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Last active August 29, 2015 14:16
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ekg/vg OSX installation issues
Raw
clone-and-make
Tue 19:54:39 ryan@mbp: c:master$ git clone --recursive https://github.com/ekg/vg.git
Cloning into 'vg'...
remote: Counting objects: 1925, done.
remote: Total 1925 (delta 0), reused 0 (delta 0), pack-reused 1925
Receiving objects: 100% (1925/1925), 2.73 MiB | 4.48 MiB/s, done.
Resolving deltas: 100% (1369/1369), done.
Checking connectivity... done.
Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'bash-tap'
Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'fastahack'
Submodule 'gssw' (https://github.com/ekg/gssw.git) registered for path 'gssw'
Submodule 'lru_cache' (https://github.com/ekg/lru_cache.git) registered for path 'lru_cache'
Submodule 'pb2json' (https://github.com/shafreeck/pb2json.git) registered for path 'pb2json'
Submodule 'progress_bar' (https://github.com/ekg/cpp_progress_bar.git) registered for path 'progress_bar'
Submodule 'rocksdb' (https://github.com/ekg/rocksdb.git) registered for path 'rocksdb'
Submodule 'snappy' (https://github.com/google/snappy.git) registered for path 'snappy'
Submodule 'sparsehash' (https://github.com/ekg/sparsehash.git) registered for path 'sparsehash'
Submodule 'vcflib' (https://github.com/ekg/vcflib.git) registered for path 'vcflib'
Cloning into 'bash-tap'...
remote: Counting objects: 49, done.
remote: Total 49 (delta 0), reused 0 (delta 0), pack-reused 49
Unpacking objects: 100% (49/49), done.
Checking connectivity... done.
Submodule path 'bash-tap': checked out 'c38fbfa401600cc81ccda66bfc0da3ea56288d03'
Cloning into 'fastahack'...
remote: Counting objects: 192, done.
remote: Total 192 (delta 0), reused 0 (delta 0), pack-reused 192
Receiving objects: 100% (192/192), 45.42 KiB | 0 bytes/s, done.
Resolving deltas: 100% (110/110), done.
Checking connectivity... done.
Submodule path 'fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
Cloning into 'gssw'...
remote: Counting objects: 1299, done.
remote: Total 1299 (delta 0), reused 0 (delta 0), pack-reused 1299
Receiving objects: 100% (1299/1299), 6.22 MiB | 4.36 MiB/s, done.
Resolving deltas: 100% (854/854), done.
Checking connectivity... done.
Submodule path 'gssw': checked out '5cbb27a77b535772132c09ee06f078ae3131e7c4'
Cloning into 'lru_cache'...
remote: Counting objects: 21, done.
remote: Total 21 (delta 0), reused 0 (delta 0), pack-reused 21
Unpacking objects: 100% (21/21), done.
Checking connectivity... done.
Submodule path 'lru_cache': checked out '4ee97e50baa89b16368096830cb1df738372e906'
Cloning into 'pb2json'...
remote: Counting objects: 154, done.
remote: Total 154 (delta 0), reused 0 (delta 0), pack-reused 154
Receiving objects: 100% (154/154), 21.45 KiB | 0 bytes/s, done.
Resolving deltas: 100% (78/78), done.
Checking connectivity... done.
Submodule path 'pb2json': checked out 'a0ad26a130c13866aff5b89b853c64e32fee6bf6'
Cloning into 'progress_bar'...
remote: Counting objects: 121, done.
remote: Total 121 (delta 0), reused 0 (delta 0), pack-reused 121
Receiving objects: 100% (121/121), 60.14 KiB | 0 bytes/s, done.
Resolving deltas: 100% (66/66), done.
Checking connectivity... done.
Submodule path 'progress_bar': checked out 'f5cc1d1a10c6c05f172717ddac545e6a6606f7d2'
Cloning into 'rocksdb'...
remote: Counting objects: 24888, done.
remote: Total 24888 (delta 0), reused 0 (delta 0), pack-reused 24888
Receiving objects: 100% (24888/24888), 42.15 MiB | 4.52 MiB/s, done.
Resolving deltas: 100% (18382/18382), done.
Checking connectivity... done.
Submodule path 'rocksdb': checked out 'e6eaf938c384d899374f4bab8852413b79dc0662'
Cloning into 'snappy'...
remote: Counting objects: 418, done.
remote: Total 418 (delta 0), reused 0 (delta 0), pack-reused 418
Receiving objects: 100% (418/418), 2.13 MiB | 0 bytes/s, done.
