=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. 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ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -MF 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ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o --- [ 4%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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/tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o -MF CMakeFiles/ngs.dir/CSRA1_Reference.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Reference.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/CSRA1_Reference.c --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o --- [ 6%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o --- [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- [ 7%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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/tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o --- [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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-I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o.d -o 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o --- [ 8%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/EBI_ReferenceSequence.c --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o --- [ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o --- [ 9%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/PileupEvent.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o --- [ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o --- [ 9%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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/tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o --- [ 9%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o --- [ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o -MF CMakeFiles/ngs.dir/SRA_Read.c.o.d -o CMakeFiles/ngs.dir/SRA_Read.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/SRA_Read.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o --- [ 10%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o --- [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include 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-Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT 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ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 12%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o --- [ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o --- [ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/SRA_ReferenceSequence.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o --- [ 12%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o -MF CMakeFiles/ngs.dir/NGS_Statistics.c.o.d -o CMakeFiles/ngs.dir/NGS_Statistics.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_Statistics.c --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/ReadGroup.cpp --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o --- [ 14%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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--- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 14%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -MF CMakeFiles/ngs.dir/NGS_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_PileupEvent.c --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 15%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/FragmentItf.cpp --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o --- [ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/ReadIterator.cpp --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o --- [ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o --- [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o -MF CMakeFiles/ngs.dir/NGS_Pileup.c.o.d -o CMakeFiles/ngs.dir/NGS_Pileup.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_Pileup.c --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o --- [ 16%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -MF CMakeFiles/ngs.dir/NGS_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_ReadGroup.c --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o --- [ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/StatisticsItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o --- [ 16%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- [ 16%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- [ 17%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Read.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/Read.cpp --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o --- [ 17%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PackageItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/PackageItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o --- [ 17%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o -MF CMakeFiles/ngs.dir/NGS_Reference.c.o.d -o CMakeFiles/ngs.dir/NGS_Reference.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_Reference.c --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o --- [ 17%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/FragmentIterator.cpp --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o --- [ 17%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 17%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- [ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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-Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StringItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/StringItf.cpp --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o --- [ 18%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o -MF CMakeFiles/ngs.dir/NGS_Read.c.o.d -o CMakeFiles/ngs.dir/NGS_Read.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_Read.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 19%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 20%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o -MF CMakeFiles/ngs-disp.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-disp.dir/Refcount.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/Refcount.cpp --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o --- [ 21%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/Statistics.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o --- [ 21%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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--- [ 21%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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-I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_Refcount.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o --- [ 21%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o -MF CMakeFiles/ngs.dir/NGS_Refcount.c.o.d -o CMakeFiles/ngs.dir/NGS_Refcount.