -DCMAKE_INSTALL_PREFIX=/data3/genome_graphs/vg-rotella -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install
-- The CXX compiler identification is GNU 5.4.0
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Found Protobuf: /usr/local/lib/libprotobuf.so;-lpthread (found version "3.11.4")
-- Checking for module 'protobuf'
-- Found protobuf, version 3.11.4
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
-- Checking for module 'htslib'
-- Found htslib, version 1.10.2
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/libvgio
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
/usr/bin/cmake -S/data3/genome_graphs/vg-rotella/deps/libvgio -B/data3/genome_graphs/vg-rotella/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
cd /data3/genome_graphs/vg-rotella/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color=
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/depend.internal".
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/link_target.dir/depend.internal".
Scanning dependencies of target link_target
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
/usr/bin/cmake -E create_symlink . vg
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[ 0%] Built target link_target
make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[ 3%] Running cpp protocol buffer compiler on deps/vg.proto
/usr/bin/miniconda3/bin/protoc --cpp_out /data3/genome_graphs/vg-rotella/deps/libvgio -I /data3/genome_graphs/vg-rotella/deps/libvgio/deps /data3/genome_graphs/vg-rotella/deps/libvgio/deps/vg.proto
cd /data3/genome_graphs/vg-rotella/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color=
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal".
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal".
Scanning dependencies of target vgio_static
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[ 7%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc
[ 11%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/stream.hpp:17:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp:8:
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Graph]’:
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp:69:31: required from here
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg/vg.pb.h:23:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/basic_stream.hpp:5,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp:7:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
[ 15%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/blocked_gzip_input_stream.cpp
[ 19%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/blocked_gzip_output_stream.cpp
[ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/hfile_cppstream.cpp
[ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_emitter.cpp
[ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp
/data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’:
/data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/message_iterator.hpp:17:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:6:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/message_iterator.hpp:17:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:6:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
[ 34%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/registry.cpp
[ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/stream.cpp
[ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/stream_multiplexer.cpp
[ 46%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o
/usr/bin/g++ -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/vpkg.cpp
[ 50%] Linking CXX static library libvgio.a
/usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1
/usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o
/usr/bin/ranlib libvgio.a
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[ 50%] Built target vgio_static
make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
cd /data3/genome_graphs/vg-rotella/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color=
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio.dir/depend.internal".
Dependee "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles/vgio.dir/depend.internal".
Scanning dependencies of target vgio
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[ 53%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/vg.pb.cc
[ 57%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/stream.hpp:17:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp:8:
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Graph]’:
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp:69:31: required from here
/data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/vg/vg.pb.h:23:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/basic_stream.hpp:5,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/basic_stream.cpp:7:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
[ 61%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/blocked_gzip_input_stream.cpp
[ 65%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/blocked_gzip_output_stream.cpp
[ 69%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/hfile_cppstream.cpp
[ 73%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_emitter.cpp
[ 76%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp
/data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’:
/data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/message_iterator.hpp:17:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:6:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
/data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2);
^
In file included from /data3/genome_graphs/vg-rotella/deps/libvgio/include/vg/io/message_iterator.hpp:17:0,
from /data3/genome_graphs/vg-rotella/deps/libvgio/src/message_iterator.cpp:6:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
[ 80%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/registry.cpp
[ 84%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/stream.cpp
[ 88%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/stream_multiplexer.cpp
[ 92%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o
/usr/bin/g++ -Dvgio_EXPORTS -I/data3/genome_graphs/vg-rotella/deps/libvgio/include -I/data3/genome_graphs/vg-rotella/deps/libvgio -I/data3/genome_graphs/vg-rotella/include/. -I/usr/local/include/. -I/data3/genome_graphs/vg-rotella/deps/libvgio/src -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /data3/genome_graphs/vg-rotella/deps/libvgio/src/vpkg.cpp
[ 96%] Linking CXX shared library libvgio.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1
/usr/bin/g++ -fPIC -O3 -g -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib: -lprotobuf -lhts -lpthread
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
[100%] Built target vgio
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
/usr/bin/cmake -E cmake_progress_start /data3/genome_graphs/vg-rotella/deps/libvgio/CMakeFiles 0
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make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
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[ 50%] Built target vgio_static
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Install the project...
-- Install configuration: ""
-- Installing: /data3/genome_graphs/vg-rotella/lib/libvgio.so
-- Set runtime path of "/data3/genome_graphs/vg-rotella/lib/libvgio.so" to ""
-- Installing: /data3/genome_graphs/vg-rotella/lib/libvgio.a
-- Up-to-date: /data3/genome_graphs/vg-rotella/include
-- Installing: /data3/genome_graphs/vg-rotella/include/vg
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/message_iterator.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/hfile_cppstream.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/protobuf_emitter.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/loader.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/basic_stream.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/blocked_gzip_output_stream.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/vpkg.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/blocked_gzip_input_stream.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/hfile_internal.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/message_emitter.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/registry.hpp
-- Installing: /data3/genome_graphs/vg-rotella/include/vg/io/fdstream.hpp
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-- Installing: /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h
-- Installing: /data3/genome_graphs/vg-rotella/lib/cmake/VGio/VGioTargets.cmake
-- Installing: /data3/genome_graphs/vg-rotella/lib/cmake/VGio/VGioTargets-noconfig.cmake
-- Installing: /data3/genome_graphs/vg-rotella/lib/cmake/VGio/VGioConfig.cmake
-- Installing: /data3/genome_graphs/vg-rotella/lib/cmake/VGio/VGioConfigVersion.cmake
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libvgio'
cp deps/BBHash/BooPHF.h /data3/genome_graphs/vg-rotella/include
cp -r deps/sparsepp/sparsepp include/
rm -Rf include/dynamic.hpp include/dynamic
# annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers
cd /data3/genome_graphs/vg-rotella/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && cmake .. && make && cp -r hopscotch_map-prefix/src/hopscotch_map/include/* /data3/genome_graphs/vg-rotella/include/
-- Setting build type to 'Debug' as none was specified.
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Building in Debug mode
-- Configuring done
-- Generating done
-- Build files have been written to: /data3/genome_graphs/vg-rotella/deps/DYNAMIC/build
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target hopscotch_map
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 4%] Creating directories for 'hopscotch_map'
[ 9%] Performing download step (git clone) for 'hopscotch_map'
Cloning into 'hopscotch_map'...
fatal: unable to access 'https://github.com/Tessil/hopscotch-map.git/': SSL certificate problem: self signed certificate in certificate chain
Cloning into 'hopscotch_map'...
-- Had to git clone more than once:
2 times.
Already on 'master'
Your branch is up to date with 'origin/master'.
[ 13%] No patch step for 'hopscotch_map'
[ 18%] No update step for 'hopscotch_map'
[ 22%] No configure step for 'hopscotch_map'
[ 27%] No build step for 'hopscotch_map'
[ 31%] No install step for 'hopscotch_map'
[ 36%] Completed 'hopscotch_map'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 36%] Built target hopscotch_map
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target h0_lz77
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 40%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o
[ 45%] Linking CXX executable h0_lz77
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 45%] Built target h0_lz77
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target cw-bwt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 50%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o
[ 54%] Linking CXX executable cw-bwt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 54%] Built target cw-bwt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target debug
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 59%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o
[ 63%] Linking CXX executable debug
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 63%] Built target debug
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target rle_bwt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 68%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o
[ 72%] Linking CXX executable rle_bwt
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 72%] Built target rle_bwt
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target rle_lz77_v1
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 77%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o
[ 81%] Linking CXX executable rle_lz77_v1
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 81%] Built target rle_lz77_v1
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target benchmark
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 86%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o
[ 90%] Linking CXX executable benchmark
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 90%] Built target benchmark
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
Scanning dependencies of target rle_lz77_v2
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[ 95%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o
[100%] Linking CXX executable rle_lz77_v2
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
[100%] Built target rle_lz77_v2
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/DYNAMIC/build'
# Do the copy of the main file last so we can tell if this recipe failed and redo it.
# Otherwise we get dynamic.hpp without its deps
mkdir -p include/dynamic && cp -r /data3/genome_graphs/vg-rotella/deps/DYNAMIC/include/* include/dynamic
. ./source_me.sh && rm -Rf /data3/genome_graphs/vg-rotella/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/data3/genome_graphs/vg-rotella/include:/data3/genome_graphs/vg-rotella/include/dynamic: CXXFLAGS="-I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2" make && cp lib/libbdsg.a /data3/genome_graphs/vg-rotella/lib && pwd && cp -r include/bdsg /data3/genome_graphs/vg-rotella/include
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libbdsg'
rm -r obj
rm -r lib
rm -r bin
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libbdsg'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/libbdsg'
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/eades_algorithm.cpp -o obj/eades_algorithm.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/hash_graph.cpp -o obj/hash_graph.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/is_single_stranded.cpp -o obj/is_single_stranded.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/node.cpp -o obj/node.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/odgi.cpp -o obj/odgi.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/packed_graph.cpp -o obj/packed_graph.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/packed_structs.cpp -o obj/packed_structs.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/path_position_overlays.cpp -o obj/path_position_overlays.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/packed_path_position_overlays.cpp -o obj/packed_path_position_overlays.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/vectorizable_overlays.cpp -o obj/vectorizable_overlays.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/split_strand_graph.cpp -o obj/split_strand_graph.o
/usr/bin/g++ -O3 -Werror=return-type -std=c++14 -ggdb -g -msse4.2 -Iinclude -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -fopenmp -c src/utility.cpp -o obj/utility.o
rm -f lib/libbdsg.a
ar rs lib/libbdsg.a obj/eades_algorithm.o obj/hash_graph.o obj/is_single_stranded.o obj/node.o obj/odgi.o obj/packed_graph.o obj/packed_structs.o obj/path_position_overlays.o obj/packed_path_position_overlays.o obj/vectorizable_overlays.o obj/split_strand_graph.o obj/utility.o
ar: creating lib/libbdsg.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/libbdsg'
/data3/genome_graphs/vg-rotella/deps/libbdsg
. ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /data3/genome_graphs/vg-rotella/include/
. ./source_me.sh && cp -r deps/ips4o/ips4o* /data3/genome_graphs/vg-rotella/include/
cp ./deps/gfakluge/src/*.hpp /data3/genome_graphs/vg-rotella/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /data3/genome_graphs/vg-rotella/include/
rm -f lib/libxg.a
cp -r deps/xg/src/*.hpp /data3/genome_graphs/vg-rotella/include
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp
ar rs lib/libxg.a deps/xg/xg.o
ar: creating lib/libxg.a
cd /data3/genome_graphs/vg-rotella/include/ && rm -Rf elfutils gelf.h libelf.h dwarf.h libdwflP.h libdwfl.h libebl.h libelf.h
. ./source_me.sh && cd deps/elfutils && autoreconf -i -f && ./configure --enable-maintainer-mode --prefix=/data3/genome_graphs/vg-rotella
configure.ac:93: installing 'config/ar-lib'
configure.ac:88: installing 'config/compile'
configure.ac:64: installing 'config/config.guess'
configure.ac:64: installing 'config/config.sub'
configure.ac:48: installing 'config/install-sh'
configure.ac:48: installing 'config/missing'
Makefile.am: installing './INSTALL'
backends/Makefile.am: installing 'config/depcomp'
configure.ac: installing 'config/ylwrap'
parallel-tests: installing 'config/test-driver'
configure: No --program-prefix given, using "eu-"
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking whether make supports nested variables... (cached) yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking whether /usr/bin/gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of /usr/bin/gcc... gcc3
checking for ranlib... ranlib
checking for bison... bison -y
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for readelf... readelf
checking for nm... nm
checking for gcc with GNU99 support... yes
checking whether gcc supports __attribute__((visibility()))... yes
checking whether gcc supports __attribute__((gcc_struct))... yes
checking whether gcc supports -fPIC... yes
checking whether gcc supports -fPIE... yes
checking whether gcc supports -Wl,-z,defs... yes
checking whether gcc supports -Wl,-z,relro... yes
checking for __thread support... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking whether fts.h is bad when included (with LFS)... no
checking whether to add -D_FORTIFY_SOURCE=2 to CFLAGS... yes
checking for library containing gzdirect... -lz
checking for library containing BZ2_bzdopen... -lbz2
checking for library containing lzma_auto_decoder... -llzma
checking whether memrchr is declared... yes
checking whether rawmemchr is declared... yes
checking whether powerof2 is declared... yes
checking whether mempcpy is declared... yes
checking for process_vm_readv... yes
checking for __cxa_demangle in -lstdc++... yes
checking whether symbol versioning is supported... yes
checking whether gcc accepts -Wstack-usage... yes
checking whether gcc has a sane -Wlogical-op... yes
checking whether gcc accepts -Wduplicated-cond... no
checking whether gcc accepts -Wnull-dereference... no
checking whether gcc accepts -Wimplicit-fallthrough... no
checking whether NLS is requested... yes
checking for msgfmt... /usr/bin/miniconda3/bin/msgfmt
checking for gmsgfmt... /usr/bin/miniconda3/bin/msgfmt
checking for xgettext... /usr/bin/miniconda3/bin/xgettext
checking for msgmerge... /usr/bin/miniconda3/bin/msgmerge
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of long... 8
checking for struct user_regs_struct... yes
checking /usr/bin/gcc option for 32-bit word size... -m32
checking for 64-bit host... yes
checking whether /usr/bin/gcc -m32 makes executables we can run... no
configure: WARNING: not running biarch tests, /usr/bin/gcc -m32 does not work
checking for flex... yes
checking for bison... yes
checking for gawk... yes
checking for bunzip2... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating config/Makefile
config.status: creating Makefile
config.status: creating m4/Makefile
config.status: creating elfutils.spec
config.status: creating lib/Makefile
config.status: creating libelf/Makefile
config.status: creating libebl/Makefile
config.status: creating libdwelf/Makefile
config.status: creating libdw/Makefile
config.status: creating libdwfl/Makefile
config.status: creating libcpu/Makefile
config.status: creating libasm/Makefile
config.status: creating backends/Makefile
config.status: creating src/Makefile
config.status: creating po/Makefile.in
config.status: creating tests/Makefile
config.status: creating config/libelf.pc
config.status: creating config/libdw.pc
config.status: creating version.h
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing po-directories commands
config.status: creating po/POTFILES
config.status: creating po/Makefile
configure:
=====================================================================
elfutils: 0.176 (eu_version: 176)
=====================================================================
Prefix : /data3/genome_graphs/vg-rotella
Program prefix ("eu-" recommended) : eu-
Source code location : .