Resolving deltas: 100% (284/284), done.
Checking connectivity... done.
Submodule path 'snappy': checked out '1ff9be9b8fafc8528ca9e055646f5932aa5db9c4'
Cloning into 'sparsehash'...
remote: Counting objects: 1277, done.
remote: Total 1277 (delta 0), reused 0 (delta 0), pack-reused 1277
Receiving objects: 100% (1277/1277), 763.75 KiB | 0 bytes/s, done.
Resolving deltas: 100% (947/947), done.
Checking connectivity... done.
Submodule path 'sparsehash': checked out '80b55f9d0f194cdacd14d884336d06017e21fac2'
Cloning into 'vcflib'...
remote: Counting objects: 1647, done.
remote: Total 1647 (delta 0), reused 0 (delta 0), pack-reused 1647
Receiving objects: 100% (1647/1647), 1.09 MiB | 0 bytes/s, done.
Resolving deltas: 100% (947/947), done.
Checking connectivity... done.
Submodule path 'vcflib': checked out 'ce69f84cf5bd2e3231948048d6eb1695e1ad2118'
Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'fastahack'
Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp'
Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'fsom'
Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree'
Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'multichoose'
Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman'
Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'tabixpp'
Cloning into 'fastahack'...
remote: Counting objects: 192, done.
remote: Total 192 (delta 0), reused 0 (delta 0), pack-reused 192
Receiving objects: 100% (192/192), 45.42 KiB | 0 bytes/s, done.
Resolving deltas: 100% (110/110), done.
Checking connectivity... done.
Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
Cloning into 'filevercmp'...
remote: Counting objects: 22, done.
remote: Total 22 (delta 0), reused 0 (delta 0), pack-reused 22
Unpacking objects: 100% (22/22), done.
Checking connectivity... done.
Submodule path 'vcflib/filevercmp': checked out '1a9b779b93d0b244040274794d402106907b71b7'
Cloning into 'fsom'...
remote: Counting objects: 38, done.
remote: Total 38 (delta 0), reused 0 (delta 0), pack-reused 38
Unpacking objects: 100% (38/38), done.
Checking connectivity... done.
Submodule path 'vcflib/fsom': checked out 'a6ef318fbd347c53189384aef7f670c0e6ce89a3'
Cloning into 'intervaltree'...
remote: Counting objects: 86, done.
remote: Total 86 (delta 0), reused 0 (delta 0), pack-reused 86
Unpacking objects: 100% (86/86), done.
Checking connectivity... done.
Submodule path 'vcflib/intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4'
Cloning into 'multichoose'...
remote: Counting objects: 94, done.
remote: Total 94 (delta 0), reused 0 (delta 0), pack-reused 94
Unpacking objects: 100% (94/94), done.
Checking connectivity... done.
Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5'
Cloning into 'smithwaterman'...
remote: Counting objects: 287, done.
remote: Total 287 (delta 0), reused 0 (delta 0), pack-reused 287
Receiving objects: 100% (287/287), 84.91 KiB | 0 bytes/s, done.
Resolving deltas: 100% (186/186), done.
Checking connectivity... done.
Submodule path 'vcflib/smithwaterman': checked out '203218b47d45ac56ef234716f1bd4c741b289be1'
Cloning into 'tabixpp'...
remote: Counting objects: 70, done.
remote: Total 70 (delta 0), reused 0 (delta 0), pack-reused 70
Unpacking objects: 100% (70/70), done.
Checking connectivity... done.
