collect2: error: ld returned 1 exit status

[mictadlo]

Hi, I have got collect2: error: ld returned 1 exit status by running ./configure --with-sparsehash=/home/lorencm/apps/ --with-bamtools=/home/lorencm/apps/bamtools --with-jemalloc=/home/lorencm/apps/ --prefix=/home/lorencm/apps/. Please find below few lines of configure output:

include -I/home/lorencm/apps/bamtools/include -I/home/lorencm/apps/bamtools/include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -std=c++98 -O3 -MT sga-haplotype-filter.o -MD -MP -MF .deps/sga-haplotype-filter.Tpo -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp
mv -f .deps/sga-haplotype-filter.Tpo .deps/sga-haplotype-filter.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/home/lorencm/apps//include -I/home/lorencm/apps/bamtools/include -I/home/lorencm/apps/bamtools/include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -std=c++98 -O3 -MT sga-OverlapCommon.o -MD -MP -MF .deps/sga-OverlapCommon.Tpo -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp
mv -f .deps/sga-OverlapCommon.Tpo .deps/sga-OverlapCommon.Po
g++ -Wall -Wextra  -Wno-unknown-pragmas -std=c++98 -O3 -pthread -fopenmp -Wl,-rpath,/home/lorencm/apps/ -L/home/lorencm/apps/ -Wl,-rpath,/home/lorencm/apps/bamtools/lib -L/home/lorencm/apps/bamtools/lib -Wl,-rpath,/home/lorencm/apps/bamtools/lib/bamtools -L/home/lorencm/apps/bamtools/lib/bamtools  -o sga sga-sga.o sga-index.o sga-overlap.o sga-assemble.o sga-correct.o sga-oview.o sga-preprocess.o sga-rmdup.o sga-merge.o sga-subgraph.o sga-scaffold.o sga-scaffold2fasta.o sga-connect.o sga-walk.o sga-filter.o sga-kmer-count.o sga-stats.o sga-fm-merge.o sga-gmap.o sga-filterBAM.o sga-cluster.o sga-gen-ssa.o sga-bwt2fa.o sga-graph-diff.o sga-graph-concordance.o sga-gapfill.o sga-preqc.o sga-overlap-long.o sga-variant-detectability.o sga-rewrite-evidence-bam.o sga-somatic-variant-filters.o sga-haplotype-filter.o sga-OverlapCommon.o ../Scaffold/libscaffold.a ../GraphDiff/libgraphdiff.a ../StringGraph/libstringgraph.a ../Concurrency/libconcurrency.a ../Algorithm/libalgorithm.a ../SuffixTools/libsuffixtools.a ../Bigraph/libbigraph.a ../Util/libutil.a ../SQG/libsqg.a ../Thirdparty/libthirdparty.a -lrt -lz  -lbamtools
sga-connect.o: In function `connectMain(int, char**)':
connect.cpp:(.text+0x1681): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
sga-filterBAM.o: In function `getErrorRate(BamTools::BamAlignment&)':
filterBAM.cpp:(.text+0x800): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const'
filterBAM.cpp:(.text+0x99b): undefined reference to `BamTools::BamAlignment::SetErrorString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
filterBAM.cpp:(.text+0xc57): undefined reference to `BamTools::BamAlignment::SetErrorString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
sga-filterBAM.o: In function `filterBAMMain(int, char**)':
filterBAM.cpp:(.text+0x1aea): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
filterBAM.cpp:(.text+0x1b1a): undefined reference to `BamTools::BamReader::GetHeaderText[abi:cxx11]() const'
filterBAM.cpp:(.text+0x1b2d): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)'
sga-rewrite-evidence-bam.o: In function `rewriteEvidenceBAMMain(int, char**)':
rewrite-evidence-bam.cpp:(.text+0x699): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
rewrite-evidence-bam.cpp:(.text+0x118d): undefined reference to `BamTools::BamReader::GetHeaderText[abi:cxx11]() const'
rewrite-evidence-bam.cpp:(.text+0x11a5): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)'
sga-somatic-variant-filters.o: In function `getVariantCoverage(BamTools::BamReader*, VCFRecord const&, ReadTable const*)':
somatic-variant-filters.cpp:(.text+0x3a8b): undefined reference to `BamTools::BamReader::GetReferenceID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
sga-somatic-variant-filters.o: In function `somaticVariantFiltersMain(int, char**)':
somatic-variant-filters.cpp:(.text+0x460f): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
somatic-variant-filters.cpp:(.text+0x4661): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
../GraphDiff/libgraphdiff.a(libgraphdiff_a-GraphCompare.o): In function `GraphCompareAggregateResults::GraphCompareAggregateResults(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, ReadTable const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
GraphCompare.cpp:(.text+0x255d): undefined reference to `BamTools::SamHeader::SamHeader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GraphCompare.cpp:(.text+0x2e26): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, BamTools::SamHeader const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)'
collect2: error: ld returned 1 exit status
make[2]: *** [sga] Error 1
make[2]: Leaving directory `/home/lorencm/apps/sga/src/SGA'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lorencm/apps/sga/src'
make: *** [all] Error 2

Did I do anything wrong?

Thank you in advance.

Mic

[walaj]

It looks like you are having trouble linking with BamTools. One thoughts is that this can happen if there is a mis-match between what the BamTools libraries were compiled with, and what SGA is compiled with. You might try recompiling bamtools and ensure it is the same compiler version used for building SGA.

Also make sure you have the libbamtools.so library where it thinks it should be.

[mictadlo]

Thank you. you were right.

[arjunud]

undefined reference to `log4cpp::Category::getInstance(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'

how to solve this//////////??