Maintainer mode : yes
libebl modules subdirectory : elfutils
build arch : x86_64-pc-linux-gnu
RECOMMENDED FEATURES (should all be yes)
gzip support : yes
bzip2 support : yes
lzma/xz support : yes
libstdc++ demangle support : yes
File textrel check : yes
Symbol versioning : yes
NOT RECOMMENDED FEATURES (should all be no)
Experimental thread safety : no
install elf.h : no
OTHER FEATURES
Deterministic archives by default : false
Native language support : yes
EXTRA TEST FEATURES (used with make check)
have bunzip2 installed (required) : yes
debug branch prediction : no
gprof support : no
gcov support : no
run all tests under valgrind : no
gcc undefined behaviour sanitizer : no
use rpath in tests : no
test biarch : no
. ./source_me.sh && cd deps/elfutils/libelf && make clean && make libelf.a
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libelf'
test -z "*.gcno *.gcda elf_version.os elf_hash.os elf_error.os elf_fill.os elf_begin.os elf_next.os elf_rand.os elf_end.os elf_kind.os gelf_getclass.os elf_getbase.os elf_getident.os elf32_fsize.os elf64_fsize.os gelf_fsize.os elf32_xlatetof.os elf32_xlatetom.os elf64_xlatetof.os elf64_xlatetom.os gelf_xlate.os elf32_getehdr.os elf64_getehdr.os gelf_getehdr.os elf32_newehdr.os elf64_newehdr.os gelf_newehdr.os gelf_update_ehdr.os elf32_getphdr.os elf64_getphdr.os gelf_getphdr.os elf32_newphdr.os elf64_newphdr.os gelf_newphdr.os gelf_update_phdr.os elf_getarhdr.os elf_getarsym.os elf_rawfile.os elf_readall.os elf_cntl.os elf_getscn.os elf_nextscn.os elf_ndxscn.os elf_newscn.os elf32_getshdr.os elf64_getshdr.os gelf_getshdr.os gelf_update_shdr.os elf_strptr.os elf_rawdata.os elf_getdata.os elf_newdata.os elf_getdata_rawchunk.os elf_flagelf.os elf_flagehdr.os elf_flagphdr.os elf_flagscn.os elf_flagshdr.os elf_flagdata.os elf_memory.os elf_update.os elf32_updatenull.os elf64_updatenull.os elf32_updatefile.os elf64_updatefile.os gelf_getsym.os gelf_update_sym.os gelf_getversym.os gelf_getverneed.os gelf_getvernaux.os gelf_getverdef.os gelf_getverdaux.os gelf_getrel.os gelf_getrela.os gelf_update_rel.os gelf_update_rela.os gelf_getdyn.os gelf_update_dyn.os gelf_getmove.os gelf_update_move.os gelf_getsyminfo.os gelf_update_syminfo.os gelf_getauxv.os gelf_update_auxv.os gelf_getnote.os gelf_xlatetof.os gelf_xlatetom.os nlist.os gelf_getsymshndx.os gelf_update_symshndx.os gelf_update_versym.os gelf_update_verneed.os gelf_update_vernaux.os gelf_update_verdef.os gelf_update_verdaux.os elf_getphdrnum.os elf_getshdrnum.os elf_getshdrstrndx.os gelf_checksum.os elf32_checksum.os elf64_checksum.os libelf_crc32.os libelf_next_prime.os elf_clone.os gelf_getlib.os gelf_update_lib.os elf32_offscn.os elf64_offscn.os gelf_offscn.os elf_getaroff.os elf_gnu_hash.os elf_scnshndx.os elf32_getchdr.os elf64_getchdr.os gelf_getchdr.os elf_compress.os elf_compress_gnu.os libelf.so.1" || rm -f *.gcno *.gcda elf_version.os elf_hash.os elf_error.os elf_fill.os elf_begin.os elf_next.os elf_rand.os elf_end.os elf_kind.os gelf_getclass.os elf_getbase.os elf_getident.os elf32_fsize.os elf64_fsize.os gelf_fsize.os elf32_xlatetof.os elf32_xlatetom.os elf64_xlatetof.os elf64_xlatetom.os gelf_xlate.os elf32_getehdr.os elf64_getehdr.os gelf_getehdr.os elf32_newehdr.os elf64_newehdr.os gelf_newehdr.os gelf_update_ehdr.os elf32_getphdr.os elf64_getphdr.os gelf_getphdr.os elf32_newphdr.os elf64_newphdr.os gelf_newphdr.os gelf_update_phdr.os elf_getarhdr.os elf_getarsym.os elf_rawfile.os elf_readall.os elf_cntl.os elf_getscn.os elf_nextscn.os elf_ndxscn.os elf_newscn.os elf32_getshdr.os elf64_getshdr.os gelf_getshdr.os gelf_update_shdr.os elf_strptr.os elf_rawdata.os elf_getdata.os elf_newdata.os elf_getdata_rawchunk.os elf_flagelf.os elf_flagehdr.os elf_flagphdr.os elf_flagscn.os elf_flagshdr.os elf_flagdata.os elf_memory.os elf_update.os elf32_updatenull.os elf64_updatenull.os elf32_updatefile.os elf64_updatefile.os gelf_getsym.os gelf_update_sym.os gelf_getversym.os gelf_getverneed.os gelf_getvernaux.os gelf_getverdef.os gelf_getverdaux.os gelf_getrel.os gelf_getrela.os gelf_update_rel.os gelf_update_rela.os gelf_getdyn.os gelf_update_dyn.os gelf_getmove.os gelf_update_move.os gelf_getsyminfo.os gelf_update_syminfo.os gelf_getauxv.os gelf_update_auxv.os gelf_getnote.os gelf_xlatetof.os gelf_xlatetom.os nlist.os gelf_getsymshndx.os gelf_update_symshndx.os gelf_update_versym.os gelf_update_verneed.os gelf_update_vernaux.os gelf_update_verdef.os gelf_update_verdaux.os elf_getphdrnum.os elf_getshdrnum.os elf_getshdrstrndx.os gelf_checksum.os elf32_checksum.os elf64_checksum.os libelf_crc32.os libelf_next_prime.os elf_clone.os gelf_getlib.os gelf_update_lib.os elf32_offscn.os elf64_offscn.os gelf_offscn.os elf_getaroff.os elf_gnu_hash.os elf_scnshndx.os elf32_getchdr.os elf64_getchdr.os gelf_getchdr.os elf_compress.os elf_compress_gnu.os libelf.so.1
test -z "libelf.a" || rm -f libelf.a
test -z "libelf_pic.a" || rm -f libelf_pic.a
test -z "libelf.so" || rm -f libelf.so
rm -f *.o
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libelf'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libelf'
CC elf_version.o
CC elf_hash.o
CC elf_error.o
CC elf_fill.o
CC elf_begin.o
CC elf_next.o
CC elf_rand.o
CC elf_end.o
CC elf_kind.o
CC gelf_getclass.o
CC elf_getbase.o
CC elf_getident.o
CC elf32_fsize.o
CC elf64_fsize.o
CC gelf_fsize.o
CC elf32_xlatetof.o
CC elf32_xlatetom.o
CC elf64_xlatetof.o
CC elf64_xlatetom.o
CC gelf_xlate.o
CC elf32_getehdr.o
CC elf64_getehdr.o
CC gelf_getehdr.o
CC elf32_newehdr.o
CC elf64_newehdr.o
CC gelf_newehdr.o
CC gelf_update_ehdr.o
CC elf32_getphdr.o
CC elf64_getphdr.o
CC gelf_getphdr.o
CC elf32_newphdr.o
CC elf64_newphdr.o
CC gelf_newphdr.o
CC gelf_update_phdr.o
CC elf_getarhdr.o
CC elf_getarsym.o
CC elf_rawfile.o
CC elf_readall.o
CC elf_cntl.o
CC elf_getscn.o
CC elf_nextscn.o
CC elf_ndxscn.o
CC elf_newscn.o
CC elf32_getshdr.o
CC elf64_getshdr.o
CC gelf_getshdr.o
CC gelf_update_shdr.o
CC elf_strptr.o
CC elf_rawdata.o
CC elf_getdata.o
CC elf_newdata.o
CC elf_getdata_rawchunk.o
CC elf_flagelf.o
CC elf_flagehdr.o
CC elf_flagphdr.o
CC elf_flagscn.o
CC elf_flagshdr.o
CC elf_flagdata.o
CC elf_memory.o
CC elf_update.o
CC elf32_updatenull.o
CC elf64_updatenull.o
CC elf32_updatefile.o
CC elf64_updatefile.o
CC gelf_getsym.o
CC gelf_update_sym.o
CC gelf_getversym.o
CC gelf_getverneed.o
CC gelf_getvernaux.o
CC gelf_getverdef.o
CC gelf_getverdaux.o
CC gelf_getrel.o
CC gelf_getrela.o
CC gelf_update_rel.o
CC gelf_update_rela.o
CC gelf_getdyn.o
CC gelf_update_dyn.o
CC gelf_getmove.o
CC gelf_update_move.o
CC gelf_getsyminfo.o
CC gelf_update_syminfo.o
CC gelf_getauxv.o
CC gelf_update_auxv.o
CC gelf_getnote.o
CC gelf_xlatetof.o
CC gelf_xlatetom.o
CC nlist.o
CC gelf_getsymshndx.o
CC gelf_update_symshndx.o
CC gelf_update_versym.o
CC gelf_update_verneed.o
CC gelf_update_vernaux.o
CC gelf_update_verdef.o
CC gelf_update_verdaux.o
CC elf_getphdrnum.o
CC elf_getshdrnum.o
CC elf_getshdrstrndx.o
CC gelf_checksum.o
CC elf32_checksum.o
CC elf64_checksum.o
CC libelf_crc32.o
CC libelf_next_prime.o
CC elf_clone.o
CC gelf_getlib.o
CC gelf_update_lib.o
CC elf32_offscn.o
CC elf64_offscn.o
CC gelf_offscn.o
CC elf_getaroff.o
CC elf_gnu_hash.o
CC elf_scnshndx.o
CC elf32_getchdr.o
CC elf64_getchdr.o
CC gelf_getchdr.o
CC elf_compress.o
CC elf_compress_gnu.o
AR libelf.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libelf'
. ./source_me.sh && cd deps/elfutils/libebl && make clean && make libebl.a
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libebl'
test -z "*.gcno *.gcda " || rm -f *.gcno *.gcda
test -z "libebl.a" || rm -f libebl.a
rm -f *.o
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libebl'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libebl'
CC eblopenbackend.o
CC eblclosebackend.o
CC eblreloctypename.o
CC eblsegmenttypename.o
CC eblsectiontypename.o
CC eblmachineflagname.o
CC eblsymboltypename.o
CC ebldynamictagname.o
CC eblsectionname.o
CC eblsymbolbindingname.o
CC eblbackendname.o
CC eblosabiname.o
CC eblmachineflagcheck.o
CC eblmachinesectionflagcheck.o
CC eblreloctypecheck.o
CC eblrelocvaliduse.o
CC eblrelocsimpletype.o
CC ebldynamictagcheck.o
CC eblcorenotetypename.o
CC eblobjnotetypename.o
CC eblcorenote.o
CC eblobjnote.o
CC ebldebugscnp.o
CC eblgotpcreloccheck.o
CC eblcopyrelocp.o
CC eblsectionstripp.o
CC eblelfclass.o
CC eblelfdata.o
CC eblelfmachine.o
CC ebl_check_special_symbol.o
CC eblbsspltp.o
CC eblretval.o
CC eblreginfo.o
CC eblnonerelocp.o
CC eblrelativerelocp.o
CC eblsysvhashentrysize.o
CC eblauxvinfo.o
CC eblcheckobjattr.o
CC ebl_check_special_section.o
CC ebl_syscall_abi.o
CC eblabicfi.o
CC eblstother.o
CC eblinitreg.o
CC ebldwarftoregno.o
CC eblnormalizepc.o
CC eblunwind.o
CC eblresolvesym.o
CC eblcheckreloctargettype.o
CC ebl_data_marker_symbol.o
AR libebl.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libebl'
. ./source_me.sh && cd deps/elfutils/libdwfl && make clean && make libdwfl.a
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwfl'
test -z "*.gcno *.gcda dwfl_begin.os dwfl_end.os dwfl_error.os dwfl_version.os dwfl_module.os dwfl_report_elf.os relocate.os dwfl_module_build_id.os dwfl_module_report_build_id.os derelocate.os offline.os segment.os dwfl_module_info.os dwfl_getmodules.os dwfl_getdwarf.os dwfl_module_getdwarf.os dwfl_module_getelf.os dwfl_validate_address.os argp-std.os find-debuginfo.os dwfl_build_id_find_elf.os dwfl_build_id_find_debuginfo.os linux-kernel-modules.os linux-proc-maps.os dwfl_addrmodule.os dwfl_addrdwarf.os cu.os dwfl_module_nextcu.os dwfl_nextcu.os dwfl_cumodule.os dwfl_module_addrdie.os dwfl_addrdie.os lines.os dwfl_lineinfo.os dwfl_line_comp_dir.os dwfl_linemodule.os dwfl_linecu.os dwfl_dwarf_line.os dwfl_getsrclines.os dwfl_onesrcline.os dwfl_module_getsrc.os dwfl_getsrc.os dwfl_module_getsrc_file.os libdwfl_crc32.os libdwfl_crc32_file.os elf-from-memory.os dwfl_module_dwarf_cfi.os dwfl_module_eh_cfi.os dwfl_module_getsym.os dwfl_module_addrname.os dwfl_module_addrsym.os dwfl_module_return_value_location.os dwfl_module_register_names.os dwfl_segment_report_module.os link_map.os core-file.os open.os image-header.os dwfl_frame.os frame_unwind.os dwfl_frame_pc.os linux-pid-attach.os linux-core-attach.os dwfl_frame_regs.os gzip.os bzip2.os lzma.os" || rm -f *.gcno *.gcda dwfl_begin.os dwfl_end.os dwfl_error.os dwfl_version.os dwfl_module.os dwfl_report_elf.os relocate.os dwfl_module_build_id.os dwfl_module_report_build_id.os derelocate.os offline.os segment.os dwfl_module_info.os dwfl_getmodules.os dwfl_getdwarf.os dwfl_module_getdwarf.os dwfl_module_getelf.os dwfl_validate_address.os argp-std.os find-debuginfo.os dwfl_build_id_find_elf.os dwfl_build_id_find_debuginfo.os linux-kernel-modules.os linux-proc-maps.os dwfl_addrmodule.os dwfl_addrdwarf.os cu.os dwfl_module_nextcu.os dwfl_nextcu.os dwfl_cumodule.os dwfl_module_addrdie.os dwfl_addrdie.os lines.os dwfl_lineinfo.os dwfl_line_comp_dir.os dwfl_linemodule.os dwfl_linecu.os dwfl_dwarf_line.os dwfl_getsrclines.os dwfl_onesrcline.os dwfl_module_getsrc.os dwfl_getsrc.os dwfl_module_getsrc_file.os libdwfl_crc32.os libdwfl_crc32_file.os elf-from-memory.os dwfl_module_dwarf_cfi.os dwfl_module_eh_cfi.os dwfl_module_getsym.os dwfl_module_addrname.os dwfl_module_addrsym.os dwfl_module_return_value_location.os dwfl_module_register_names.os dwfl_segment_report_module.os link_map.os core-file.os open.os image-header.os dwfl_frame.os frame_unwind.os dwfl_frame_pc.os linux-pid-attach.os linux-core-attach.os dwfl_frame_regs.os gzip.os bzip2.os lzma.os
test -z "libdwfl.a libdwfl_pic.a" || rm -f libdwfl.a libdwfl_pic.a
rm -f *.o
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwfl'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwfl'
CC dwfl_begin.o
CC dwfl_end.o
CC dwfl_error.o
CC dwfl_version.o
CC dwfl_module.o
CC dwfl_report_elf.o
CC relocate.o
CC dwfl_module_build_id.o
CC dwfl_module_report_build_id.o
CC derelocate.o
CC offline.o
CC segment.o
CC dwfl_module_info.o
CC dwfl_getmodules.o
CC dwfl_getdwarf.o
CC dwfl_module_getdwarf.o
CC dwfl_module_getelf.o
CC dwfl_validate_address.o
CC argp-std.o
CC find-debuginfo.o
CC dwfl_build_id_find_elf.o
CC dwfl_build_id_find_debuginfo.o
CC linux-kernel-modules.o
CC linux-proc-maps.o
CC dwfl_addrmodule.o
CC dwfl_addrdwarf.o
CC cu.o
CC dwfl_module_nextcu.o
CC dwfl_nextcu.o
CC dwfl_cumodule.o
CC dwfl_module_addrdie.o
CC dwfl_addrdie.o
CC lines.o
CC dwfl_lineinfo.o
CC dwfl_line_comp_dir.o
CC dwfl_linemodule.o
CC dwfl_linecu.o
CC dwfl_dwarf_line.o
CC dwfl_getsrclines.o
CC dwfl_onesrcline.o
CC dwfl_module_getsrc.o
CC dwfl_getsrc.o
CC dwfl_module_getsrc_file.o
CC libdwfl_crc32.o
CC libdwfl_crc32_file.o
CC elf-from-memory.o
CC dwfl_module_dwarf_cfi.o
CC dwfl_module_eh_cfi.o
CC dwfl_module_getsym.o
CC dwfl_module_addrname.o
CC dwfl_module_addrsym.o
CC dwfl_module_return_value_location.o
CC dwfl_module_register_names.o
CC dwfl_segment_report_module.o
CC link_map.o
CC core-file.o
CC open.o
CC image-header.o
CC dwfl_frame.o
CC frame_unwind.o
CC dwfl_frame_pc.o
CC linux-pid-attach.o
CC linux-core-attach.o
CC dwfl_frame_regs.o
CC gzip.o
CC bzip2.o
CC lzma.o
AR libdwfl.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwfl'
. ./source_me.sh && cd deps/elfutils/libdwelf && make clean && make libdwelf.a
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwelf'
test -z "*.gcno *.gcda dwelf_elf_gnu_debuglink.os dwelf_dwarf_gnu_debugaltlink.os dwelf_elf_gnu_build_id.os dwelf_scn_gnu_compressed_size.os dwelf_strtab.os dwelf_elf_begin.os" || rm -f *.gcno *.gcda dwelf_elf_gnu_debuglink.os dwelf_dwarf_gnu_debugaltlink.os dwelf_elf_gnu_build_id.os dwelf_scn_gnu_compressed_size.os dwelf_strtab.os dwelf_elf_begin.os
test -z "libdwelf.a libdwelf_pic.a" || rm -f libdwelf.a libdwelf_pic.a
rm -f *.o
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwelf'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwelf'
CC dwelf_elf_gnu_debuglink.o
CC dwelf_dwarf_gnu_debugaltlink.o
CC dwelf_elf_gnu_build_id.o
CC dwelf_scn_gnu_compressed_size.o
CC dwelf_strtab.o
CC dwelf_elf_begin.o
AR libdwelf.a
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdwelf'
. ./source_me.sh && cd deps/elfutils/libdw && make clean && make libdw.a known-dwarf.h
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdw'
test -z "*.gcno *.gcda" || rm -f *.gcno *.gcda
test -z "libdw.a" || rm -f libdw.a
test -z "libdw_pic.a" || rm -f libdw_pic.a
test -z "libdw.so" || rm -f libdw.so
rm -f *.o