Submodule path 'vcflib/tabixpp': checked out 'bbc63a49acc52212199f92e9e3b8fba0a593e3f7'
Tue 19:55:16 ryan@mbp: c:master$
Tue 19:56:08 ryan@mbp: c:master$
Tue 19:56:08 ryan@mbp: c:master$ cd vg
Tue 19:56:09 ryan@mbp: vg:master$ g++ --version
g++ (Homebrew gcc 4.9.2_1) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Tue 19:56:13 ryan@mbp: vg:master$ gcc --version
gcc (Homebrew gcc 4.9.2_1) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Tue 19:56:16 ryan@mbp: vg:master$ make
mkdir -p cpp
protoc vg.proto --cpp_out=cpp
cd gssw/src && /Applications/Xcode.app/Contents/Developer/usr/bin/make libgssw.a
gcc -Wall -O3 -msse2 -c -o gssw.o gssw.c
ar rvs libgssw.a gssw.o
ar: creating archive libgssw.a
a - gssw.o
g++ -std=c++11 -fopenmp -g -O3 -c -o gssw_aligner.o gssw_aligner.cpp -I./ -Ipb2json -Icpp -Ivcflib/src -Ivcflib -Ifastahack -Igssw/src -Irocksdb/include -Iprogress_bar -Isparsehash/build/include -Ilru_cache
cd vcflib && /Applications/Xcode.app/Contents/Developer/usr/bin/make libvcflib.a
cd tabixpp && /Applications/Xcode.app/Contents/Developer/usr/bin/make
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count, block_length = deflate_block(fp, 0);
^
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
ranlib libtabix.a
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o
gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o
gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
g++ -g -Wall -O2 -fPIC -c tabix.cpp
g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz
g++ -c -o src/Variant.o src/Variant.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64
g++ -c -o src/split.o src/split.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64
cd smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make
c++ -c -o smithwaterman.o smithwaterman.cpp
c++ -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp
c++ -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp
c++ -c -o Repeats.o Repeats.cpp
c++ -c -o LeftAlign.o LeftAlign.cpp
LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses]
&& (indel.insertion && indel.position == referenceSequence.size()
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning
&& (indel.insertion && indel.position == referenceSequence.size()
^
( )
1 warning generated.
c++ -c -o IndelAllele.o IndelAllele.cpp
g++ -c -o disorder.o disorder.c
* linking smithwaterman
ld: warning: option -s is obsolete and being ignored
ld: internal error: atom not found in symbolIndex(__ZNKSt3__16vectorINS_4pairIicEENS_9allocatorIS2_EEE8max_sizeEv) for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [smithwaterman] Error 1
make[1]: *** [smithwaterman/SmithWatermanGotoh.o] Error 2
make: *** [vcflib/libvcflib.a] Error 2
Raw
make-clean
Tue 19:57:05 ryan@mbp: vg:master$ make clean
rm -f vg
rm -f cpp/*
rm -f *.o
cd progress_bar && make clean
cd test && /Applications/Xcode.app/Contents/Developer/usr/bin/make clean
rm -f build_graph
cd pb2json && /Applications/Xcode.app/Contents/Developer/usr/bin/make clean
rm -f *.o *.so *.a test_pb2json
cd test && make clean
rm -f test_person test_json person.pb.cc person.pb.h dump
cd vcflib && /Applications/Xcode.app/Contents/Developer/usr/bin/make clean
rm -f bin/vcfecho 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/vcfsom 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/vcfinfosummarize src/Variant.o src/split.o
rm -f ssw_cpp.o ssw.o
rm -f libvcflib.a
cd tabixpp && make clean
rm -fr gmon.out *.o a.out *.dSYM tabix bgzip tabix++ *~ *.a tabix.aux tabix.log tabix.pdf *.class libtabix.*.dylib libtabix.so*
cd smithwaterman && make clean
Cleaning up.
cd fastahack && make clean
rm -f fastahack *.o
cd snappy && /Applications/Xcode.app/Contents/Developer/usr/bin/make clean
make[1]: *** No rule to make target `clean'. Stop.
make: *** [clean] Error 2
Raw
make-need-to-clean
Tue 19:56:38 ryan@mbp: vg:master$ make
cd vcflib && /Applications/Xcode.app/Contents/Developer/usr/bin/make libvcflib.a
cd fastahack && /Applications/Xcode.app/Contents/Developer/usr/bin/make
g++ -O3 -D_FILE_OFFSET_BITS=64 -c Fasta.cpp
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
cc -c -o src/ssw.o src/ssw.c
g++ -O3 -D_FILE_OFFSET_BITS=64 -c -o src/ssw_cpp.o src/ssw_cpp.cpp
cd fsom && g++ -O3 -D_FILE_OFFSET_BITS=64 -c fsom.c -lm
cd filevercmp && make
gcc -c filevercmp.c
gcc -o filevercmp main.c filevercmp.o
ar rvs libvcflib.a src/Variant.o src/split.o smithwaterman/sw.o fastahack/Fasta.o src/ssw.o src/ssw_cpp.o fsom/fsom.o filevercmp/filevercmp.o tabixpp/tabix.o tabixpp/bgzf.o tabixpp/index.o tabixpp/knetfile.o tabixpp/kstring.o
ar: creating archive libvcflib.a
a - src/Variant.o