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_Refcount.c --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 22%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o -MF CMakeFiles/ngs.dir/NGS_String.c.o.d -o CMakeFiles/ngs.dir/NGS_String.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/NGS_String.c --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- [ 22%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/StringRef.cpp --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- [ 22%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_StringItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 22%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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/tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o 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"CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- /usr/bin/ar qc ../../../../ilib/libngs-bind-python.a "CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- /usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- /usr/bin/ranlib ../../../../ilib/libngs-bind-python.a --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 25%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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CMakeFiles/ngs-disp.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../ilib/libngs-disp.a "CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "CMakeFiles/ngs-disp.dir/VTable.cpp.o" "CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" /usr/bin/ranlib ../../../ilib/libngs-disp.a [ 25%] Built target ngs-disp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o --- --- 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-Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/PileupItf.cpp --- libs/loader/CMakeFiles/loader.dir/all --- [ 26%] Building C object libs/loader/CMakeFiles/loader.dir/progressbar.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/FragmentBlobIterator.cpp --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o --- [ 32%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ReadGroupItf.cpp --- libs/loader/CMakeFiles/loader.dir/all --- --- libs/loader/CMakeFiles/loader.dir/mmarray.c.o --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o --- --- libs/loader/CMakeFiles/loader.dir/all --- [ 32%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/all --- --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o --- --- libs/loader/CMakeFiles/loader.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ReadItf.cpp --- libs/loader/CMakeFiles/loader.dir/all --- --- libs/loader/CMakeFiles/loader.dir/reference-writer.c.o --- [ 32%] Building C object libs/loader/CMakeFiles/loader.dir/reference-writer.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o -MF CMakeFiles/loader.dir/sequence-writer.c.o.d -o CMakeFiles/loader.dir/sequence-writer.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/sequence-writer.c --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- [ 33%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o --- [ 33%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/VdbReference.cpp --- libs/loader/CMakeFiles/loader.dir/all --- --- ilib/libloader.a --- [ 33%] Linking C static library ../../ilib/libloader.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /usr/pkg/bin/cmake -P CMakeFiles/loader.dir/cmake_clean_target.cmake cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/loader.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libloader.a CMakeFiles/loader.dir/progressbar.c.o "CMakeFiles/loader.dir/loader-file.c.o" "CMakeFiles/loader.dir/loader-meta.c.o" "CMakeFiles/loader.dir/queue-file.c.o" "CMakeFiles/loader.dir/alignment-writer.c.o" "CMakeFiles/loader.dir/common-reader.c.o" "CMakeFiles/loader.dir/common-writer.c.o" CMakeFiles/loader.dir/mmarray.c.o "CMakeFiles/loader.dir/reference-writer.c.o" "CMakeFiles/loader.dir/sequence-writer.c.o" /usr/bin/ranlib ../../ilib/libloader.a [ 33%] Built target loader --- libs/ascp/CMakeFiles/ascp.dir/all --- /usr/bin/make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend --- libs/ascp/CMakeFiles/ascp.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp/CMakeFiles/ascp.dir/DependInfo.cmake "--color=" /usr/bin/make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/build --- libs/ascp/CMakeFiles/ascp.dir/ascp.c.o --- [ 34%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o --- --- libs/ascp/CMakeFiles/ascp.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/ascp/CMakeFiles/ascp.dir/ascp.c.o -MF CMakeFiles/ascp.dir/ascp.c.o.d -o CMakeFiles/ascp.dir/ascp.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/ascp.c --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- [ 35%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/StatisticsItf.cpp --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/all --- --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o --- [ 35%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -s--- libs/ascp/CMakeFiles/ascp.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/unix/connect.c --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/all --- --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o --- [ 36%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/ReferenceBlobIterator.cpp --- libs/ascp/CMakeFiles/ascp.dir/all --- --- libs/ascp/CMakeFiles/ascp.dir/bsd/ascp-path.c.o --- [ 36%] Building C object libs/ascp/CMakeFiles/ascp.dir/bsd/ascp-path.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/ascp/CMakeFiles/ascp.dir/bsd/ascp-path.c.o -MF CMakeFiles/ascp.dir/bsd/ascp-path.c.o.d -o CMakeFiles/ascp.dir/bsd/ascp-path.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/bsd/ascp-path.c --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o --- [ 36%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/Refcount.cpp --- libs/ascp/CMakeFiles/ascp.dir/all --- --- ilib/libascp.a --- [ 36%] Linking C static library ../../ilib/libascp.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /usr/pkg/bin/cmake -P CMakeFiles/ascp.dir/cmake_clean_target.cmake cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ascp.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libascp.a CMakeFiles/ascp.dir/ascp.c.o CMakeFiles/ascp.dir/unix/connect.c.o "CMakeFiles/ascp.dir/bsd/ascp-path.c.o" /usr/bin/ranlib ../../ilib/libascp.a [ 36%] Built target ascp --- libs/diagnose/CMakeFiles/diagnose.dir/all --- /usr/bin/make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/depend --- libs/diagnose/CMakeFiles/diagnose.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/diagnose /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/diagnose/CMakeFiles/diagnose.dir/DependInfo.cmake "--color=" /usr/bin/make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/build --- libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o --- [ 36%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/diagnose && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -MF CMakeFiles/diagnose.dir/diagnose.c.o.d -o CMakeFiles/diagnose.dir/diagnose.