test -z "dwarf_begin.os dwarf_begin_elf.os dwarf_end.os dwarf_getelf.os dwarf_getpubnames.os dwarf_getabbrev.os dwarf_tag.os dwarf_error.os dwarf_nextcu.os dwarf_diename.os dwarf_offdie.os dwarf_attr.os dwarf_formstring.os dwarf_abbrev_hash.os dwarf_sig8_hash.os dwarf_attr_integrate.os dwarf_hasattr_integrate.os dwarf_child.os dwarf_haschildren.os dwarf_formaddr.os dwarf_formudata.os dwarf_formsdata.os dwarf_lowpc.os dwarf_entrypc.os dwarf_haspc.os dwarf_highpc.os dwarf_ranges.os dwarf_formref.os dwarf_formref_die.os dwarf_siblingof.os dwarf_dieoffset.os dwarf_cuoffset.os dwarf_diecu.os dwarf_hasattr.os dwarf_hasform.os dwarf_whatform.os dwarf_whatattr.os dwarf_bytesize.os dwarf_arrayorder.os dwarf_bitsize.os dwarf_bitoffset.os dwarf_srclang.os dwarf_getabbrevtag.os dwarf_getabbrevcode.os dwarf_abbrevhaschildren.os dwarf_getattrcnt.os dwarf_getabbrevattr.os dwarf_getsrclines.os dwarf_getsrc_die.os dwarf_getscopes.os dwarf_getscopes_die.os dwarf_getscopevar.os dwarf_linesrc.os dwarf_lineno.os dwarf_lineaddr.os dwarf_linecol.os dwarf_linebeginstatement.os dwarf_lineendsequence.os dwarf_lineblock.os dwarf_lineprologueend.os dwarf_lineepiloguebegin.os dwarf_lineisa.os dwarf_linediscriminator.os dwarf_lineop_index.os dwarf_line_file.os dwarf_onesrcline.os dwarf_formblock.os dwarf_getsrcfiles.os dwarf_filesrc.os dwarf_getsrcdirs.os dwarf_getlocation.os dwarf_getstring.os dwarf_offabbrev.os dwarf_getaranges.os dwarf_onearange.os dwarf_getarangeinfo.os dwarf_getarange_addr.os dwarf_getattrs.os dwarf_formflag.os dwarf_getmacros.os dwarf_macro_getparamcnt.os dwarf_macro_opcode.os dwarf_macro_param.os dwarf_macro_param1.os dwarf_macro_param2.os dwarf_macro_getsrcfiles.os dwarf_addrdie.os dwarf_getfuncs.os dwarf_decl_file.os dwarf_decl_line.os dwarf_decl_column.os dwarf_func_inline.os dwarf_getsrc_file.os libdw_findcu.os libdw_form.os libdw_alloc.os libdw_visit_scopes.os dwarf_entry_breakpoints.os dwarf_next_cfi.os cie.os fde.os cfi.os frame-cache.os dwarf_frame_info.os dwarf_frame_cfa.os dwarf_frame_register.os dwarf_cfi_addrframe.os dwarf_getcfi.os dwarf_getcfi_elf.os dwarf_cfi_end.os dwarf_aggregate_size.os dwarf_getlocation_implicit_pointer.os dwarf_getlocation_die.os dwarf_getlocation_attr.os dwarf_getalt.os dwarf_setalt.os dwarf_cu_getdwarf.os dwarf_cu_die.os dwarf_peel_type.os dwarf_default_lower_bound.os dwarf_die_addr_die.os dwarf_get_units.os libdw_find_split_unit.os dwarf_cu_info.os dwarf_next_lines.os libdw.so.1" || rm -f dwarf_begin.os dwarf_begin_elf.os dwarf_end.os dwarf_getelf.os dwarf_getpubnames.os dwarf_getabbrev.os dwarf_tag.os dwarf_error.os dwarf_nextcu.os dwarf_diename.os dwarf_offdie.os dwarf_attr.os dwarf_formstring.os dwarf_abbrev_hash.os dwarf_sig8_hash.os dwarf_attr_integrate.os dwarf_hasattr_integrate.os dwarf_child.os dwarf_haschildren.os dwarf_formaddr.os dwarf_formudata.os dwarf_formsdata.os dwarf_lowpc.os dwarf_entrypc.os dwarf_haspc.os dwarf_highpc.os dwarf_ranges.os dwarf_formref.os dwarf_formref_die.os dwarf_siblingof.os dwarf_dieoffset.os dwarf_cuoffset.os dwarf_diecu.os dwarf_hasattr.os dwarf_hasform.os dwarf_whatform.os dwarf_whatattr.os dwarf_bytesize.os dwarf_arrayorder.os dwarf_bitsize.os dwarf_bitoffset.os dwarf_srclang.os dwarf_getabbrevtag.os dwarf_getabbrevcode.os dwarf_abbrevhaschildren.os dwarf_getattrcnt.os dwarf_getabbrevattr.os dwarf_getsrclines.os dwarf_getsrc_die.os dwarf_getscopes.os dwarf_getscopes_die.os dwarf_getscopevar.os dwarf_linesrc.os dwarf_lineno.os dwarf_lineaddr.os dwarf_linecol.os dwarf_linebeginstatement.os dwarf_lineendsequence.os dwarf_lineblock.os dwarf_lineprologueend.os dwarf_lineepiloguebegin.os dwarf_lineisa.os dwarf_linediscriminator.os dwarf_lineop_index.os dwarf_line_file.os dwarf_onesrcline.os dwarf_formblock.os dwarf_getsrcfiles.os dwarf_filesrc.os dwarf_getsrcdirs.os dwarf_getlocation.os dwarf_getstring.os dwarf_offabbrev.os dwarf_getaranges.os dwarf_onearange.os dwarf_getarangeinfo.os dwarf_getarange_addr.os dwarf_getattrs.os dwarf_formflag.os dwarf_getmacros.os dwarf_macro_getparamcnt.os dwarf_macro_opcode.os dwarf_macro_param.os dwarf_macro_param1.os dwarf_macro_param2.os dwarf_macro_getsrcfiles.os dwarf_addrdie.os dwarf_getfuncs.os dwarf_decl_file.os dwarf_decl_line.os dwarf_decl_column.os dwarf_func_inline.os dwarf_getsrc_file.os libdw_findcu.os libdw_form.os libdw_alloc.os libdw_visit_scopes.os dwarf_entry_breakpoints.os dwarf_next_cfi.os cie.os fde.os cfi.os frame-cache.os dwarf_frame_info.os dwarf_frame_cfa.os dwarf_frame_register.os dwarf_cfi_addrframe.os dwarf_getcfi.os dwarf_getcfi_elf.os dwarf_cfi_end.os dwarf_aggregate_size.os dwarf_getlocation_implicit_pointer.os dwarf_getlocation_die.os dwarf_getlocation_attr.os dwarf_getalt.os dwarf_setalt.os dwarf_cu_getdwarf.os dwarf_cu_die.os dwarf_peel_type.os dwarf_default_lower_bound.os dwarf_die_addr_die.os dwarf_get_units.os libdw_find_split_unit.os dwarf_cu_info.os dwarf_next_lines.os libdw.so.1
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdw'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdw'
CC dwarf_begin.o
CC dwarf_begin_elf.o
CC dwarf_end.o
CC dwarf_getelf.o
CC dwarf_getpubnames.o
CC dwarf_getabbrev.o
CC dwarf_tag.o
CC dwarf_error.o
CC dwarf_nextcu.o
CC dwarf_diename.o
CC dwarf_offdie.o
CC dwarf_attr.o
CC dwarf_formstring.o
CC dwarf_abbrev_hash.o
CC dwarf_sig8_hash.o
CC dwarf_attr_integrate.o
CC dwarf_hasattr_integrate.o
CC dwarf_child.o
CC dwarf_haschildren.o
CC dwarf_formaddr.o
CC dwarf_formudata.o
CC dwarf_formsdata.o
CC dwarf_lowpc.o
CC dwarf_entrypc.o
CC dwarf_haspc.o
CC dwarf_highpc.o
CC dwarf_ranges.o
CC dwarf_formref.o
CC dwarf_formref_die.o
CC dwarf_siblingof.o
CC dwarf_dieoffset.o
CC dwarf_cuoffset.o
CC dwarf_diecu.o
CC dwarf_hasattr.o
CC dwarf_hasform.o
CC dwarf_whatform.o
CC dwarf_whatattr.o
CC dwarf_bytesize.o
CC dwarf_arrayorder.o
CC dwarf_bitsize.o
CC dwarf_bitoffset.o
CC dwarf_srclang.o
CC dwarf_getabbrevtag.o
CC dwarf_getabbrevcode.o
CC dwarf_abbrevhaschildren.o
CC dwarf_getattrcnt.o
CC dwarf_getabbrevattr.o
CC dwarf_getsrclines.o
CC dwarf_getsrc_die.o
CC dwarf_getscopes.o
CC dwarf_getscopes_die.o
CC dwarf_getscopevar.o
CC dwarf_linesrc.o
CC dwarf_lineno.o
CC dwarf_lineaddr.o
CC dwarf_linecol.o
CC dwarf_linebeginstatement.o
CC dwarf_lineendsequence.o
CC dwarf_lineblock.o
CC dwarf_lineprologueend.o
CC dwarf_lineepiloguebegin.o
CC dwarf_lineisa.o
CC dwarf_linediscriminator.o
CC dwarf_lineop_index.o
CC dwarf_line_file.o
CC dwarf_onesrcline.o
CC dwarf_formblock.o
CC dwarf_getsrcfiles.o
CC dwarf_filesrc.o
CC dwarf_getsrcdirs.o
CC dwarf_getlocation.o
CC dwarf_getstring.o
CC dwarf_offabbrev.o
CC dwarf_getaranges.o
CC dwarf_onearange.o
CC dwarf_getarangeinfo.o
CC dwarf_getarange_addr.o
CC dwarf_getattrs.o
CC dwarf_formflag.o
CC dwarf_getmacros.o
CC dwarf_macro_getparamcnt.o
CC dwarf_macro_opcode.o
CC dwarf_macro_param.o
CC dwarf_macro_param1.o
CC dwarf_macro_param2.o
CC dwarf_macro_getsrcfiles.o
CC dwarf_addrdie.o
CC dwarf_getfuncs.o
CC dwarf_decl_file.o
CC dwarf_decl_line.o
CC dwarf_decl_column.o
CC dwarf_func_inline.o
CC dwarf_getsrc_file.o
CC libdw_findcu.o
CC libdw_form.o
CC libdw_alloc.o
CC libdw_visit_scopes.o
CC dwarf_entry_breakpoints.o
CC dwarf_next_cfi.o
CC cie.o
CC fde.o
CC cfi.o
CC frame-cache.o
CC dwarf_frame_info.o
CC dwarf_frame_cfa.o
CC dwarf_frame_register.o
CC dwarf_cfi_addrframe.o
CC dwarf_getcfi.o
CC dwarf_getcfi_elf.o
CC dwarf_cfi_end.o
CC dwarf_aggregate_size.o
CC dwarf_getlocation_implicit_pointer.o
CC dwarf_getlocation_die.o
CC dwarf_getlocation_attr.o
CC dwarf_getalt.o
CC dwarf_setalt.o
CC dwarf_cu_getdwarf.o
CC dwarf_cu_die.o
CC dwarf_peel_type.o
CC dwarf_default_lower_bound.o
CC dwarf_die_addr_die.o
CC dwarf_get_units.o
CC libdw_find_split_unit.o
CC dwarf_cu_info.o
CC dwarf_next_lines.o
AR libdw.a
gawk -f ../config/known-dwarf.awk dwarf.h > known-dwarf.h.new
mv -f known-dwarf.h.new known-dwarf.h
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/elfutils/libdw'
cd deps/elfutils && mkdir -p /data3/genome_graphs/vg-rotella/include/elfutils && cp libdw/known-dwarf.h libdw/libdw.h libebl/libebl.h libelf/elf-knowledge.h version.h libdwfl/libdwfl.h libdwelf/libdwelf.h /data3/genome_graphs/vg-rotella/include/elfutils && cp libelf/gelf.h libelf/libelf.h libdw/dwarf.h /data3/genome_graphs/vg-rotella/include && cp libebl/libebl.a libdw/libdw.a libdwfl/libdwfl.a libdwelf/libdwelf.a libelf/libelf.a /data3/genome_graphs/vg-rotella/lib/
cd ./deps/lru_cache && cp *.h* /data3/genome_graphs/vg-rotella/include/
. ./source_me.sh && cd deps/sparsehash && ./autogen.sh && LDFLAGS="-L/opt/local/lib" ./configure --prefix=/data3/genome_graphs/vg-rotella && make && make install
+ rm -rf autom4te.cache
+ aclocal --force -I m4
+ autoconf -f -W all,no-obsolete
+ autoheader -f -W all
+ automake -a -c -f -W all
configure.ac:16: installing './compile'
Makefile.am:156: warning: source file 'src/hashtable_test.cc' is in a subdirectory,
Makefile.am:156: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
Makefile.am:140: warning: source file 'src/libc_allocator_with_realloc_test.cc' is in a subdirectory,
Makefile.am:140: but option 'subdir-objects' is disabled
Makefile.am:172: warning: source file 'src/simple_compat_test.cc' is in a subdirectory,
Makefile.am:172: but option 'subdir-objects' is disabled
Makefile.am:166: warning: source file 'src/simple_test.cc' is in a subdirectory,
Makefile.am:166: but option 'subdir-objects' is disabled
Makefile.am:148: warning: source file 'src/sparsetable_unittest.cc' is in a subdirectory,
Makefile.am:148: but option 'subdir-objects' is disabled
Makefile.am:125: warning: source file 'src/template_util_unittest.cc' is in a subdirectory,
Makefile.am:125: but option 'subdir-objects' is disabled
Makefile.am:179: warning: source file 'src/time_hash_map.cc' is in a subdirectory,
Makefile.am:179: but option 'subdir-objects' is disabled
Makefile.am:132: warning: source file 'src/type_traits_unittest.cc' is in a subdirectory,
Makefile.am:132: but option 'subdir-objects' is disabled
parallel-tests: installing './test-driver'
+ rm -rf autom4te.cache
+ exit 0
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/miniconda3/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of /usr/bin/g++... gcc3
checking for gcc... /usr/bin/gcc
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking whether /usr/bin/gcc understands -c and -o together... yes
checking dependency style of /usr/bin/gcc... gcc3
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for memcpy... yes
checking for memmove... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for uint16_t... yes
checking for u_int16_t... yes
checking for __uint16... no
checking for long long... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for unistd.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking google/malloc_extension.h usability... yes
checking google/malloc_extension.h presence... yes
checking for google/malloc_extension.h... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking whether what we have so far is sufficient with -nostdlib... no
checking whether -lpthread saves the day... yes
checking whether the compiler implements namespaces... yes
checking the location of hash_map... <unordered_map>
checking how to include hash_fun directly... <functional>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
[ -d src/sparsehash/internal ] || mkdir -p src/sparsehash/internal
echo "/*" > src/sparsehash/internal/_sparsehash_config
echo " * NOTE: This file is for internal use only." >> src/sparsehash/internal/_sparsehash_config
echo " * Do not use these #defines in your own program!" >> src/sparsehash/internal/_sparsehash_config
echo " */" >> src/sparsehash/internal/_sparsehash_config
gawk '{prevline=currline; currline=$0;} \
/^#/ {in_second_file = 1;} \
!in_second_file {if (currline !~ /^ *$/) {inc[currline]=0}}; \
in_second_file { for (i in inc) { \
if (index(currline, i) != 0) { \
print "\n"prevline"\n"currline; \
delete inc[i]; \
} \
} }' \
./src/config.h.include ./src/config.h \
>> src/sparsehash/internal/_sparsehash_config
mv -f src/sparsehash/internal/_sparsehash_config src/sparsehash/internal/sparseconfig.h
make all-am
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT template_util_unittest.o -MD -MP -MF .deps/template_util_unittest.Tpo -c -o template_util_unittest.o `test -f 'src/template_util_unittest.cc' || echo './'`src/template_util_unittest.cc
mv -f .deps/template_util_unittest.Tpo .deps/template_util_unittest.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o template_util_unittest template_util_unittest.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT type_traits_unittest.o -MD -MP -MF .deps/type_traits_unittest.Tpo -c -o type_traits_unittest.o `test -f 'src/type_traits_unittest.cc' || echo './'`src/type_traits_unittest.cc
mv -f .deps/type_traits_unittest.Tpo .deps/type_traits_unittest.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o type_traits_unittest type_traits_unittest.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT libc_allocator_with_realloc_test.o -MD -MP -MF .deps/libc_allocator_with_realloc_test.Tpo -c -o libc_allocator_with_realloc_test.o `test -f 'src/libc_allocator_with_realloc_test.cc' || echo './'`src/libc_allocator_with_realloc_test.cc
mv -f .deps/libc_allocator_with_realloc_test.Tpo .deps/libc_allocator_with_realloc_test.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o libc_allocator_with_realloc_test libc_allocator_with_realloc_test.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT sparsetable_unittest.o -MD -MP -MF .deps/sparsetable_unittest.Tpo -c -o sparsetable_unittest.o `test -f 'src/sparsetable_unittest.cc' || echo './'`src/sparsetable_unittest.cc
mv -f .deps/sparsetable_unittest.Tpo .deps/sparsetable_unittest.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o sparsetable_unittest sparsetable_unittest.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT hashtable_test.o -MD -MP -MF .deps/hashtable_test.Tpo -c -o hashtable_test.o `test -f 'src/hashtable_test.cc' || echo './'`src/hashtable_test.cc
mv -f .deps/hashtable_test.Tpo .deps/hashtable_test.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o hashtable_test hashtable_test.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT simple_test.o -MD -MP -MF .deps/simple_test.Tpo -c -o simple_test.o `test -f 'src/simple_test.cc' || echo './'`src/simple_test.cc
mv -f .deps/simple_test.Tpo .deps/simple_test.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o simple_test simple_test.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT simple_compat_test.o -MD -MP -MF .deps/simple_compat_test.Tpo -c -o simple_compat_test.o `test -f 'src/simple_compat_test.cc' || echo './'`src/simple_compat_test.cc
mv -f .deps/simple_compat_test.Tpo .deps/simple_compat_test.Po
/usr/bin/g++ -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -L/opt/local/lib -o simple_compat_test simple_compat_test.o
/usr/bin/g++ -DHAVE_CONFIG_H -I. -I./src -I./src -pthread -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -MT time_hash_map-time_hash_map.o -MD -MP -MF .deps/time_hash_map-time_hash_map.Tpo -c -o time_hash_map-time_hash_map.o `test -f 'src/time_hash_map.cc' || echo './'`src/time_hash_map.cc
In file included from src/time_hash_map.cc:391:0:
/usr/include/google/malloc_extension.h:34:2: warning: #warning "google/malloc_extension.h is deprecated. Use gperftools/malloc_extension.h instead" [-Wcpp]
#warning "google/malloc_extension.h is deprecated. Use gperftools/malloc_extension.h instead"
^
mv -f .deps/time_hash_map-time_hash_map.Tpo .deps/time_hash_map-time_hash_map.Po
/usr/bin/g++ -pthread -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -pthread -L/opt/local/lib -o time_hash_map time_hash_map-time_hash_map.o -ltcmalloc -lpthread
echo 'prefix=/data3/genome_graphs/vg-rotella' > "libsparsehash.pc".tmp
echo 'exec_prefix='`echo '/data3/genome_graphs/vg-rotella' | sed 's@^/data3/genome_graphs/vg-rotella@${prefix}@'` >> "libsparsehash.pc".tmp
echo 'libdir='`echo '/data3/genome_graphs/vg-rotella/lib' | sed 's@^/data3/genome_graphs/vg-rotella@${exec_prefix}@'` >> "libsparsehash.pc".tmp
echo 'includedir='`echo '/data3/genome_graphs/vg-rotella/include' | sed 's@^/data3/genome_graphs/vg-rotella@${prefix}@'` >> "libsparsehash.pc".tmp
echo '' >> "libsparsehash.pc".tmp
echo 'Name: sparsehash' >> "libsparsehash.pc".tmp
echo 'Version: 2.0.2' >> "libsparsehash.pc".tmp
grep '^Summary:' ./packages/rpm/rpm.spec | sed s/^Summary:/Description:/ | head -n1 >> "libsparsehash.pc".tmp
grep '^URL: ' ./packages/rpm/rpm.spec >> "libsparsehash.pc".tmp
echo 'Requires:' >> "libsparsehash.pc".tmp
echo 'Libs:' >> "libsparsehash.pc".tmp
echo 'Cflags: -I${includedir}' >> "libsparsehash.pc".tmp
mv -f "libsparsehash.pc".tmp "libsparsehash.pc"
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
make[1]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
make install-am
make[2]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
make[3]: Entering directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/share/doc/sparsehash-2.0.2'
/usr/bin/miniconda3/bin/install -c -m 644 AUTHORS COPYING ChangeLog INSTALL NEWS README README_windows.txt TODO doc/dense_hash_map.html doc/dense_hash_set.html doc/sparse_hash_map.html doc/sparse_hash_set.html doc/sparsetable.html doc/implementation.html doc/performance.html doc/index.html doc/designstyle.css '/data3/genome_graphs/vg-rotella/share/doc/sparsehash-2.0.2'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/include/google'
/usr/bin/miniconda3/bin/install -c -m 644 src/google/dense_hash_map src/google/dense_hash_set src/google/sparse_hash_map src/google/sparse_hash_set src/google/sparsetable src/google/template_util.h src/google/type_traits.h '/data3/genome_graphs/vg-rotella/include/google'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/include/google/sparsehash'
/usr/bin/miniconda3/bin/install -c -m 644 src/google/sparsehash/densehashtable.h src/google/sparsehash/sparsehashtable.h src/google/sparsehash/hashtable-common.h src/google/sparsehash/libc_allocator_with_realloc.h '/data3/genome_graphs/vg-rotella/include/google/sparsehash'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/include/sparsehash/internal'