a - src/split.o
a - smithwaterman/sw.o
ar: smithwaterman/sw.o: No such file or directory
a - fastahack/Fasta.o
a - src/ssw.o
a - src/ssw_cpp.o
a - fsom/fsom.o
a - filevercmp/filevercmp.o
a - tabixpp/tabix.o
a - tabixpp/bgzf.o
a - tabixpp/index.o
a - tabixpp/knetfile.o
a - tabixpp/kstring.o
make[1]: *** [libvcflib.a] Error 1
make: *** [vcflib/libvcflib.a] Error 2
Raw
make-pb2json
Tue 19:57:26 ryan@mbp: vg:master$ make
mkdir -p cpp
protoc vg.proto --cpp_out=cpp
g++ -std=c++11 -fopenmp -g -O3 -c -o gssw_aligner.o gssw_aligner.cpp -I./ -Ipb2json -Icpp -Ivcflib/src -Ivcflib -Ifastahack -Igssw/src -Irocksdb/include -Iprogress_bar -Isparsehash/build/include -Ilru_cache
cd vcflib && /Applications/Xcode.app/Contents/Developer/usr/bin/make libvcflib.a
cd tabixpp && /Applications/Xcode.app/Contents/Developer/usr/bin/make
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count, block_length = deflate_block(fp, 0);
^
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
ranlib libtabix.a
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o
gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o
gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
g++ -g -Wall -O2 -fPIC -c tabix.cpp
g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz
g++ -c -o src/Variant.o src/Variant.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64
g++ -c -o src/split.o src/split.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64
cd smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make
c++ -c -o smithwaterman.o smithwaterman.cpp
c++ -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp
c++ -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp
c++ -c -o Repeats.o Repeats.cpp
c++ -c -o LeftAlign.o LeftAlign.cpp
LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses]
&& (indel.insertion && indel.position == referenceSequence.size()
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning
&& (indel.insertion && indel.position == referenceSequence.size()
^
( )
1 warning generated.
c++ -c -o IndelAllele.o IndelAllele.cpp
g++ -c -o disorder.o disorder.c
* linking smithwaterman
ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o
cd fastahack && /Applications/Xcode.app/Contents/Developer/usr/bin/make
g++ -O3 -D_FILE_OFFSET_BITS=64 -c Fasta.cpp
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
ar rvs libvcflib.a src/Variant.o src/split.o smithwaterman/sw.o fastahack/Fasta.o src/ssw.o src/ssw_cpp.o fsom/fsom.o filevercmp/filevercmp.o tabixpp/tabix.o tabixpp/bgzf.o tabixpp/index.o tabixpp/knetfile.o tabixpp/kstring.o
ar: creating archive libvcflib.a
a - src/Variant.o
a - src/split.o
a - smithwaterman/sw.o
a - fastahack/Fasta.o
a - src/ssw.o
a - src/ssw_cpp.o
a - fsom/fsom.o
a - filevercmp/filevercmp.o
a - tabixpp/tabix.o
a - tabixpp/bgzf.o
a - tabixpp/index.o
a - tabixpp/knetfile.o
a - tabixpp/kstring.o
cd pb2json && /Applications/Xcode.app/Contents/Developer/usr/bin/make libpb2json.a
c++ -c -o pb2json.o pb2json.cpp
ar cr libpb2json.a pb2json.o
cd test && make -f Makefile
protoc --cpp_out=./ person.proto
g++ -g -o test_person test_person.cpp person.pb.cc -lprotobuf -lpthread
Undefined symbols for architecture x86_64:
"google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&))", referenced from:
protobuf_AddDesc_person_2eproto() in ccB5xx3E.o
"google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned char*)", referenced from:
Person_PhoneNumber::SerializeWithCachedSizesToArray(unsigned char*) const in ccB5xx3E.o
Person::SerializeWithCachedSizesToArray(unsigned char*) const in ccB5xx3E.o
"google::protobuf::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)", referenced from:
Person_PhoneNumber::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in ccB5xx3E.o
Person::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in ccB5xx3E.o
"google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::io::CodedOutputStream*)", referenced from:
Person_PhoneNumber::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in ccB5xx3E.o
Person::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in ccB5xx3E.o
"google::protobuf::DescriptorPool::FindFileByName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
protobuf_AssignDesc_person_2eproto() in ccB5xx3E.o
"google::protobuf::Message::SerializeToOstream(std::basic_ostream<char, std::char_traits<char> >*) const", referenced from:
_main in ccW1ghcy.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [test_person] Error 1
make[1]: *** [libpb2json.a] Error 2
make: *** [pb2json/libpb2json.a] Error 2
Raw
snappy-linker-errors
Tue 22:09:49 ryan@mbp: vg:master$ make