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose/diagnose.c --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/all --- --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o --- [ 36%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/VdbAlignment.cpp --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o --- [ 36%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ErrorMsg.cpp --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/all --- --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o --- [ 36%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -MF CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o.d -o CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/NGS-VDB.cpp --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o --- [ 37%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ErrBlock.cpp --- ilib/libngs-adapt-c++.a --- [ 37%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /usr/pkg/bin/cmake -P CMakeFiles/ngs-adapt-c++.dir/cmake_clean_target.cmake cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ngs-adapt-c++.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../ilib/libngs-adapt-c++.a "CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o" /usr/bin/ranlib ../../../ilib/libngs-adapt-c++.a [ 37%] Built target ngs-adapt-c++ --- libs/general-writer/CMakeFiles/general-writer.dir/all --- /usr/bin/make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/depend --- libs/general-writer/CMakeFiles/general-writer.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/general-writer /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/general-writer /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/general-writer/CMakeFiles/general-writer.dir/DependInfo.cmake "--color=" /usr/bin/make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/build --- libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o --- [ 37%] Building CXX object libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/general-writer && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/general-writer/general-writer.cpp --- libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/all --- --- ilib/libngs-vdb.a --- [ 38%] Linking CXX static library ../../ilib/libngs-vdb.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /usr/pkg/bin/cmake -P CMakeFiles/ngs-vdb.dir/cmake_clean_target.cmake cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ngs-vdb.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libngs-vdb.a "CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o" "CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o" /usr/bin/ranlib ../../ilib/libngs-vdb.a [ 38%] Built target ngs-vdb --- tools/external/prefetch/CMakeFiles/prefetch.dir/all --- /usr/bin/make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend --- tools/external/prefetch/CMakeFiles/prefetch.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/prefetch /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch/CMakeFiles/prefetch.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/build --- tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o --- [ 38%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/prefetch\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/prefetch\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/usr/bin/make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/build --- tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o --- [ 40%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config/tui && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"libs/tui\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config/tui && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"libs/tui\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc 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tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/prefetch\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config/tui && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"libs/tui\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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-I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o -MF CMakeFiles/sra-pileup.dir/out_redir.c.o.d -o CMakeFiles/sra-pileup.dir/out_redir.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/out_redir.c --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o --- [ 53%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o -MF CMakeFiles/sra-pileup.dir/reref.c.o.d -o CMakeFiles/sra-pileup.dir/reref.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/reref.c --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o --- --- tools/external/sra-dump/CMakeFiles/illumina-dump.dir/all --- --- tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o --- --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/all --- [ 53%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o -MF CMakeFiles/sra-pileup.dir/cg_tools.c.o.d -o 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tools/external/sra-pileup/CMakeFiles/sam-dump.dir/all --- [ 56%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o -MF CMakeFiles/sam-dump.dir/perf_log.c.o.d -o CMakeFiles/sam-dump.dir/perf_log.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/perf_log.c --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/all --- --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o --- [ 56%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker_0.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/ref_walker_0.c --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/all --- --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o --- [ 57%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o -MF CMakeFiles/sam-dump.dir/rna_splice_log.c.o.d -o CMakeFiles/sam-dump.dir/rna_splice_log.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/rna_splice_log.c --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/all --- --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o --- [ 58%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/ref_walker.c --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o --- --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/all --- --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- [ 58%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o -MF CMakeFiles/fasterq-dump.dir/arg_helper.c.o.d -o CMakeFiles/fasterq-dump.dir/arg_helper.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump/arg_helper.c --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/all --- [ 58%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -MF CMakeFiles/sam-dump.dir/sam-dump-opts.