/usr/bin/miniconda3/bin/install -c -m 644 src/sparsehash/internal/densehashtable.h src/sparsehash/internal/sparsehashtable.h src/sparsehash/internal/hashtable-common.h src/sparsehash/internal/libc_allocator_with_realloc.h '/data3/genome_graphs/vg-rotella/include/sparsehash/internal'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/include/sparsehash/internal'
/usr/bin/miniconda3/bin/install -c -m 644 src/sparsehash/internal/sparseconfig.h '/data3/genome_graphs/vg-rotella/include/sparsehash/internal'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/lib/pkgconfig'
/usr/bin/miniconda3/bin/install -c -m 644 libsparsehash.pc '/data3/genome_graphs/vg-rotella/lib/pkgconfig'
/usr/bin/miniconda3/bin/mkdir -p '/data3/genome_graphs/vg-rotella/include/sparsehash'
/usr/bin/miniconda3/bin/install -c -m 644 src/sparsehash/dense_hash_map src/sparsehash/dense_hash_set src/sparsehash/sparse_hash_map src/sparsehash/sparse_hash_set src/sparsehash/sparsetable src/sparsehash/template_util.h src/sparsehash/type_traits.h '/data3/genome_graphs/vg-rotella/include/sparsehash'
make[3]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
make[2]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
make[1]: Leaving directory '/data3/genome_graphs/vg-rotella/deps/sparsehash'
cp deps/sha1/*.h* /data3/genome_graphs/vg-rotella/include/
cp deps/progress_bar/progress_bar.hpp /data3/genome_graphs/vg-rotella/include
cp deps/backward-cpp/backward.hpp /data3/genome_graphs/vg-rotella/include/
mkdir -p /data3/genome_graphs/vg-rotella/include/dozeu && cp deps/dozeu/*.h /data3/genome_graphs/vg-rotella/include/dozeu/
cd deps/raptor/build && mkdir -p /data3/genome_graphs/vg-rotella/include/raptor2 && cp src/*.h /data3/genome_graphs/vg-rotella/include/raptor2
touch include/raptor2/raptor2.h
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/main.o src/main.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/stream_sorter.o src/stream_sorter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/path.o src/path.cpp
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/path.cpp:2:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Path]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Path; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Path; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Path; std::istream = std::basic_istream<char>]’
src/path.cpp:116:32: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/path.hpp:11,
from src/path.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/readfilter.o src/readfilter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/graph.o src/graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/gff_reader.o src/gff_reader.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/feature_set.o src/feature_set.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/snarls.o src/snarls.cpp
In file included from src/snarls.hpp:18:0,
from src/snarls.cpp:10:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Snarl]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Snarl; std::istream = std::basic_istream<char>]’
src/snarls.cpp:603:49: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/message_emitter.hpp:18:0,
from /data3/genome_graphs/vg-rotella/include/vg/io/protobuf_emitter.hpp:18,
from src/snarls.cpp:8:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
diff: include/vg_git_version.hpp: No such file or directory
diff: include/vg_environment_version.hpp: No such file or directory
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/version.o src/version.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/mapper.o src/mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/utility.o src/utility.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/variant_adder.o src/variant_adder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/genotyper.o src/genotyper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/packer.o src/packer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/filter.o src/filter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/graph_caller.o src/graph_caller.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/traversal_support.o src/traversal_support.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/aligner.o src/aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/progressive.o src/progressive.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/alignment_emitter.o src/alignment_emitter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/viz.o src/viz.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/haplotypes.o src/haplotypes.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/region.o src/region.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/prune.o src/prune.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/ssw_aligner.o src/ssw_aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/reverse_graph.o src/reverse_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/alignment.o src/alignment.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/scanner.o src/scanner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/stream_index.o src/stream_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/subgraph.o src/subgraph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/extra_node_graph.o src/extra_node_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/watchdog.o src/watchdog.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/name_mapper.o src/name_mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/variant_recall.o src/variant_recall.cpp
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/variant_recall.hpp:16,
from src/variant_recall.cpp:2:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Alignment]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
src/variant_recall.cpp:353:45: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/variant_recall.hpp:15,
from src/variant_recall.cpp:2:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/path_component_index.o src/path_component_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/surjector.o src/surjector.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/gfa.o src/gfa.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/min_distance.o src/min_distance.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/phased_genome.o src/phased_genome.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/genome_state.o src/genome_state.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/gbwt_helper.o src/gbwt_helper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/funnel.o src/funnel.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/vg.o src/vg.cpp
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/vg.cpp:1:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Graph]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
src/vg.cpp:79:32: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/aligner.hpp:12,
from src/vg.hpp:20,
from src/vg.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/memoizing_graph.o src/memoizing_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/crash.o src/crash.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/multipath_alignment.o src/multipath_alignment.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/translator.o src/translator.cpp
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/translator.hpp:16,
from src/translator.cpp:1:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Translation]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
src/translator.cpp:14:32: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/translator.hpp:15,
from src/translator.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/seed_clusterer.o src/seed_clusterer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/dagified_graph.o src/dagified_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/option.o src/option.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/phase_unfolder.o src/phase_unfolder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/sampler.o src/sampler.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/multipath_mapper.o src/multipath_mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/region_expander.o src/region_expander.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/build_index.o src/build_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/vg_set.o src/vg_set.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/transcriptome.o src/transcriptome.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/msa_converter.o src/msa_converter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/deconstructor.o src/deconstructor.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/cluster.o src/cluster.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/gapless_extender.o src/gapless_extender.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/homogenizer.o src/homogenizer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/proto_handle_graph.o src/proto_handle_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/preflight.o src/preflight.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/genotypekit.o src/genotypekit.cpp
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/genotypekit.hpp:19,
from src/genotypekit.cpp:1:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Translation]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
src/genotypekit.cpp:291:37: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/genotypekit.hpp:18,
from src/genotypekit.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/genotypekit.hpp:19,
from src/genotypekit.cpp:1:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::LocationSupport]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::LocationSupport; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::LocationSupport; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::LocationSupport; std::istream = std::basic_istream<char>]’
src/genotypekit.cpp:334:37: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/genotypekit.hpp:18,
from src/genotypekit.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/srpe.o src/srpe.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/edit.o src/edit.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/kmer.o src/kmer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/traversal_finder.o src/traversal_finder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/snarl_caller.o src/snarl_caller.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/split_strand_graph.o src/split_strand_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/memusage.o src/memusage.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/benchmark.o src/benchmark.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/path_index.o src/path_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/cactus.o src/cactus.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/convert_handle.o src/convert_handle.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/flow_sort.o src/flow_sort.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/augment.o src/augment.cpp
In file included from /data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/augment.cpp:1:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Alignment]’:
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-rotella/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
src/augment.cpp:38:54: required from here
/data3/genome_graphs/vg-rotella/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-rotella/include/vg/vg.pb.h:23:0,
from src/aligner.hpp:12,
from src/vg.hpp:20,
from src/augment.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/entropy.o src/entropy.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/tree_subgraph.o src/tree_subgraph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/json2pb.o src/json2pb.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/index.o src/index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/identity_overlay.o src/identity_overlay.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/vcf_buffer.o src/vcf_buffer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/vectorizer.o src/vectorizer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-rotella/include -I. -I/data3/genome_graphs/vg-rotella/src -I/data3/genome_graphs/vg-rotella/src/unittest -I/data3/genome_graphs/vg-rotella/src/subcommand -I/data3/genome_graphs/vg-rotella/include/dynamic -I/data3/genome_graphs/vg-rotella/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -I /data3/genome_graphs/vg-rotella/include -I/data3/genome_graphs/vg-rotella/include/dynamic -fopenmp -msse4.2 -c -o obj/index_manager.o src/index_manager.cpp
In file included from src/index_manager.cpp:18:0:
src/haplotype_indexer.hpp:79:54: error: expected ‘;’ at end of member declaration
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:79:54: error: declaration of ‘std::pair<long unsigned int, long unsigned int> vg::HaplotypeIndexer::size_t’ [-fpermissive]
In file included from /usr/include/wchar.h:51:0,
from /usr/include/c++/5/cwchar:44,
from /usr/include/c++/5/bits/postypes.h:40,
from /usr/include/c++/5/iosfwd:40,
from /usr/include/c++/5/ios:38,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from src/index_manager.cpp:5:
/usr/lib/gcc/x86_64-linux-gnu/5/include/stddef.h:216:23: error: changes meaning of ‘size_t’ from ‘typedef long unsigned int size_t’ [-fpermissive]
typedef __SIZE_TYPE__ size_t;
^
In file included from src/index_manager.cpp:18:0:
src/haplotype_indexer.hpp:79:60: error: expected unqualified-id before ‘>’ token
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:22: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:22: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:22: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:30: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:30: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:30: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:83:30: error: template argument 1 is invalid
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:83:30: error: template argument 2 is invalid
src/haplotype_indexer.hpp:83:36: error: template argument 2 is invalid
map<string, pair<size_t, size_t>> regions;
^
src/haplotype_indexer.hpp:83:36: error: template argument 4 is invalid
src/haplotype_indexer.hpp:121:5: error: ‘size_t’ does not name a type
size_t parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& cont
^
src/haplotype_indexer.hpp:157:27: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
tuple<vector<string>, size_t, vector<string>> generate_threads(const PathHandleGraph* graph, map<string, Path>
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:157:27: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
tuple<vector<string>, size_t, vector<string>> generate_threads(const PathHandleGraph* graph, map<string, Path>
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:157:27: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
tuple<vector<string>, size_t, vector<string>> generate_threads(const PathHandleGraph* graph, map<string, Path>
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:157:48: error: template argument 2 is invalid
tuple<vector<string>, size_t, vector<string>> generate_threads(const PathHandleGraph* graph, map<string, Path>
^
src/haplotype_indexer.hpp:159:29: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
const function<void(size_t)>& bit_width_ready, const function<void(const gbwt::vector_type&, const gbwt::s
^
src/haplotype_indexer.hpp:79:54: note: declared here
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
src/haplotype_indexer.hpp:159:36: error: template argument 1 is invalid
const function<void(size_t)>& bit_width_ready, const function<void(const gbwt::vector_type&, const gbwt::s
^
src/haplotype_indexer.hpp:79:46: error: wrong number of template arguments (1, should be 2)
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from src/index_manager.cpp:5:
/usr/include/c++/5/bits/stl_pair.h:96:12: note: provided for ‘template<class _T1, class _T2> struct std::pair’
struct pair
^
Makefile:702: recipe for target 'obj/index_manager.o' failed
make: *** [obj/index_manager.o] Error 1
This does not look promising. 🙈 It ran for quite some time again, but the first error message to pop up was
src/haplotype_indexer.hpp:79:54: error: expected ‘;’ at end of member declaration
pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
and that is absolutely nothing I know how to deal with. There is a chance that this is caused by whatever C++ version we have.