cd snappy && mkdir -p build && ./autogen.sh && ./configure --prefix=`pwd`/build/ && /Applications/Xcode.app/Contents/Developer/usr/bin/make && /Applications/Xcode.app/Contents/Developer/usr/bin/make install
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/local/Cellar/automake/1.14/share/automake-1.14/am/ltlibrary.am: warning: 'libsnappy.la': linking libtool libraries using a non-POSIX
/usr/local/Cellar/automake/1.14/share/automake-1.14/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/local/bin/ginstall -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/local/bin/gmkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-apple-darwin14.1.0
checking host system type... x86_64-apple-darwin14.1.0
checking how to print strings... printf
checking for style of include used by make... GNU
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 gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/local/bin/ggrep
checking for egrep... /usr/local/bin/ggrep -E
checking for fgrep... /usr/local/bin/ggrep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin14.1.0 file names to x86_64-apple-darwin14.1.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin14.1.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
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... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... 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 gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.1.0 dyld
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 for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.1.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether byte ordering is bigendian... no
checking for size_t... yes
checking for ssize_t... yes
checking for stdint.h... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking byteswap.h usability... no
checking byteswap.h presence... no
checking for byteswap.h... no
checking sys/byteswap.h usability... no
checking sys/byteswap.h presence... no
checking for sys/byteswap.h... no
checking sys/endian.h usability... no
checking sys/endian.h presence... no
checking for sys/endian.h... no
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for mmap... yes
checking for 'gtest-config'... checking for gtest-config... no
no
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for gflags... no
checking if the compiler supports __builtin_expect... yes
checking if the compiler supports __builtin_ctzll... yes
checking for zlibVersion in -lz... yes
checking for lzo1x_1_15_compress in -llzo2... no
checking for lzf_compress in -llzf... no
checking for fastlz_compress in -lfastlz... no
checking for qlz_compress in -lquicklz... no
checking that generated files are newer than configure... done
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
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c -o snappy.lo snappy.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c snappy.cc -fno-common -DPIC -o .libs/snappy.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -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/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-sinksource.lo -MD -MP -MF .deps/snappy-sinksource.Tpo -c -o snappy-sinksource.lo snappy-sinksource.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-sinksource.lo -MD -MP -MF .deps/snappy-sinksource.Tpo -c snappy-sinksource.cc -fno-common -DPIC -o .libs/snappy-sinksource.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -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/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -g -O2 -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: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-stubs-internal.lo -MD -MP -MF .deps/snappy-stubs-internal.Tpo -c snappy-stubs-internal.cc -fno-common -DPIC -o .libs/snappy-stubs-internal.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -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/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c -o snappy-c.lo snappy-c.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c snappy-c.cc -fno-common -DPIC -o .libs/snappy-c.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -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/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -version-info 3:1:2 -o libsnappy.la -rpath /Users/ryan/c/vg/snappy/build/lib snappy.lo snappy-sinksource.lo snappy-stubs-internal.lo snappy-c.lo
libtool: link: g++ -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libsnappy.1.dylib .libs/snappy.o .libs/snappy-sinksource.o .libs/snappy-stubs-internal.o .libs/snappy-c.o -g -O2 -install_name /Users/ryan/c/vg/snappy/build/lib/libsnappy.1.dylib -compatibility_version 4 -current_version 4.1 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libsnappy.dylib" && ln -s "libsnappy.1.dylib" "libsnappy.dylib")