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump-opts.c --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/all --- /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/ref_walker.c: In function 'ref_walker_add_iterator.constprop': /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/ref_walker.c:571:14: warning: 'cursor_ids' may be used uninitialized in this function [-Wmaybe-uninitialized] rc = VCursorAddColumn ( *cursor, &cursor_ids->idx_read_filter, COL_READ_FILTER ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/ref_walker.c:590:22: note: 'cursor_ids' was declared here walker_col_ids * cursor_ids; ^~~~~~~~~~ --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o --- [ 58%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -MF CMakeFiles/fasterq-dump.dir/dflt_defline.c.o.d -o CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump/dflt_defline.c --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o --- [ 58%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/all --- --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o --- [ 58%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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/tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_varcount.c.o -MF CMakeFiles/sra-pileup.dir/pileup_varcount.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_varcount.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/pileup_varcount.c --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump/inspector.c: In function 'insp_report': /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump/inspector.c:1165:12: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] rc = KOutMsg( "... is %s\n", s_acc_type ); ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/all --- [ 60%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-hdr1.c --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o --- [ 61%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_v2.c.o -MF CMakeFiles/sra-pileup.dir/pileup_v2.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_v2.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/pileup_v2.c --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o --- [ 62%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o --- [ 62%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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-D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o -MF CMakeFiles/sra-pileup.dir/sra-pileup.c.o.d -o 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o -MF CMakeFiles/fasterq-dump.dir/var_fmt.c.o.d -o CMakeFiles/fasterq-dump.dir/var_fmt.c.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump/var_fmt.c --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/all --- --- tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o --- [ 63%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o --- [ 63%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT 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tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump/raw_read_iter.c --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o --- [ 70%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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"CMakeFiles/fasterq-dump.dir/ref_inventory.c.o" "CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o" -o ../../../bin/fasterq-dump -L/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm --- tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/all --- --- bin/vdb-validate --- [ 76%] Linking C executable ../../../bin/vdb-validate cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-validate && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/vdb-validate.dir/link.txt --verbose=1 --- tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f fasterq-dump.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv fasterq-dump fasterq-dump.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s fasterq-dump.3.0.6 fasterq-dump.3 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s fasterq-dump.3 fasterq-dump cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 fasterq-dump-driver --- tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/all --- /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm --- ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/all --- [ 86%] Linking CXX shared library ../../lib/libngs-c++.so cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++-shared.dir/link.txt --verbose=1 /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -fPIC -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -shared -Wl,-soname,libngs-c++.so -o ../../lib/libngs-c++.so "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" 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tools/external/vdb-config/CMakeFiles/vdb-config.dir/all --- --- tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o --- [ 90%] Building C object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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-I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o -MF CMakeFiles/sratools.dir/config.cpp.o.d -o CMakeFiles/sratools.dir/config.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/config.cpp --- tools/external/sra-info/CMakeFiles/sra-info.dir/all --- --- bin/sra-info --- [ 91%] Linking CXX executable ../../../bin/sra-info cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-info && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/sra-info.dir/link.txt --verbose=1 /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib "CMakeFiles/sra-info.dir/main.cpp.o" "CMakeFiles/sra-info.dir/sra-info.cpp.o" "CMakeFiles/sra-info.dir/formatter.cpp.o" -o ../../../bin/sra-info -L/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sra-info.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sra-info sra-info.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-info.3.0.6 sra-info.3 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-info.3 sra-info [ 91%] Built target sra-info --- ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/all --- /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend --- ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build --- lib/libncbi-ngs.a --- [ 91%] Linking CXX static library ../../lib/libncbi-ngs.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk && /usr/pkg/bin/cmake -P CMakeFiles/ncbi-ngs.dir/cmake_clean_target.cmake --- tools/external/vdb-config/CMakeFiles/vdb-config.dir/all --- --- tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o --- --- ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs.dir/link.txt --verbose=1 --- tools/external/vdb-config/CMakeFiles/vdb-config.dir/all --- [ 91%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config -Wall -O2 -I/usr/pkg/include 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--- ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && rm -f libncbi-ngs.so.