Maybe I should listen to the advice of the vg team and download the “build-able source tarball”.
Clean install from tarball
wget https://github.com/vgteam/vg/releases/download/v1.22.0/vg-v1.22.0.tar.gz
tar -xzvf vg-v1.22.0.tar.gz
cd vg-v1.22.0/
screen -S vg-install
. ./source_me.sh && make
screen -r 8234.vg-install
include/jemalloc/internal/atomic_gcc_atomic.h:79:11: warning: parameter ‘expected’ set but not used [-Wunused-but-set-parameter]
type *expected, type desired, atomic_memory_order_t success_mo, \
^
include/jemalloc/internal/atomic_gcc_atomic.h:90:1: note: in expansion of macro ‘JEMALLOC_GENERATE_ATOMICS’
JEMALLOC_GENERATE_ATOMICS(type, short_type, /* unused */ lg_size) \
^
include/jemalloc/internal/atomic.h:78:1: note: in expansion of macro ‘JEMALLOC_GENERATE_INT_ATOMICS’
JEMALLOC_GENERATE_INT_ATOMICS(uint32_t, u32, 2)
^
include/jemalloc/internal/atomic.h: In function ‘bool atomic_compare_exchange_weak_u64(atomic_u64_t*, uint64_t*, uint64_t, atomic_memory_order_t, atomic_memory_order_t)’:
include/jemalloc/internal/atomic_gcc_atomic.h:70:11: warning: parameter ‘expected’ set but not used [-Wunused-but-set-parameter]
type *expected, type desired, atomic_memory_order_t success_mo, \
^
include/jemalloc/internal/atomic_gcc_atomic.h:90:1: note: in expansion of macro ‘JEMALLOC_GENERATE_ATOMICS’
JEMALLOC_GENERATE_ATOMICS(type, short_type, /* unused */ lg_size) \
^
include/jemalloc/internal/atomic.h:81:1: note: in expansion of macro ‘JEMALLOC_GENERATE_INT_ATOMICS’
JEMALLOC_GENERATE_INT_ATOMICS(uint64_t, u64, 3)
^
include/jemalloc/internal/atomic.h: In function ‘bool atomic_compare_exchange_strong_u64(atomic_u64_t*, uint64_t*, uint64_t, atomic_memory_order_t, atomic_memory_order_t)’:
include/jemalloc/internal/atomic_gcc_atomic.h:79:11: warning: parameter ‘expected’ set but not used [-Wunused-but-set-parameter]
type *expected, type desired, atomic_memory_order_t success_mo, \
^
include/jemalloc/internal/atomic_gcc_atomic.h:90:1: note: in expansion of macro ‘JEMALLOC_GENERATE_ATOMICS’
JEMALLOC_GENERATE_ATOMICS(type, short_type, /* unused */ lg_size) \
^
include/jemalloc/internal/atomic.h:81:1: note: in expansion of macro ‘JEMALLOC_GENERATE_INT_ATOMICS’
JEMALLOC_GENERATE_INT_ATOMICS(uint64_t, u64, 3)
^
In file included from /usr/include/c++/5/mutex:35:0,
from src/jemalloc_cpp.cpp:1:
/usr/include/c++/5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support \
^
Makefile:412: recipe for target 'src/jemalloc_cpp.pic.o' failed
make[1]: *** [src/jemalloc_cpp.pic.o] Error 1
make[1]: Leaving directory '/data3/genome_graphs/vg-v1.22.0/deps/jemalloc'
Makefile:382: recipe for target 'lib/libjemalloc.a' failed
make: *** [lib/libjemalloc.a] Error 2
Unfortunately, screen doesn’t save all the output, so this is a short one. I should have used screen -L to save the complete log. Noted for next time, since the installation did again not work. On the positive side, I’ve seen this error before, so maybe I’m close…
cd deps/jemalloc/
git pull origin master
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
OK, that is new. I’ll remove the directory and clone from GitHub.
cd ../
rm -r jemallock/
git clone git@github.com:jemalloc/jemalloc.git
cd jemalloc/
./autogen.sh
make
make install
sudo make install
-> click here for the output of the above commands <-
autoconf
./configure --enable-autogen
checking for xsltproc... /usr/bin/miniconda3/bin/xsltproc
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether compiler is cray... no
checking whether compiler supports -std=gnu11... yes
checking whether compiler supports -Wall... yes
checking whether compiler supports -Wextra... yes
checking whether compiler supports -Wshorten-64-to-32... no
checking whether compiler supports -Wsign-compare... yes
checking whether compiler supports -Wundef... yes
checking whether compiler supports -Wno-format-zero-length... yes
checking whether compiler supports -Wpointer-arith... yes
checking whether compiler supports -Wno-missing-braces... yes
checking whether compiler supports -pipe... yes
checking whether compiler supports -g3... yes
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... no
checking whether g++ supports C++17 features with +std=c++17... no
checking whether g++ supports C++17 features with -h std=c++17... no
checking whether g++ supports C++17 features with -std=c++1z... no
checking whether g++ supports C++17 features with +std=c++1z... no
checking whether g++ supports C++17 features with -h std=c++1z... no
configure: No compiler with C++17 support was found
checking whether g++ supports C++14 features with -std=c++14... yes
checking whether compiler supports -Wall... yes
checking whether compiler supports -Wextra... yes
checking whether compiler supports -g3... yes
checking whether libstdc++ linkage is compilable... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking size of void *... 8
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of intmax_t... 8
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking whether pause instruction is compilable... yes
checking number of significant virtual address bits... 48
checking for ar... ar
checking for nm... nm
checking for gawk... gawk
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking whether malloc_usable_size definition can use const argument... no
checking for library containing log... -lm
checking whether __attribute__ syntax is compilable... yes
checking whether compiler supports -fvisibility=hidden... yes
checking whether compiler supports -fvisibility=hidden... yes
checking whether compiler supports -Werror... yes
checking whether compiler supports -herror_on_warning... no
checking whether tls_model attribute is compilable... yes
checking whether compiler supports -Werror... yes
checking whether compiler supports -herror_on_warning... no
checking whether alloc_size attribute is compilable... yes
checking whether compiler supports -Werror... yes
checking whether compiler supports -herror_on_warning... no
checking whether format(gnu_printf, ...) attribute is compilable... yes
checking whether compiler supports -Werror... yes
checking whether compiler supports -herror_on_warning... no
checking whether format(printf, ...) attribute is compilable... yes
checking whether compiler supports -Werror... yes
checking whether compiler supports -herror_on_warning... no
checking whether format(printf, ...) attribute is compilable... yes
checking whether compiler supports -Wimplicit-fallthrough... no
checking whether fallthrough attribute is compilable... no
checking for a BSD-compatible install... /usr/bin/miniconda3/bin/install -c
checking for ranlib... ranlib
checking for ld... /usr/bin/ld
checking for autoconf... /usr/bin/autoconf
checking for memalign... yes
checking for valloc... yes
checking for __libc_calloc... yes
checking for __libc_free... yes
checking for __libc_malloc... yes
checking for __libc_memalign... yes
checking for __libc_realloc... yes
checking for __libc_valloc... yes
checking for __posix_memalign... no
checking whether compiler supports -O3... yes
checking whether compiler supports -O3... yes
checking whether compiler supports -funroll-loops... yes
checking configured backtracing method... N/A
checking for sbrk... yes
checking whether utrace(2) is compilable... no
checking whether a program using __builtin_unreachable is compilable... yes
checking whether a program using __builtin_ffsl is compilable... yes
checking whether a program using __builtin_popcountl is compilable... yes
checking LG_PAGE... 12
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for pthread_create in -lpthread... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for dlsym... no
checking for dlsym in -ldl... yes
checking whether pthread_atfork(3) is compilable... yes
checking whether pthread_setname_np(3) is compilable... yes
checking for library containing clock_gettime... none required
checking whether clock_gettime(CLOCK_MONOTONIC_COARSE, ...) is compilable... yes
checking whether clock_gettime(CLOCK_MONOTONIC, ...) is compilable... yes
checking whether mach_absolute_time() is compilable... no
checking whether compiler supports -Werror... yes
checking whether syscall(2) is compilable... yes
checking for secure_getenv... yes
checking for sched_getcpu... yes
checking for sched_setaffinity... yes
checking for issetugid... no
checking for _malloc_thread_cleanup... no
checking for _pthread_mutex_init_calloc_cb... no
checking for TLS... yes
checking whether C11 atomics is compilable... yes
checking whether GCC __atomic atomics is compilable... yes
checking whether GCC 8-bit __atomic atomics is compilable... yes
checking whether GCC __sync atomics is compilable... yes
checking whether GCC 8-bit __sync atomics is compilable... yes
checking whether Darwin OSAtomic*() is compilable... no
checking whether madvise(2) is compilable... yes
checking whether madvise(..., MADV_FREE) is compilable... no
checking whether madvise(..., MADV_DONTNEED) is compilable... yes
checking whether madvise(..., MADV_DO[NT]DUMP) is compilable... yes
checking whether madvise(..., MADV_[NO]HUGEPAGE) is compilable... yes
checking for __builtin_clz... yes
checking whether Darwin os_unfair_lock_*() is compilable... no
checking whether glibc malloc hook is compilable... yes
checking whether glibc memalign hook is compilable... yes
checking whether pthreads adaptive mutexes is compilable... yes
checking whether compiler supports -D_GNU_SOURCE... yes
checking whether compiler supports -Werror... yes
checking whether compiler supports -herror_on_warning... no
checking whether strerror_r returns char with gnu source is compilable... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating jemalloc.pc
config.status: creating doc/html.xsl
config.status: creating doc/manpages.xsl
config.status: creating doc/jemalloc.xml
config.status: creating include/jemalloc/jemalloc_macros.h
config.status: creating include/jemalloc/jemalloc_protos.h
config.status: creating include/jemalloc/jemalloc_typedefs.h
config.status: creating include/jemalloc/internal/jemalloc_preamble.h
config.status: creating test/test.sh
config.status: creating test/include/test/jemalloc_test.h
config.status: creating config.stamp
config.status: creating bin/jemalloc-config
config.status: creating bin/jemalloc.sh
config.status: creating bin/jeprof
config.status: creating include/jemalloc/jemalloc_defs.h
config.status: creating include/jemalloc/internal/jemalloc_internal_defs.h
config.status: creating test/include/test/jemalloc_test_defs.h
config.status: executing include/jemalloc/internal/public_symbols.txt commands
config.status: executing include/jemalloc/internal/private_symbols.awk commands
config.status: executing include/jemalloc/internal/private_symbols_jet.awk commands
config.status: executing include/jemalloc/internal/public_namespace.h commands
config.status: executing include/jemalloc/internal/public_unnamespace.h commands
config.status: executing include/jemalloc/jemalloc_protos_jet.h commands
config.status: executing include/jemalloc/jemalloc_rename.h commands
config.status: executing include/jemalloc/jemalloc_mangle.h commands
config.status: executing include/jemalloc/jemalloc_mangle_jet.h commands
config.status: executing include/jemalloc/jemalloc.h commands
===============================================================================
jemalloc version : 5.2.1-266-gccdc70a5ce7b9dd723d947025f99006e7e78d17e
library revision : 2
CONFIG : --enable-autogen
CC : gcc
CONFIGURE_CFLAGS : -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops
SPECIFIED_CFLAGS :
EXTRA_CFLAGS :
CPPFLAGS : -D_GNU_SOURCE -D_REENTRANT
CXX : g++ -std=c++14
CONFIGURE_CXXFLAGS : -Wall -Wextra -g3 -fvisibility=hidden -O3
SPECIFIED_CXXFLAGS :
EXTRA_CXXFLAGS :
LDFLAGS :
EXTRA_LDFLAGS :
DSO_LDFLAGS : -shared -Wl,-soname,$(@F)
LIBS : -lm -lstdc++ -pthread -ldl
RPATH_EXTRA :
XSLTPROC : /usr/bin/miniconda3/bin/xsltproc
XSLROOT : /usr/share/xml/docbook/stylesheet/docbook-xsl
PREFIX : /usr/local
BINDIR : /usr/local/bin
DATADIR : /usr/local/share
INCLUDEDIR : /usr/local/include
LIBDIR : /usr/local/lib
MANDIR : /usr/local/share/man
srcroot :
abs_srcroot : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/
objroot :
abs_objroot : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/
JEMALLOC_PREFIX :
JEMALLOC_PRIVATE_NAMESPACE
: je_
install_suffix :
malloc_conf :
documentation : 1
shared libs : 1
static libs : 1
autogen : 1
debug : 0
stats : 1
experimetal_smallocx : 0
prof : 0
prof-libunwind : 0
prof-libgcc : 0
prof-gcc : 0
fill : 1
utrace : 0
xmalloc : 0
log : 0
lazy_lock : 0
cache-oblivious : 1
cxx : 1
===============================================================================
spo12@CPI-SL64001:/data3/genome_graphs/vg-v1.22.0/deps/jemalloc$ make
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/jemalloc.sym.o src/jemalloc.c
nm -a src/jemalloc.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/jemalloc.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/arena.sym.o src/arena.c
nm -a src/arena.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/arena.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/background_thread.sym.o src/background_thread.c
nm -a src/background_thread.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/background_thread.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/base.sym.o src/base.c
nm -a src/base.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/base.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/bin.sym.o src/bin.c
nm -a src/bin.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/bin.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/bin_info.sym.o src/bin_info.c
nm -a src/bin_info.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/bin_info.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/bitmap.sym.o src/bitmap.c
nm -a src/bitmap.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/bitmap.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/buf_writer.sym.o src/buf_writer.c
nm -a src/buf_writer.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/buf_writer.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/cache_bin.sym.o src/cache_bin.c
nm -a src/cache_bin.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/cache_bin.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ckh.sym.o src/ckh.c
nm -a src/ckh.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ckh.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/counter.sym.o src/counter.c
nm -a src/counter.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/counter.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ctl.sym.o src/ctl.c
nm -a src/ctl.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ctl.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/div.sym.o src/div.c
nm -a src/div.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/div.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ecache.sym.o src/ecache.c
nm -a src/ecache.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ecache.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/edata.sym.o src/edata.c
nm -a src/edata.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/edata.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/edata_cache.sym.o src/edata_cache.c
nm -a src/edata_cache.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/edata_cache.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ehooks.sym.o src/ehooks.c
nm -a src/ehooks.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ehooks.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/emap.sym.o src/emap.c
nm -a src/emap.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/emap.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/eset.sym.o src/eset.c
nm -a src/eset.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/eset.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/extent.sym.o src/extent.c
nm -a src/extent.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/extent.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/extent_dss.sym.o src/extent_dss.c
nm -a src/extent_dss.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/extent_dss.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/extent_mmap.sym.o src/extent_mmap.c
nm -a src/extent_mmap.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/extent_mmap.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/hash.sym.o src/hash.c
nm -a src/hash.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/hash.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/hook.sym.o src/hook.c
nm -a src/hook.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/hook.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/inspect.sym.o src/inspect.c
nm -a src/inspect.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/inspect.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/large.sym.o src/large.c
nm -a src/large.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/large.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/log.sym.o src/log.c
nm -a src/log.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/log.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/malloc_io.sym.o src/malloc_io.c
nm -a src/malloc_io.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/malloc_io.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/mutex.sym.o src/mutex.c
nm -a src/mutex.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/mutex.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/mutex_pool.sym.o src/mutex_pool.c
nm -a src/mutex_pool.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/mutex_pool.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/nstime.sym.o src/nstime.c
nm -a src/nstime.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/nstime.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/pages.sym.o src/pages.c
nm -a src/pages.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/pages.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prng.sym.o src/prng.c
nm -a src/prng.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prng.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof.sym.o src/prof.c
nm -a src/prof.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof_data.sym.o src/prof_data.c
nm -a src/prof_data.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof_data.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof_log.sym.o src/prof_log.c
nm -a src/prof_log.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof_log.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof_recent.sym.o src/prof_recent.c
nm -a src/prof_recent.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof_recent.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/rtree.sym.o src/rtree.c
nm -a src/rtree.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/rtree.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/safety_check.sym.o src/safety_check.c