libtool: link: ar cru .libs/libsnappy.a snappy.o snappy-sinksource.o snappy-stubs-internal.o snappy-c.o
libtool: link: ranlib .libs/libsnappy.a
libtool: link: ( cd ".libs" && rm -f "libsnappy.la" && ln -s "../libsnappy.la" "libsnappy.la" )
g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy_unittest-snappy_unittest.o -MD -MP -MF .deps/snappy_unittest-snappy_unittest.Tpo -c -o snappy_unittest-snappy_unittest.o `test -f 'snappy_unittest.cc' || echo './'`snappy_unittest.cc
mv -f .deps/snappy_unittest-snappy_unittest.Tpo .deps/snappy_unittest-snappy_unittest.Po
g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy_unittest-snappy-test.o -MD -MP -MF .deps/snappy_unittest-snappy-test.Tpo -c -o snappy_unittest-snappy-test.o `test -f 'snappy-test.cc' || echo './'`snappy-test.cc
mv -f .deps/snappy_unittest-snappy-test.Tpo .deps/snappy_unittest-snappy-test.Po
/bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -o snappy_unittest snappy_unittest-snappy_unittest.o snappy_unittest-snappy-test.o libsnappy.la -lz
/usr/local/bin/ggrep: warning: GREP_OPTIONS is deprecated; please use an alias or script
libtool: link: g++ -g -O2 -o .libs/snappy_unittest snappy_unittest-snappy_unittest.o snappy_unittest-snappy-test.o -Wl,-bind_at_load ./.libs/libsnappy.dylib -lz
/usr/local/bin/gmkdir -p '/Users/ryan/c/vg/snappy/build/lib'
/bin/sh ./libtool --mode=install /usr/local/bin/ginstall -c libsnappy.la '/Users/ryan/c/vg/snappy/build/lib'
libtool: install: /usr/local/bin/ginstall -c .libs/libsnappy.1.dylib /Users/ryan/c/vg/snappy/build/lib/libsnappy.1.dylib
libtool: install: (cd /Users/ryan/c/vg/snappy/build/lib && { ln -s -f libsnappy.1.dylib libsnappy.dylib || { rm -f libsnappy.dylib && ln -s libsnappy.1.dylib libsnappy.dylib; }; })
libtool: install: /usr/local/bin/ginstall -c .libs/libsnappy.lai /Users/ryan/c/vg/snappy/build/lib/libsnappy.la
libtool: install: /usr/local/bin/ginstall -c .libs/libsnappy.a /Users/ryan/c/vg/snappy/build/lib/libsnappy.a
libtool: install: chmod 644 /Users/ryan/c/vg/snappy/build/lib/libsnappy.a
libtool: install: ranlib /Users/ryan/c/vg/snappy/build/lib/libsnappy.a
/usr/local/bin/gmkdir -p '/Users/ryan/c/vg/snappy/build/share/doc/snappy'
/usr/local/bin/ginstall -c -m 644 ChangeLog COPYING INSTALL NEWS README format_description.txt framing_format.txt '/Users/ryan/c/vg/snappy/build/share/doc/snappy'
/usr/local/bin/gmkdir -p '/Users/ryan/c/vg/snappy/build/include'
/usr/local/bin/ginstall -c -m 644 snappy.h snappy-sinksource.h snappy-stubs-public.h snappy-c.h '/Users/ryan/c/vg/snappy/build/include'
cp snappy/build/lib/libsnappy.a snappy/
g++ -std=c++11 -fopenmp -g -O3 -o vg gssw_aligner.o vg.o cpp/vg.pb.o main.o index.o mapper.o region.o progress_bar/progress_bar.o vg_set.o utility.o path.o json.o -I./ -Ipb2json -Icpp -Ivcflib/src -Ivcflib -Ifastahack -Igssw/src -Irocksdb/include -Iprogress_bar -Isparsehash/build/include -Ilru_cache -L./ -Lpb2json -Lvcflib -Lgssw/src -Lsnappy -Lrocksdb -Lprogressbar -lpb2json -lvcflib -lgssw -lprotobuf -lpthread -ljansson -lncurses -lrocksdb -lsnappy -lz -lbz2
ld: warning: directory not found for option '-Lprogressbar'
Undefined symbols for architecture x86_64:
"CSmithWatermanGotoh::Align(unsigned int&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
vcf::Variant::parsedAlternates(bool, bool, bool, float, float, float, float, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) in libvcflib.a(Variant.o)
"google::protobuf::MessageLite::ParseFromString(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
bool stream::for_each<vg::Graph>(std::basic_istream<char, std::char_traits<char> >&, std::function<void (vg::Graph&)>&, std::function<void (unsigned long long)>&) in vg.o
vg::Index::parse_node(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long long&, vg::Node&) in index.o
vg::Index::parse_node_path(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long long&, long long&, long long&, vg::Mapping&) in index.o
vg::Index::parse_path_position(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long long&, long long&, long long&, vg::Mapping&) in index.o
vg::Index::get_node(long long, vg::Node&) in index.o
vg::Index::get_edge(long long, long long, vg::Edge&) in index.o
vg::Index::get_range(long long, long long, vg::VG&)::{lambda(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)#1}::operator()(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const in index.o
...
