freebayes build

gistfile1.txt

$ make
cd ../bamtools && mkdir -p build && cd build && cmake .. && make
-- Configuring done
-- Generating done
-- Build files have been written to: /home/james/src/freebayes/bamtools/build
make[1]: Entering directory `/home/james/src/freebayes/bamtools/build'
make[2]: Entering directory `/home/james/src/freebayes/bamtools/build'
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[  0%] Exporting SharedHeaders
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[  1%] Built target SharedHeaders
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[  1%] Exporting APIHeaders
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[  2%] Built target APIHeaders
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
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make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
[  4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp: In member function ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const’:
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp:1769:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp: In member function ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const’:
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp:1856:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp: In member function ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const’:
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp:1944:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
[  5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[  7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
[  8%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
[ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
[ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BamHeader_p.cpp.o
[ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BamIndexFactory_p.cpp.o
[ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BamMultiReader_p.cpp.o
[ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BamRandomAccessController_p.cpp.o
[ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BamReader_p.cpp.o
[ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BamStandardIndex_p.cpp.o
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[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/BgzfStream_p.cpp.o
[ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/SamFormatParser_p.cpp.o
[ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/SamFormatPrinter_p.cpp.o
[ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/SamHeaderValidator_p.cpp.o
Linking CXX shared library ../../../lib/libbamtools.so
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build'
[ 36%] Built target BamTools
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build'
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
[ 37%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp: In member function ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const’:
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp:1769:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp: In member function ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const’:
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp:1856:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp: In member function ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const’:
/home/james/src/freebayes/bamtools/src/api/BamAlignment.cpp:1944:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
[ 39%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[ 40%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
[ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
[ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamHeader_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamIndexFactory_p.cpp.o
[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamMultiReader_p.cpp.o
[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamRandomAccessController_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamReader_p.cpp.o
[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamStandardIndex_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamToolsIndex_p.cpp.o
[ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BamWriter_p.cpp.o
[ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/BgzfStream_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/SamFormatParser_p.cpp.o
[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/SamFormatPrinter_p.cpp.o
[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/SamHeaderValidator_p.cpp.o
Linking CXX static library ../../../lib/libbamtools.a
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build'
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make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
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make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
[ 71%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
[ 72%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 73%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 75%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
Linking CXX shared library ../../../lib/libbamtools-utils.so
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build'
[ 75%] Built target BamTools-utils
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
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[ 76%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
[ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
[ 79%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
Linking CXX shared library ../../../../lib/libjsoncpp.so
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[ 79%] Built target jsoncpp
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
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make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
[ 81%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 82%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 84%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 85%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
/home/james/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp: In member function ‘const string BamTools::FilterTool::FilterToolPrivate::GetScriptContents()’:
/home/james/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:483:16: warning: converting ‘false’ to pointer type for argument 1 of ‘std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ [-Wconversion-null]
/home/james/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:499:20: warning: converting ‘false’ to pointer type for argument 1 of ‘std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ [-Wconversion-null]
/home/james/src/freebayes/bamtools/src/utils/bamtools_filter_ruleparser.h: In function ‘int BamTools::priority(const BamTools::RuleToken&)’:
/home/james/src/freebayes/bamtools/src/utils/bamtools_filter_ruleparser.h:59:1: warning: control reaches end of non-void function [-Wreturn-type]
[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
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[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
[ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
Linking CXX executable ../../../bin/bamtools
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build'
[100%] Built target bamtools_cmd
make[2]: Leaving directory `/home/james/src/freebayes/bamtools/build'
make[1]: Leaving directory `/home/james/src/freebayes/bamtools/build'
g++ -O3 -I../bamtools/src -c freebayes.cpp
g++ -O3 -I../bamtools/src -c BedReader.cpp
g++ -O3 -I../bamtools/src -c CNV.cpp
gcc -O3 -I../bamtools/src -c fastlz.c	
g++ -O3 -I../bamtools/src -c Fasta.cpp
g++ -O3 -I../bamtools/src -c Parameters.cpp
g++ -O3 -I../bamtools/src -c Allele.cpp
g++ -O3 -I../bamtools/src -c Sample.cpp
g++ -O3 -I../bamtools/src -c Result.cpp
g++ -O3 -I../bamtools/src -c AlleleParser.cpp
g++ -O3 -I../bamtools/src -c Utility.cpp
g++ -O3 -I../bamtools/src -c Genotype.cpp
g++ -O3 -I../bamtools/src -c DataLikelihood.cpp
g++ -O3 -I../bamtools/src -c Multinomial.cpp
g++ -O3 -I../bamtools/src -c Ewens.cpp
g++ -O3 -I../bamtools/src -c ResultData.cpp
g++ -O3 -I../bamtools/src -c Dirichlet.cpp
g++ -O3 -I../bamtools/src -c Marginals.cpp
g++ -O3 -I../bamtools/src -c split.cpp
g++ -O3 -I../bamtools/src -c LeftAlign.cpp
g++ -O3 -I../bamtools/src -c IndelAllele.cpp
g++    -c -o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/tabix.cpp
cd ../vcflib/tabixpp && make
make[1]: Entering directory `/home/james/src/freebayes/vcflib/tabixpp'
make[2]: Entering directory `/home/james/src/freebayes/vcflib/tabixpp'
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]
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  -lz -L. -ltabix
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  -o tabix++ main.cpp tabix.o bgzf.o -lm  -lz -L. -ltabix
make[2]: Leaving directory `/home/james/src/freebayes/vcflib/tabixpp'
make[1]: Leaving directory `/home/james/src/freebayes/vcflib/tabixpp'
cd ../vcflib/smithwaterman && make
make[1]: Entering directory `/home/james/src/freebayes/vcflib/smithwaterman'
g++    -c -o smithwaterman.o smithwaterman.cpp
g++    -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp
g++    -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp
  * linking smithwaterman
make[1]: Leaving directory `/home/james/src/freebayes/vcflib/smithwaterman'
g++ -O3 -I../bamtools/src -c ../vcflib/Variant.cpp
g++ -O3 -I../bamtools/src freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/bgzf.o ../vcflib/smithwaterman/SmithWatermanGotoh.o Variant.o ../bamtools/lib/libbamtools.a -o ../bin/freebayes -lz -lm -L./ -L../vcflib/tabixpp/ -L../bamtools/lib -ltabix
g++ -O3 -I../bamtools/src -c bamleftalign.cpp
g++ -O3 -I../bamtools/src bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o ../bamtools/lib/libbamtools.a -o ../bin/bamleftalign -lz -lm -L./ -L../vcflib/tabixpp/ -L../bamtools/lib -ltabix