nm -a src/safety_check.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/safety_check.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/sc.sym.o src/sc.c
nm -a src/sc.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/sc.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/stats.sym.o src/stats.c
nm -a src/stats.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/stats.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/sz.sym.o src/sz.c
nm -a src/sz.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/sz.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/tcache.sym.o src/tcache.c
nm -a src/tcache.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/tcache.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/test_hooks.sym.o src/test_hooks.c
nm -a src/test_hooks.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/test_hooks.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/thread_event.sym.o src/thread_event.c
nm -a src/thread_event.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/thread_event.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ticker.sym.o src/ticker.c
nm -a src/ticker.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ticker.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/tsd.sym.o src/tsd.c
nm -a src/tsd.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/tsd.sym
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/witness.sym.o src/witness.c
nm -a src/witness.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/witness.sym
/bin/sh include/jemalloc/internal/private_namespace.sh src/jemalloc.sym src/arena.sym src/background_thread.sym src/base.sym src/bin.sym src/bin_info.sym src/bitmap.sym src/buf_writer.sym src/cache_bin.sym src/ckh.sym src/counter.sym src/ctl.sym src/div.sym src/ecache.sym src/edata.sym src/edata_cache.sym src/ehooks.sym src/emap.sym src/eset.sym src/extent.sym src/extent_dss.sym src/extent_mmap.sym src/hash.sym src/hook.sym src/inspect.sym src/large.sym src/log.sym src/malloc_io.sym src/mutex.sym src/mutex_pool.sym src/nstime.sym src/pages.sym src/prng.sym src/prof.sym src/prof_data.sym src/prof_log.sym src/prof_recent.sym src/rtree.sym src/safety_check.sym src/sc.sym src/stats.sym src/sz.sym src/tcache.sym src/test_hooks.sym src/thread_event.sym src/ticker.sym src/tsd.sym src/witness.sym > include/jemalloc/internal/private_namespace.gen.h
cp include/jemalloc/internal/private_namespace.gen.h include/jemalloc/internal/private_namespace.h
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc.pic.o src/jemalloc.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/arena.pic.o src/arena.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/background_thread.pic.o src/background_thread.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/base.pic.o src/base.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bin.pic.o src/bin.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bin_info.pic.o src/bin_info.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bitmap.pic.o src/bitmap.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/buf_writer.pic.o src/buf_writer.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/cache_bin.pic.o src/cache_bin.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ckh.pic.o src/ckh.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/counter.pic.o src/counter.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ctl.pic.o src/ctl.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/div.pic.o src/div.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ecache.pic.o src/ecache.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/edata.pic.o src/edata.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/edata_cache.pic.o src/edata_cache.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ehooks.pic.o src/ehooks.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/emap.pic.o src/emap.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/eset.pic.o src/eset.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent.pic.o src/extent.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent_dss.pic.o src/extent_dss.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent_mmap.pic.o src/extent_mmap.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hash.pic.o src/hash.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hook.pic.o src/hook.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/inspect.pic.o src/inspect.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/large.pic.o src/large.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/log.pic.o src/log.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/malloc_io.pic.o src/malloc_io.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex.pic.o src/mutex.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex_pool.pic.o src/mutex_pool.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/nstime.pic.o src/nstime.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/pages.pic.o src/pages.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prng.pic.o src/prng.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof.pic.o src/prof.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_data.pic.o src/prof_data.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_log.pic.o src/prof_log.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_recent.pic.o src/prof_recent.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/rtree.pic.o src/rtree.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/safety_check.pic.o src/safety_check.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/sc.pic.o src/sc.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/stats.pic.o src/stats.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/sz.pic.o src/sz.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tcache.pic.o src/tcache.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/test_hooks.pic.o src/test_hooks.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/thread_event.pic.o src/thread_event.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ticker.pic.o src/ticker.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tsd.pic.o src/tsd.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/witness.pic.o src/witness.c
g++ -std=c++14 -Wall -Wextra -g3 -fvisibility=hidden -O3 -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc_cpp.pic.o src/jemalloc_cpp.cpp
gcc -shared -Wl,-soname,libjemalloc.so.2 -o lib/libjemalloc.so.2 src/jemalloc.pic.o src/arena.pic.o src/background_thread.pic.o src/base.pic.o src/bin.pic.o src/bin_info.pic.o src/bitmap.pic.o src/buf_writer.pic.o src/cache_bin.pic.o src/ckh.pic.o src/counter.pic.o src/ctl.pic.o src/div.pic.o src/ecache.pic.o src/edata.pic.o src/edata_cache.pic.o src/ehooks.pic.o src/emap.pic.o src/eset.pic.o src/extent.pic.o src/extent_dss.pic.o src/extent_mmap.pic.o src/hash.pic.o src/hook.pic.o src/inspect.pic.o src/large.pic.o src/log.pic.o src/malloc_io.pic.o src/mutex.pic.o src/mutex_pool.pic.o src/nstime.pic.o src/pages.pic.o src/prng.pic.o src/prof.pic.o src/prof_data.pic.o src/prof_log.pic.o src/prof_recent.pic.o src/rtree.pic.o src/safety_check.pic.o src/sc.pic.o src/stats.pic.o src/sz.pic.o src/tcache.pic.o src/test_hooks.pic.o src/thread_event.pic.o src/ticker.pic.o src/tsd.pic.o src/witness.pic.o src/jemalloc_cpp.pic.o -lm -lstdc++ -pthread -ldl
ln -sf libjemalloc.so.2 lib/libjemalloc.so
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc.o src/jemalloc.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/arena.o src/arena.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/background_thread.o src/background_thread.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/base.o src/base.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bin.o src/bin.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bin_info.o src/bin_info.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bitmap.o src/bitmap.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/buf_writer.o src/buf_writer.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/cache_bin.o src/cache_bin.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ckh.o src/ckh.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/counter.o src/counter.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ctl.o src/ctl.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/div.o src/div.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ecache.o src/ecache.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/edata.o src/edata.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/edata_cache.o src/edata_cache.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ehooks.o src/ehooks.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/emap.o src/emap.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/eset.o src/eset.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent.o src/extent.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent_dss.o src/extent_dss.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent_mmap.o src/extent_mmap.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hash.o src/hash.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hook.o src/hook.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/inspect.o src/inspect.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/large.o src/large.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/log.o src/log.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/malloc_io.o src/malloc_io.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex.o src/mutex.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex_pool.o src/mutex_pool.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/nstime.o src/nstime.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/pages.o src/pages.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prng.o src/prng.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof.o src/prof.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_data.o src/prof_data.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_log.o src/prof_log.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_recent.o src/prof_recent.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/rtree.o src/rtree.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/safety_check.o src/safety_check.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/sc.o src/sc.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/stats.o src/stats.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/sz.o src/sz.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tcache.o src/tcache.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/test_hooks.o src/test_hooks.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/thread_event.o src/thread_event.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ticker.o src/ticker.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tsd.o src/tsd.c
gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/witness.o src/witness.c
g++ -std=c++14 -Wall -Wextra -g3 -fvisibility=hidden -O3 -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc_cpp.o src/jemalloc_cpp.cpp
ar crus lib/libjemalloc.a src/jemalloc.o src/arena.o src/background_thread.o src/base.o src/bin.o src/bin_info.o src/bitmap.o src/buf_writer.o src/cache_bin.o src/ckh.o src/counter.o src/ctl.o src/div.o src/ecache.o src/edata.o src/edata_cache.o src/ehooks.o src/emap.o src/eset.o src/extent.o src/extent_dss.o src/extent_mmap.o src/hash.o src/hook.o src/inspect.o src/large.o src/log.o src/malloc_io.o src/mutex.o src/mutex_pool.o src/nstime.o src/pages.o src/prng.o src/prof.o src/prof_data.o src/prof_log.o src/prof_recent.o src/rtree.o src/safety_check.o src/sc.o src/stats.o src/sz.o src/tcache.o src/test_hooks.o src/thread_event.o src/ticker.o src/tsd.o src/witness.o src/jemalloc_cpp.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar crus lib/libjemalloc_pic.a src/jemalloc.pic.o src/arena.pic.o src/background_thread.pic.o src/base.pic.o src/bin.pic.o src/bin_info.pic.o src/bitmap.pic.o src/buf_writer.pic.o src/cache_bin.pic.o src/ckh.pic.o src/counter.pic.o src/ctl.pic.o src/div.pic.o src/ecache.pic.o src/edata.pic.o src/edata_cache.pic.o src/ehooks.pic.o src/emap.pic.o src/eset.pic.o src/extent.pic.o src/extent_dss.pic.o src/extent_mmap.pic.o src/hash.pic.o src/hook.pic.o src/inspect.pic.o src/large.pic.o src/log.pic.o src/malloc_io.pic.o src/mutex.pic.o src/mutex_pool.pic.o src/nstime.pic.o src/pages.pic.o src/prng.pic.o src/prof.pic.o src/prof_data.pic.o src/prof_log.pic.o src/prof_recent.pic.o src/rtree.pic.o src/safety_check.pic.o src/sc.pic.o src/stats.pic.o src/sz.pic.o src/tcache.pic.o src/test_hooks.pic.o src/thread_event.pic.o src/ticker.pic.o src/tsd.pic.o src/witness.pic.o src/jemalloc_cpp.pic.o
ar: `u' modifier ignored since `D' is the default (see `U')
spo12@CPI-SL64001:/data3/genome_graphs/vg-v1.22.0/deps/jemalloc$ make install
/usr/bin/miniconda3/bin/install -c -d /usr/local/bin
/usr/bin/miniconda3/bin/install -c -m 755 bin/jemalloc-config /usr/local/bin
/usr/bin/miniconda3/bin/install: cannot create regular file '/usr/local/bin/jemalloc-config': Permission denied
/usr/bin/miniconda3/bin/install -c -m 755 bin/jemalloc.sh /usr/local/bin
/usr/bin/miniconda3/bin/install: cannot create regular file '/usr/local/bin/jemalloc.sh': Permission denied
/usr/bin/miniconda3/bin/install -c -m 755 bin/jeprof /usr/local/bin
/usr/bin/miniconda3/bin/install: cannot create regular file '/usr/local/bin/jeprof': Permission denied
Makefile:487: recipe for target 'install_bin' failed
make: *** [install_bin] Error 1
spo12@CPI-SL64001:/data3/genome_graphs/vg-v1.22.0/deps/jemalloc$ sudo make install
[sudo] password for spo12:
/usr/bin/miniconda3/bin/install -c -d /usr/local/bin
/usr/bin/miniconda3/bin/install -c -m 755 bin/jemalloc-config /usr/local/bin
/usr/bin/miniconda3/bin/install -c -m 755 bin/jemalloc.sh /usr/local/bin
/usr/bin/miniconda3/bin/install -c -m 755 bin/jeprof /usr/local/bin
/usr/bin/miniconda3/bin/install -c -d /usr/local/include/jemalloc
/usr/bin/miniconda3/bin/install -c -m 644 include/jemalloc/jemalloc.h /usr/local/include/jemalloc
/usr/bin/miniconda3/bin/install -c -d /usr/local/lib
/usr/bin/miniconda3/bin/install -c -m 755 lib/libjemalloc.so.2 /usr/local/lib
ln -sf libjemalloc.so.2 /usr/local/lib/libjemalloc.so
/usr/bin/miniconda3/bin/install -c -d /usr/local/lib
/usr/bin/miniconda3/bin/install -c -m 755 lib/libjemalloc.a /usr/local/lib
/usr/bin/miniconda3/bin/install -c -m 755 lib/libjemalloc_pic.a /usr/local/lib
/usr/bin/miniconda3/bin/install -c -d /usr/local/lib/pkgconfig
/usr/bin/miniconda3/bin/install -c -m 644 jemalloc.pc /usr/local/lib/pkgconfig
/usr/bin/miniconda3/bin/xsltproc -o doc/jemalloc.html doc/html.xsl doc/jemalloc.xml
/usr/bin/miniconda3/bin/xsltproc -o doc/jemalloc.3 doc/manpages.xsl doc/jemalloc.xml
Note: Writing jemalloc.3
/usr/bin/miniconda3/bin/install -c -d /usr/local/share/doc/jemalloc
/usr/bin/miniconda3/bin/install -c -m 644 doc/jemalloc.html /usr/local/share/doc/jemalloc
/usr/bin/miniconda3/bin/install -c -d /usr/local/share/man/man3
/usr/bin/miniconda3/bin/install -c -m 644 doc/jemalloc.3 /usr/local/share/man/man3
I’m not sure if using sudo here was a good idea, but we’ll see…
cd ../../
. ./source_me.sh && make
-> click here for the final make results <-
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/main.o src/main.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/path.o src/path.cpp
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/path.cpp:2:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Path]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Path; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Path; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Path; std::istream = std::basic_istream<char>]’
src/path.cpp:116:32: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/path.hpp:11,
from src/path.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/readfilter.o src/readfilter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/snarls.o src/snarls.cpp
In file included from src/snarls.hpp:18:0,
from src/snarls.cpp:8:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Snarl]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Snarl; std::istream = std::basic_istream<char>]’
src/snarls.cpp:601:49: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/message_emitter.hpp:18:0,
from /data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_emitter.hpp:18,
from src/snarls.hpp:17,
from src/snarls.cpp:8:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/mapper.o src/mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/utility.o src/utility.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/variant_adder.o src/variant_adder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/region_expander.o src/region_expander.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/genotyper.o src/genotyper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/packer.o src/packer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/filter.o src/filter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/graph_caller.o src/graph_caller.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/traversal_support.o src/traversal_support.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/aligner.o src/aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/alignment_emitter.o src/alignment_emitter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/viz.o src/viz.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/haplotypes.o src/haplotypes.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/prune.o src/prune.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/ssw_aligner.o src/ssw_aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/reverse_graph.o src/reverse_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/alignment.o src/alignment.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/extra_node_graph.o src/extra_node_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/variant_recall.o src/variant_recall.cpp
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/variant_recall.hpp:16,
from src/variant_recall.cpp:2:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Alignment]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
src/variant_recall.cpp:353:45: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/variant_recall.hpp:15,
from src/variant_recall.cpp:2:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/edit.o src/edit.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/surjector.o src/surjector.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/gfa.o src/gfa.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/min_distance.o src/min_distance.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/phased_genome.o src/phased_genome.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/genome_state.o src/genome_state.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/gbwt_helper.o src/gbwt_helper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/vg.o src/vg.cpp