"google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&))", referenced from:
vg::protobuf_AddDesc_vg_2eproto() in vg.pb.o
"google::protobuf::io::CodedInputStream::ReadString(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)", referenced from:
bool stream::for_each<vg::Graph>(std::basic_istream<char, std::char_traits<char> >&, std::function<void (vg::Graph&)>&, std::function<void (unsigned long long)>&) in vg.o
bool stream::for_each<vg::Path>(std::basic_istream<char, std::char_traits<char> >&, std::function<void (vg::Path&)>&, std::function<void (unsigned long long)>&) in path.o
"google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned char*)", referenced from:
vg::KmerMatch::SerializeWithCachedSizesToArray(unsigned char*) const in vg.pb.o
vg::Edit::SerializeWithCachedSizesToArray(unsigned char*) const in vg.pb.o
vg::Path::SerializeWithCachedSizesToArray(unsigned char*) const in vg.pb.o
vg::Alignment::SerializeWithCachedSizesToArray(unsigned char*) const in vg.pb.o
vg::Edge::SerializeWithCachedSizesToArray(unsigned char*) const in vg.pb.o
vg::Node::SerializeWithCachedSizesToArray(unsigned char*) const in vg.pb.o
"google::protobuf::io::IstreamInputStream::IstreamInputStream(std::basic_istream<char, std::char_traits<char> >*, int)", referenced from:
bool stream::for_each<vg::Graph>(std::basic_istream<char, std::char_traits<char> >&, std::function<void (vg::Graph&)>&, std::function<void (unsigned long long)>&) in vg.o
bool stream::for_each<vg::Path>(std::basic_istream<char, std::char_traits<char> >&, std::function<void (vg::Path&)>&, std::function<void (unsigned long long)>&) in path.o
"google::protobuf::io::OstreamOutputStream::OstreamOutputStream(std::basic_ostream<char, std::char_traits<char> >*, int)", referenced from:
bool stream::write<vg::Graph>(std::basic_ostream<char, std::char_traits<char> >&, unsigned long long, std::function<vg::Graph (unsigned long long)>&) in vg.o
bool stream::write<vg::Path>(std::basic_ostream<char, std::char_traits<char> >&, unsigned long long, std::function<vg::Path (unsigned long long)>&) in path.o
"google::protobuf::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)", referenced from:
vg::KmerMatch::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
vg::Edit::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
vg::Node::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
vg::Path::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
vg::Alignment::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
"google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::io::CodedOutputStream*)", referenced from:
vg::Alignment::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
vg::Edge::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
vg::Node::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
"google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::io::CodedOutputStream*)", referenced from:
vg::Path::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
vg::Edit::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
vg::Alignment::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
vg::Node::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
vg::KmerMatch::SerializeWithCachedSizes(google::protobuf::io::CodedOutputStream*) const in vg.pb.o
"google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)", referenced from:
vg::Edge::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
vg::Node::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
vg::Alignment::MergePartialFromCodedStream(google::protobuf::io::CodedInputStream*) in vg.pb.o
"google::protobuf::MessageLite::SerializeToString(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*) const", referenced from:
bool stream::write<vg::Graph>(std::basic_ostream<char, std::char_traits<char> >&, unsigned long long, std::function<vg::Graph (unsigned long long)>&) in vg.o
std::_Function_handler<void (vg::Node*), vg::Index::load_graph(vg::VG&)::{lambda(vg::Node*)#1}>::_M_invoke(std::_Any_data const&, vg::Node*) in index.o
vg::Index::put_node(vg::Node const*) in index.o
vg::Index::batch_node(vg::Node const*, rocksdb::WriteBatch&) in index.o
vg::Index::put_edge(vg::Edge const*) in index.o
vg::Index::batch_edge(vg::Edge const*, rocksdb::WriteBatch&) in index.o
vg::Index::put_node_path(long long, long long, long long, vg::Mapping const&) in index.o
...