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/vg.cpp:1:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Graph]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Graph; std::istream = std::basic_istream<char>]’
src/vg.cpp:79:32: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/aligner.hpp:12,
from src/vg.hpp:20,
from src/vg.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/multipath_alignment.o src/multipath_alignment.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/translator.o src/translator.cpp
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/translator.hpp:16,
from src/translator.cpp:1:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Translation]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
src/translator.cpp:14:32: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/translator.hpp:15,
from src/translator.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/seed_clusterer.o src/seed_clusterer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/phase_unfolder.o src/phase_unfolder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/sampler.o src/sampler.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/multipath_mapper.o src/multipath_mapper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/vcf_buffer.o src/vcf_buffer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/build_index.o src/build_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/vg_set.o src/vg_set.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/transcriptome.o src/transcriptome.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/msa_converter.o src/msa_converter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/deconstructor.o src/deconstructor.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/gapless_extender.o src/gapless_extender.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/homogenizer.o src/homogenizer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/genotypekit.o src/genotypekit.cpp
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/genotypekit.hpp:19,
from src/genotypekit.cpp:1:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Translation]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Translation; std::istream = std::basic_istream<char>]’
src/genotypekit.cpp:291:37: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/genotypekit.hpp:18,
from src/genotypekit.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/genotypekit.hpp:19,
from src/genotypekit.cpp:1:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::LocationSupport]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::LocationSupport; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::LocationSupport; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::LocationSupport; std::istream = std::basic_istream<char>]’
src/genotypekit.cpp:334:37: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/genotypekit.hpp:18,
from src/genotypekit.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/srpe.o src/srpe.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/cluster.o src/cluster.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/kmer.o src/kmer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/traversal_finder.o src/traversal_finder.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/snarl_caller.o src/snarl_caller.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/split_strand_graph.o src/split_strand_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/path_index.o src/path_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/cactus.o src/cactus.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/convert_handle.o src/convert_handle.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/flow_sort.o src/flow_sort.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/augment.o src/augment.cpp
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:17:0,
from src/vg.hpp:29,
from src/augment.cpp:1:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Alignment]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:124:15: required from ‘vg::io::ProtobufIterator<T>::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:108:34: required from ‘void vg::io::for_each(std::istream&, const std::function<void(long int, T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
/data3/genome_graphs/vg-v1.22.0/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function<void(T&)>&) [with T = vg::Alignment; std::istream = std::basic_istream<char>]’
src/augment.cpp:38:54: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/aligner.hpp:12,
from src/vg.hpp:20,
from src/augment.cpp:1:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/index.o src/index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/vectorizer.o src/vectorizer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/position.o src/position.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/mem.o src/mem.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/statistics.o src/statistics.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/path_subgraph.o src/path_subgraph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/constructor.o src/constructor.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/indexed_vg.o src/indexed_vg.cpp
In file included from src/stream_index.hpp:17:0,
from src/indexed_vg.hpp:15,
from src/indexed_vg.cpp:6:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘void vg::io::ProtobufIterator<T>::fill_value() [with T = vg::Graph]’:
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:185:19: required from ‘bool vg::io::ProtobufIterator<T>::seek_group(int64_t) [with T = vg::Graph; int64_t = long int]’
src/indexed_vg.cpp:41:13: required from here
/data3/genome_graphs/vg-v1.22.0/include/vg/io/protobuf_iterator.hpp:240:40: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations]
coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE *
^
In file included from /data3/genome_graphs/vg-v1.22.0/include/vg/vg.pb.h:23:0,
from src/stream_index.hpp:16,
from src/indexed_vg.hpp:15,
from src/indexed_vg.cpp:6:
/usr/local/include/google/protobuf/io/coded_stream.h:397:8: note: declared here
void SetTotalBytesLimit(int total_bytes_limit, int) {
^
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/chunker.o src/chunker.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/stream_sorter.o src/stream_sorter.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/reverse_complement.o src/algorithms/reverse_complement.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/dijkstra.o src/algorithms/dijkstra.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/find_shortest_paths.o src/algorithms/find_shortest_paths.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/count_walks.o src/algorithms/count_walks.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/walk.o src/algorithms/walk.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/extend.o src/algorithms/extend.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/split_strands.o src/algorithms/split_strands.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/algorithms/topological_sort.o src/algorithms/topological_sort.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp
rm -f lib/libvg.a
ar rs lib/libvg.a obj/path.o obj/readfilter.o obj/graph.o obj/gff_reader.o obj/feature_set.o obj/snarls.o obj/version.o obj/mapper.o obj/utility.o obj/variant_adder.o obj/region_expander.o obj/genotyper.o obj/packer.o obj/filter.o obj/graph_caller.o obj/traversal_support.o obj/aligner.o obj/minimizer_mapper.o obj/subgraph_overlay.o obj/alignment_emitter.o obj/viz.o obj/haplotypes.o obj/region.o obj/prune.o obj/ssw_aligner.o obj/graph_synchronizer.o obj/reverse_graph.o obj/alignment.o obj/scanner.o obj/rare_variant_simplifier.o obj/stream_index.o obj/banded_global_aligner.o obj/subgraph.o obj/extra_node_graph.o obj/watchdog.o obj/name_mapper.o obj/variant_recall.o obj/edit.o obj/path_component_index.o obj/surjector.o obj/gfa.o obj/small_snarl_simplifier.o obj/min_distance.o obj/phased_genome.o obj/genome_state.o obj/gbwt_helper.o obj/funnel.o obj/vg.o obj/memoizing_graph.o obj/crash.o obj/multipath_alignment.o obj/translator.o obj/seed_clusterer.o obj/dagified_graph.o obj/option.o obj/source_sink_overlay.o obj/phase_unfolder.o obj/sampler.o obj/multipath_mapper.o obj/vcf_buffer.o obj/build_index.o obj/vg_set.o obj/transcriptome.o obj/msa_converter.o obj/deconstructor.o obj/nested_traversal_finder.o obj/progressive.o obj/gapless_extender.o obj/homogenizer.o obj/proto_handle_graph.o obj/preflight.o obj/genotypekit.o obj/srpe.o obj/cluster.o obj/mcmc_genotyper.o obj/kmer.o obj/traversal_finder.o obj/snarl_caller.o obj/split_strand_graph.o obj/memusage.o obj/benchmark.o obj/path_index.o obj/multipath_alignment_graph.o obj/cactus.o obj/convert_handle.o obj/flow_sort.o obj/augment.o obj/entropy.o obj/tree_subgraph.o obj/json2pb.o obj/index.o obj/xdrop_aligner.o obj/identity_overlay.o obj/vectorizer.o obj/position.o obj/mem.o obj/null_masking_graph.o obj/statistics.o obj/path_subgraph.o obj/constructor.o obj/haplotype_extracter.o obj/indexed_vg.o obj/chunker.o obj/stream_sorter.o obj/algorithms/is_single_stranded.o obj/algorithms/apply_bulk_modifications.o obj/algorithms/reverse_complement.o obj/algorithms/shortest_cycle.o obj/algorithms/dijkstra.o obj/algorithms/jump_along_path.o obj/algorithms/kmer.o obj/algorithms/dfs.o obj/algorithms/weakly_connected_components.o obj/algorithms/alignment_path_offsets.o obj/algorithms/coverage_depth.o obj/algorithms/remove_high_degree.o obj/algorithms/are_equivalent.o obj/algorithms/sorted_id_ranges.o obj/algorithms/copy_graph.o obj/algorithms/is_acyclic.o obj/algorithms/dagify.o obj/algorithms/find_shortest_paths.o obj/algorithms/normalize.o obj/algorithms/merge.o obj/algorithms/extract_extending_graph.o obj/algorithms/expand_context.o obj/algorithms/extract_containing_graph.o obj/algorithms/eades_algorithm.o obj/algorithms/to_gfa.o obj/algorithms/subgraph.o obj/algorithms/count_walks.o obj/algorithms/strongly_connected_components.o obj/algorithms/simplify_siblings.o obj/algorithms/approx_path_distance.o obj/algorithms/unchop.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/next_pos_chars.o obj/algorithms/walk.o obj/algorithms/path_string.o obj/algorithms/id_sort.o obj/algorithms/extend.o obj/algorithms/split_strands.o obj/algorithms/extract_connecting_graph.o obj/algorithms/topological_sort.o obj/algorithms/nearest_offsets_in_paths.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_xg.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_gcsa.o obj/io/register_libvg_io.o obj/io/load_proto_to_graph.o obj/progress_bar.o obj/sha1.o obj/Fasta.o
ar: creating lib/libvg.a
. ./source_me.sh && cd deps/jemalloc && ./autogen.sh && ./configure --disable-libdl --prefix=`pwd` && make && cp -r lib/* /data3/genome_graphs/vg-v1.22.0/lib/ && cp -r include/* /data3/genome_graphs/vg-v1.22.0/include/
autoconf
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configure: creating ./config.status
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===============================================================================
jemalloc version : 5.2.1-266-gccdc70a5ce7b9dd723d947025f99006e7e78d17e
library revision : 2
CONFIG : --enable-autogen CC=/usr/bin/gcc 'CFLAGS=-I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include ' CXX=/usr/bin/g++ 'CXXFLAGS=-I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2'
CC : /usr/bin/gcc
CONFIGURE_CFLAGS : -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops
SPECIFIED_CFLAGS : -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include
EXTRA_CFLAGS :
CPPFLAGS : -D_GNU_SOURCE -D_REENTRANT
CXX : /usr/bin/g++ -std=c++14
CONFIGURE_CXXFLAGS : -Wall -Wextra -g3 -fvisibility=hidden -O3
SPECIFIED_CXXFLAGS : -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2
EXTRA_CXXFLAGS :
LDFLAGS :
EXTRA_LDFLAGS :
DSO_LDFLAGS : -shared -Wl,-soname,$(@F)
LIBS : -lm -lstdc++ -pthread -ldl
RPATH_EXTRA :
XSLTPROC : /usr/bin/miniconda3/bin/xsltproc
XSLROOT : /usr/share/xml/docbook/stylesheet/docbook-xsl
PREFIX : /usr/local
BINDIR : /usr/local/bin
DATADIR : /usr/local/share
INCLUDEDIR : /usr/local/include
LIBDIR : /usr/local/lib
MANDIR : /usr/local/share/man
srcroot :
abs_srcroot : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/
objroot :
abs_objroot : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/
JEMALLOC_PREFIX :
JEMALLOC_PRIVATE_NAMESPACE
: je_
install_suffix :
malloc_conf :
documentation : 1
shared libs : 1
static libs : 1
autogen : 1
debug : 0
stats : 1
experimetal_smallocx : 0
prof : 0
prof-libunwind : 0
prof-libgcc : 0
prof-gcc : 0
fill : 1
utrace : 0
xmalloc : 0
log : 0
lazy_lock : 0
cache-oblivious : 1
cxx : 1
===============================================================================
checking for xsltproc... /usr/bin/miniconda3/bin/xsltproc
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
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checking whether compiler is cray... no
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checking whether compiler supports -Wshorten-64-to-32... no
checking whether compiler supports -Wsign-compare... yes
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checking whether compiler supports -Wno-format-zero-length... yes
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checking whether compiler supports -Wextra... yes
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checking whether byte ordering is bigendian... no
checking size of void *... 8
checking size of int... 4
checking size of long... 8
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checking size of intmax_t... 8
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
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checking malloc.h usability... yes
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config.status: executing include/jemalloc/internal/private_symbols_jet.awk commands
config.status: executing include/jemalloc/internal/public_namespace.h commands
config.status: executing include/jemalloc/internal/public_unnamespace.h commands
config.status: executing include/jemalloc/jemalloc_protos_jet.h commands
config.status: executing include/jemalloc/jemalloc_rename.h commands
config.status: executing include/jemalloc/jemalloc_mangle.h commands
config.status: executing include/jemalloc/jemalloc_mangle_jet.h commands
config.status: executing include/jemalloc/jemalloc.h commands
===============================================================================
jemalloc version : 5.2.1-266-gccdc70a5ce7b9dd723d947025f99006e7e78d17e
library revision : 2
CONFIG : --disable-libdl --prefix=/data3/genome_graphs/vg-v1.22.0/deps/jemalloc CC=/usr/bin/gcc 'CFLAGS=-I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include ' CXX=/usr/bin/g++ 'CXXFLAGS=-I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2'
CC : /usr/bin/gcc
CONFIGURE_CFLAGS : -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops
SPECIFIED_CFLAGS : -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include
EXTRA_CFLAGS :
CPPFLAGS : -D_GNU_SOURCE -D_REENTRANT
CXX : /usr/bin/g++ -std=c++14
CONFIGURE_CXXFLAGS : -Wall -Wextra -g3 -fvisibility=hidden -O3
SPECIFIED_CXXFLAGS : -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2
EXTRA_CXXFLAGS :
LDFLAGS :
EXTRA_LDFLAGS :
DSO_LDFLAGS : -shared -Wl,-soname,$(@F)
LIBS : -lm -lstdc++ -pthread
RPATH_EXTRA :
XSLTPROC : /usr/bin/miniconda3/bin/xsltproc
XSLROOT : /usr/share/xml/docbook/stylesheet/docbook-xsl
PREFIX : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc
BINDIR : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/bin
DATADIR : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/share
INCLUDEDIR : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/include
LIBDIR : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/lib
MANDIR : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/share/man
srcroot :
abs_srcroot : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/
objroot :
abs_objroot : /data3/genome_graphs/vg-v1.22.0/deps/jemalloc/
JEMALLOC_PREFIX :
JEMALLOC_PRIVATE_NAMESPACE
: je_
install_suffix :
malloc_conf :
documentation : 1
shared libs : 1
static libs : 1
autogen : 0
debug : 0
stats : 1
experimetal_smallocx : 0
prof : 0
prof-libunwind : 0
prof-libgcc : 0
prof-gcc : 0
fill : 1
utrace : 0
xmalloc : 0
log : 0
lazy_lock : 0
cache-oblivious : 1
cxx : 1
===============================================================================
make[1]: Entering directory '/data3/genome_graphs/vg-v1.22.0/deps/jemalloc'
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/jemalloc.sym.o src/jemalloc.c
nm -a src/jemalloc.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/jemalloc.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/arena.sym.o src/arena.c
nm -a src/arena.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/arena.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/background_thread.sym.o src/background_thread.c
nm -a src/background_thread.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/background_thread.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/base.sym.o src/base.c
nm -a src/base.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/base.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/bin.sym.o src/bin.c
nm -a src/bin.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/bin.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/bin_info.sym.o src/bin_info.c
nm -a src/bin_info.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/bin_info.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/bitmap.sym.o src/bitmap.c
nm -a src/bitmap.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/bitmap.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/buf_writer.sym.o src/buf_writer.c
nm -a src/buf_writer.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/buf_writer.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/cache_bin.sym.o src/cache_bin.c
nm -a src/cache_bin.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/cache_bin.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ckh.sym.o src/ckh.c
nm -a src/ckh.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ckh.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/counter.sym.o src/counter.c
nm -a src/counter.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/counter.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ctl.sym.o src/ctl.c
nm -a src/ctl.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ctl.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/div.sym.o src/div.c