"google::protobuf::DescriptorPool::FindFileByName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
vg::protobuf_AssignDesc_vg_2eproto() in vg.pb.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::find(char const*, unsigned long, unsigned long) const", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::rfind(char const*, unsigned long, unsigned long) const", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::compare(char const*) const", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
countMismatches(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in libvcflib.a(sw.o)
"std::__1::__vector_base_common<true>::__throw_length_error() const", referenced from:
void std::__1::vector<float, std::__1::allocator<float> >::__push_back_slow_path<float const>(float const&) in libvcflib.a(sw.o)
void std::__1::vector<std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > >, std::__1::allocator<std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > > > >::__push_back_slow_path<std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > > const>(std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > > const&) in libvcflib.a(sw.o)
void std::__1::vector<std::__1::pair<int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > >::__push_back_slow_path<std::__1::pair<int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > const>(std::__1::pair<int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > const&) in libvcflib.a(sw.o)
void std::__1::vector<IndelAllele, std::__1::allocator<IndelAllele> >::__push_back_slow_path<IndelAllele const>(IndelAllele const&) in libvcflib.a(sw.o)
"std::__1::__vector_base_common<true>::__throw_out_of_range() const", referenced from:
std::__1::vector<std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > >, std::__1::allocator<std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > > > >::at(unsigned long) in libvcflib.a(sw.o)
std::__1::vector<float, std::__1::allocator<float> >::at(unsigned long) in libvcflib.a(sw.o)
"std::__1::__basic_string_common<true>::__throw_length_error() const", referenced from:
__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6__initIPcEENS_9enable_ifIXsr21__is_forward_iteratorIT_EE5valueEvE4typeES9_S9_ in libvcflib.a(sw.o)
"std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libvcflib.a(sw.o)
"std::__1::ios_base::getloc() const", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::at(unsigned long)", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
countMismatches(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(char const*, unsigned long)", referenced from:
pb2json(google::protobuf::Message*, char const*, int) in libpb2json.a(pb2json.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, IndelAllele const&) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(char const*, unsigned long, unsigned long)", referenced from:
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > std::__1::operator+<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > std::__1::operator+<char, std::__1::char_traits<char>, std::__1::allocator<char> >(char, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(unsigned long, char)", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::append(char const*, unsigned long)", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
joinCIGAR(std::__1::vector<std::__1::pair<int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > > const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > std::__1::operator+<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > std::__1::operator+<char, std::__1::char_traits<char>, std::__1::allocator<char> >(char, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::insert(unsigned long, char const*, unsigned long)", referenced from:
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::resize(unsigned long, char)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::reserve(unsigned long)", referenced from:
hex_encode(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libpb2json.a(pb2json.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::push_back(char)", referenced from:
hex_encode(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libpb2json.a(pb2json.o)
splitCIGAR(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
repeatCounts(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
splitCIGAR(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
countMismatches(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in libvcflib.a(sw.o)
std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int>::pair(std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> const&) in libvcflib.a(sw.o)
std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, int> > >::__construct_node_with_key(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long, std::__1::allocator<char> const&)", referenced from:
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
repeatCounts(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) in libvcflib.a(sw.o)
isRepeatUnit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_string()", referenced from:
hex_encode(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libpb2json.a(pb2json.o)
parse_msg(google::protobuf::Message const*) in libpb2json.a(pb2json.o)
pb2json(google::protobuf::Message*, char const*, int) in libpb2json.a(pb2json.o)
parse_repeated_field(google::protobuf::Message const*, google::protobuf::Reflection const*, google::protobuf::FieldDescriptor const*) in libpb2json.a(pb2json.o)
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
repeatCounts(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) in libvcflib.a(sw.o)
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::operator=(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
parse_msg(google::protobuf::Message const*) in libpb2json.a(pb2json.o)
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
repeatCounts(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
mergeCIGAR(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::put(char)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::flush()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::sentry(std::__1::basic_ostream<char, std::__1::char_traits<char> >&)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::~sentry()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(int)", referenced from:
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
operator<<(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned int)", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned long)", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::sync()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::uflow()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::setbuf(char*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsgetn(char*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsputn(char const*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::showmanyc()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::basic_streambuf()", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::~basic_streambuf()", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
"std::__1::cerr", referenced from:
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
leftAlign(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int&, bool) in libvcflib.a(sw.o)
"std::__1::cout", referenced from:
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
"std::__1::ctype<char>::id", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libvcflib.a(sw.o)
"std::__1::locale::~locale()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libvcflib.a(sw.o)
"std::__1::ios_base::__set_badbit_and_consider_rethrow()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
"std::__1::ios_base::init(void*)", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
"std::__1::ios_base::clear(unsigned int)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libvcflib.a(sw.o)
"std::__1::basic_ios<char, std::__1::char_traits<char> >::~basic_ios()", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
"typeinfo for std::__1::basic_ostream<char, std::__1::char_traits<char> >", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
typeinfo for std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"typeinfo for std::__1::basic_streambuf<char, std::__1::char_traits<char> >", referenced from:
typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"vtable for std::__1::ios_base", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
"vtable for std::__1::basic_ios<char, std::__1::char_traits<char> >", referenced from:
CBandedSmithWaterman::Traceback(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, unsigned int, unsigned int, unsigned int) in libvcflib.a(sw.o)
CSmithWatermanGotoh::Align(unsigned int&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libvcflib.a(sw.o)
operator<(IndelAllele const&, IndelAllele const&) in libvcflib.a(sw.o)
std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > convert<int>(int const&) in libvcflib.a(sw.o)
NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
"virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
"virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libvcflib.a(sw.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [vg] Error 1
Tue 22:10:12 ryan@mbp: vg:master$
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