nm -a src/div.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/div.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ecache.sym.o src/ecache.c
nm -a src/ecache.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ecache.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/edata.sym.o src/edata.c
nm -a src/edata.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/edata.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/edata_cache.sym.o src/edata_cache.c
nm -a src/edata_cache.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/edata_cache.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ehooks.sym.o src/ehooks.c
nm -a src/ehooks.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ehooks.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/emap.sym.o src/emap.c
nm -a src/emap.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/emap.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/eset.sym.o src/eset.c
nm -a src/eset.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/eset.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/extent.sym.o src/extent.c
nm -a src/extent.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/extent.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/extent_dss.sym.o src/extent_dss.c
nm -a src/extent_dss.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/extent_dss.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/extent_mmap.sym.o src/extent_mmap.c
nm -a src/extent_mmap.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/extent_mmap.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/hash.sym.o src/hash.c
nm -a src/hash.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/hash.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/hook.sym.o src/hook.c
nm -a src/hook.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/hook.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/inspect.sym.o src/inspect.c
nm -a src/inspect.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/inspect.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/large.sym.o src/large.c
nm -a src/large.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/large.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/log.sym.o src/log.c
nm -a src/log.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/log.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/malloc_io.sym.o src/malloc_io.c
nm -a src/malloc_io.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/malloc_io.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/mutex.sym.o src/mutex.c
nm -a src/mutex.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/mutex.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/mutex_pool.sym.o src/mutex_pool.c
nm -a src/mutex_pool.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/mutex_pool.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/nstime.sym.o src/nstime.c
nm -a src/nstime.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/nstime.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/pages.sym.o src/pages.c
nm -a src/pages.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/pages.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prng.sym.o src/prng.c
nm -a src/prng.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prng.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof.sym.o src/prof.c
nm -a src/prof.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof_data.sym.o src/prof_data.c
nm -a src/prof_data.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof_data.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof_log.sym.o src/prof_log.c
nm -a src/prof_log.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof_log.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/prof_recent.sym.o src/prof_recent.c
nm -a src/prof_recent.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/prof_recent.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/rtree.sym.o src/rtree.c
nm -a src/rtree.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/rtree.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/safety_check.sym.o src/safety_check.c
nm -a src/safety_check.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/safety_check.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/sc.sym.o src/sc.c
nm -a src/sc.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/sc.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/stats.sym.o src/stats.c
nm -a src/stats.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/stats.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/sz.sym.o src/sz.c
nm -a src/sz.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/sz.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/tcache.sym.o src/tcache.c
nm -a src/tcache.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/tcache.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/test_hooks.sym.o src/test_hooks.c
nm -a src/test_hooks.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/test_hooks.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/thread_event.sym.o src/thread_event.c
nm -a src/thread_event.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/thread_event.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/ticker.sym.o src/ticker.c
nm -a src/ticker.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/ticker.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/tsd.sym.o src/tsd.c
nm -a src/tsd.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/tsd.sym
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -DJEMALLOC_NO_PRIVATE_NAMESPACE -o src/witness.sym.o src/witness.c
nm -a src/witness.sym.o | gawk -f include/jemalloc/internal/private_symbols.awk > src/witness.sym
/bin/sh include/jemalloc/internal/private_namespace.sh src/jemalloc.sym src/arena.sym src/background_thread.sym src/base.sym src/bin.sym src/bin_info.sym src/bitmap.sym src/buf_writer.sym src/cache_bin.sym src/ckh.sym src/counter.sym src/ctl.sym src/div.sym src/ecache.sym src/edata.sym src/edata_cache.sym src/ehooks.sym src/emap.sym src/eset.sym src/extent.sym src/extent_dss.sym src/extent_mmap.sym src/hash.sym src/hook.sym src/inspect.sym src/large.sym src/log.sym src/malloc_io.sym src/mutex.sym src/mutex_pool.sym src/nstime.sym src/pages.sym src/prng.sym src/prof.sym src/prof_data.sym src/prof_log.sym src/prof_recent.sym src/rtree.sym src/safety_check.sym src/sc.sym src/stats.sym src/sz.sym src/tcache.sym src/test_hooks.sym src/thread_event.sym src/ticker.sym src/tsd.sym src/witness.sym > include/jemalloc/internal/private_namespace.gen.h
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc.pic.o src/jemalloc.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/arena.pic.o src/arena.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/background_thread.pic.o src/background_thread.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/base.pic.o src/base.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bin.pic.o src/bin.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bin_info.pic.o src/bin_info.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bitmap.pic.o src/bitmap.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/buf_writer.pic.o src/buf_writer.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/cache_bin.pic.o src/cache_bin.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ckh.pic.o src/ckh.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/counter.pic.o src/counter.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ctl.pic.o src/ctl.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/div.pic.o src/div.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ecache.pic.o src/ecache.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/edata.pic.o src/edata.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/edata_cache.pic.o src/edata_cache.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ehooks.pic.o src/ehooks.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/emap.pic.o src/emap.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/eset.pic.o src/eset.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent.pic.o src/extent.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent_dss.pic.o src/extent_dss.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent_mmap.pic.o src/extent_mmap.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hash.pic.o src/hash.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hook.pic.o src/hook.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/inspect.pic.o src/inspect.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/large.pic.o src/large.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/log.pic.o src/log.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/malloc_io.pic.o src/malloc_io.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -fPIC -DPIC -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex.pic.o src/mutex.c
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/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/malloc_io.o src/malloc_io.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex.o src/mutex.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex_pool.o src/mutex_pool.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/nstime.o src/nstime.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/pages.o src/pages.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prng.o src/prng.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof.o src/prof.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_data.o src/prof_data.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_log.o src/prof_log.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof_recent.o src/prof_recent.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/rtree.o src/rtree.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/safety_check.o src/safety_check.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/sc.o src/sc.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/stats.o src/stats.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/sz.o src/sz.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tcache.o src/tcache.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/test_hooks.o src/test_hooks.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/thread_event.o src/thread_event.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ticker.o src/ticker.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tsd.o src/tsd.c
/usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -pipe -g3 -fvisibility=hidden -O3 -funroll-loops -I /data3/genome_graphs/vg-v1.22.0/include -I /data3/genome_graphs/vg-v1.22.0/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/witness.o src/witness.c
/usr/bin/g++ -std=c++14 -Wall -Wextra -g3 -fvisibility=hidden -O3 -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc_cpp.o src/jemalloc_cpp.cpp
ar crus lib/libjemalloc.a src/jemalloc.o src/arena.o src/background_thread.o src/base.o src/bin.o src/bin_info.o src/bitmap.o src/buf_writer.o src/cache_bin.o src/ckh.o src/counter.o src/ctl.o src/div.o src/ecache.o src/edata.o src/edata_cache.o src/ehooks.o src/emap.o src/eset.o src/extent.o src/extent_dss.o src/extent_mmap.o src/hash.o src/hook.o src/inspect.o src/large.o src/log.o src/malloc_io.o src/mutex.o src/mutex_pool.o src/nstime.o src/pages.o src/prng.o src/prof.o src/prof_data.o src/prof_log.o src/prof_recent.o src/rtree.o src/safety_check.o src/sc.o src/stats.o src/sz.o src/tcache.o src/test_hooks.o src/thread_event.o src/ticker.o src/tsd.o src/witness.o src/jemalloc_cpp.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar crus lib/libjemalloc_pic.a src/jemalloc.pic.o src/arena.pic.o src/background_thread.pic.o src/base.pic.o src/bin.pic.o src/bin_info.pic.o src/bitmap.pic.o src/buf_writer.pic.o src/cache_bin.pic.o src/ckh.pic.o src/counter.pic.o src/ctl.pic.o src/div.pic.o src/ecache.pic.o src/edata.pic.o src/edata_cache.pic.o src/ehooks.pic.o src/emap.pic.o src/eset.pic.o src/extent.pic.o src/extent_dss.pic.o src/extent_mmap.pic.o src/hash.pic.o src/hook.pic.o src/inspect.pic.o src/large.pic.o src/log.pic.o src/malloc_io.pic.o src/mutex.pic.o src/mutex_pool.pic.o src/nstime.pic.o src/pages.pic.o src/prng.pic.o src/prof.pic.o src/prof_data.pic.o src/prof_log.pic.o src/prof_recent.pic.o src/rtree.pic.o src/safety_check.pic.o src/sc.pic.o src/stats.pic.o src/sz.pic.o src/tcache.pic.o src/test_hooks.pic.o src/thread_event.pic.o src/ticker.pic.o src/tsd.pic.o src/witness.pic.o src/jemalloc_cpp.pic.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/data3/genome_graphs/vg-v1.22.0/deps/jemalloc'
rm -f lib/vg_is_static
. ./source_me.sh && /usr/bin/g++ -I/data3/genome_graphs/vg-v1.22.0/include -I. -I/data3/genome_graphs/vg-v1.22.0/src -I/data3/genome_graphs/vg-v1.22.0/src/unittest -I/data3/genome_graphs/vg-v1.22.0/src/subcommand -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -I/data3/genome_graphs/vg-v1.22.0/include/sonLib -I/usr/local/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg-v1.22.0/include -I/data3/genome_graphs/vg-v1.22.0/include/dynamic -fopenmp -msse4.2 -o bin/vg obj/main.o obj/unittest/constructor.o obj/unittest/gapless_extender.o obj/unittest/haplotypes.o obj/unittest/snarls.o obj/unittest/mapper.o obj/unittest/tree_subgraph.o obj/unittest/dijkstra.o obj/unittest/cluster.o obj/unittest/overlays.o obj/unittest/vcf_buffer.o obj/unittest/handle.o obj/unittest/mcmc_genotyper.o obj/unittest/mapping.o obj/unittest/banded_global_aligner.o obj/unittest/cactus.o obj/unittest/random_graph.o obj/unittest/convert_handle.o obj/unittest/min_distance.o obj/unittest/distributions.o obj/unittest/dagify.o obj/unittest/flow_sort_test.o obj/unittest/driver.o obj/unittest/pinned_alignment.o obj/unittest/phased_genome.o obj/unittest/xdrop_aligner.o obj/unittest/genotypekit.o obj/unittest/gfa.o obj/unittest/stream.o obj/unittest/minimizer_mapper.o obj/unittest/position.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/mem.o obj/unittest/statistics.o obj/unittest/packed_graph.o obj/unittest/multipath_mapper.o obj/unittest/multipath_alignment.o obj/unittest/vpkg.o obj/unittest/chunker.o obj/unittest/xg.o obj/unittest/vg_algorithms.o obj/unittest/indexed_vg.o obj/unittest/readfilter.o obj/unittest/phase_unfolder.o obj/unittest/stream_index.o obj/unittest/hfile_cppstream.o obj/unittest/annotation.o obj/unittest/sampler.o obj/unittest/vg.o obj/unittest/source_sink_overlay.o obj/unittest/variant_adder.o obj/unittest/seed_clusterer.o obj/unittest/genotyper.o obj/unittest/alignment.o obj/unittest/dagified_graph.o obj/unittest/multipath_alignment_graph.o obj/unittest/hash_graph.o obj/unittest/feature_set.o obj/unittest/path_component_index.o obj/unittest/aligner.o obj/unittest/genome_state.o obj/unittest/srpe_filter.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/path_index.o obj/unittest/msa_converter.o obj/unittest/surject.o obj/unittest/packed_structs.o obj/subcommand/mod_main.o obj/subcommand/mcmc_main.o obj/subcommand/circularize_main.o obj/subcommand/help_main.o obj/subcommand/annotate_main.o obj/subcommand/depth_main.o obj/subcommand/version_main.o obj/subcommand/translate_main.o obj/subcommand/index_main.o obj/subcommand/bugs_main.o obj/subcommand/sort_main.o obj/subcommand/test_main.o obj/subcommand/pack_main.o obj/subcommand/filter_main.o obj/subcommand/add_main.o obj/subcommand/augment_main.o obj/subcommand/gaffe_main.o obj/subcommand/surject_main.o obj/subcommand/call_main.o obj/subcommand/genotype_main.o obj/subcommand/stats_main.o obj/subcommand/gamcompare_main.o obj/subcommand/concat_main.o obj/subcommand/kmers_main.o obj/subcommand/paths_main.o obj/subcommand/snarls_main.o obj/subcommand/srpe_main.o obj/subcommand/map_main.o obj/subcommand/locify_main.o obj/subcommand/msga_main.o obj/subcommand/ids_main.o obj/subcommand/prune_main.o obj/subcommand/align_main.o obj/subcommand/simplify_main.o obj/subcommand/minimizer_main.o obj/subcommand/mpmap_main.o obj/subcommand/rna_main.o obj/subcommand/explode_main.o obj/subcommand/subcommand.o obj/subcommand/view_main.o obj/subcommand/trace_main.o obj/subcommand/inject_main.o obj/subcommand/dotplot_main.o obj/subcommand/find_main.o obj/subcommand/sift_main.o obj/subcommand/vectorize_main.o obj/subcommand/gamsort_main.o obj/subcommand/compare_main.o obj/subcommand/deconstruct_main.o obj/subcommand/benchmark_main.o obj/subcommand/join_main.o obj/subcommand/gbwt_main.o obj/subcommand/construct_main.o obj/subcommand/chunk_main.o obj/subcommand/combine_main.o obj/subcommand/sim_main.o obj/subcommand/validate_main.o obj/subcommand/viz_main.o obj/subcommand/crash_main.o obj/subcommand/cluster_main.o obj/subcommand/convert_main.o obj/subcommand/recalibrate_main.o -lvg -L/data3/genome_graphs/vg-v1.22.0/lib /data3/genome_graphs/vg-v1.22.0/lib/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS /data3/genome_graphs/vg-v1.22.0/lib/libhts.a /data3/genome_graphs/vg-v1.22.0/lib/libdeflate.a -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -L/usr/local/lib -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -lexpat -lfreetype -lexpat -lfreetype -lz -lpng12 -lz -lm -lpng12 -lz -lm -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -Wl,-rpath,/data3/genome_graphs/vg-v1.22.0/lib -rdynamic -ldwfl -ldw -ldwelf -lelf -lebl -ldl -llzma -lrocksdb -ljemalloc -lpthread -lrt -lsnappy -lz -lbz2 -llz4 -lnuma
Done!
./bin/vg
vg: variation graph tool, version v1.22.0 "Rotella"
usage: ./bin/vg <command> [options]
main mapping and calling pipeline:
-- construct graph construction
-- index index graphs or alignments for random access or mapping
-- map MEM-based read alignment
-- augment augment a graph from an alignment
-- pack convert alignments to a compact coverage index
-- call call or genotype VCF variants
-- help show all subcommands
For more commands, type `vg help`.
For technical support, please visit: https://www.biostars.org/t/vg/
I will keep the old version of vg for now, just to be safe, and just remove the cloned repo that I couldn’t use. I will change the symbolic link, though, since I don’t expect that I’d want to keep using the old version (and even if, I’ll still have the executable).
cd ..
sudo rm -r vg-rotella/
rm vg-v1.22.0.tar.gz
sudo rm /usr/bin/vg
sudo ln -s /data3/genome_graphs/vg-v1.22.0/bin/vg /usr/bin/vg
vg
vg: variation graph tool, version v1.22.0 "Rotella"
usage: ./bin/vg <command> [options]
main mapping and calling pipeline:
-- construct graph construction
-- index index graphs or alignments for random access or mapping
-- map MEM-based read alignment
-- augment augment a graph from an alignment
-- pack convert alignments to a compact coverage index
-- call call or genotype VCF variants
-- help show all subcommands
For more commands, type `vg help`.
For technical support, please visit: https://www.biostars.org/t/vg/