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && mv libncbi-ngs.so libncbi-ngs.so.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs.so.3.0.6 libncbi-ngs.so.3 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs.so.3 libncbi-ngs.so [ 91%] Built target ncbi-ngs-shared --- tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/all --- /usr/bin/make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/depend --- tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ngs-pileup /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ngs-pileup /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build --- tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o --- [ 91%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ngs-pileup && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -MF CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o.d -o CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ngs-pileup/ngs-pileup.cpp --- tools/external/driver-tool/CMakeFiles/sratools.dir/all --- --- tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o --- [ 91%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ngs-pileup/main.cpp --- tools/external/vdb-config/CMakeFiles/vdb-config.dir/all --- --- tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o --- [ 91%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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Linking CXX executable ../../../bin/ngs-pileup cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ngs-pileup && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ngs-pileup.dir/link.txt --verbose=1 /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib "CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o" "CMakeFiles/ngs-pileup.dir/main.cpp.o" -o ../../../bin/ngs-pileup -L/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f ngs-pileup.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv ngs-pileup ngs-pileup.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s ngs-pileup.3.0.6 ngs-pileup.3 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s ngs-pileup.3 ngs-pileup [ 92%] Built target ngs-pileup --- tools/external/ref-variation/CMakeFiles/ref-variation.dir/all --- /usr/bin/make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/depend --- tools/external/ref-variation/CMakeFiles/ref-variation.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ref-variation /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation/CMakeFiles/ref-variation.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/build --- tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o --- [ 92%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/tmp/biology/sra-tools/work/.cwrapper/bin/c++ -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib "CMakeFiles/vdb-config.dir/configure.cpp.o" "CMakeFiles/vdb-config.dir/util.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config.c.o" "CMakeFiles/vdb-config.dir/interactive2.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o" -o ../../../bin/vdb-config -L/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../ilib/libtui_cpp.a ../../../ilib/libtui.a /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o --- [ 93%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/vdb-sqlite && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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-D__mod__=\"tools/ref-variation\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /usr/pkg/bin/cmake -E copy /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/kfg/ncbi/default.kfg /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin/ncbi/default.kfg [ 93%] Built target vdb-config --- tools/external/ref-variation/CMakeFiles/var-expand.dir/all --- /usr/bin/make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/depend --- tools/external/ref-variation/CMakeFiles/var-expand.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c 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vdb-sqlite --- tools/external/sra-search/CMakeFiles/sra-search.dir/all --- /usr/bin/make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/depend --- tools/external/sra-search/CMakeFiles/sra-search.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-search /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search 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tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o --- [ 98%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-search\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o -MF CMakeFiles/sratools.dir/json-parse.cpp.o.d -o CMakeFiles/sratools.dir/json-parse.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/json-parse.cpp --- tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o --- [ 99%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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--- tools/external/sra-search/CMakeFiles/sra-search.dir/all --- --- bin/sra-search --- [ 99%] Linking CXX executable ../../../bin/sra-search cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/sra-search.dir/link.txt --verbose=1 /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib "CMakeFiles/sra-search.dir/main.cpp.o" "CMakeFiles/sra-search.dir/searchblock.cpp.o" "CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/referencematchiterator.cpp.o" "CMakeFiles/sra-search.dir/vdb-search.cpp.o" -o ../../../bin/sra-search -L/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libtk-version.a -lkapp /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sra-search.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sra-search sra-search.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-search.3.0.6 sra-search.3 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-search.3 sra-search [ 99%] Built target sra-search --- tools/external/driver-tool/CMakeFiles/sratools.dir/all --- --- tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o --- --- tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o --- --- tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o --- [ 99%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o --- tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o --- [ 99%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o --- tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -MF CMakeFiles/sratools.dir/tool-args.cpp.o.d -o CMakeFiles/sratools.dir/tool-args.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/tool-args.cpp --- tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o --- cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -MF CMakeFiles/sratools.dir/build-version.cpp.o.d -o CMakeFiles/sratools.dir/build-version.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/build-version.cpp --- tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o --- [ 99%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -MF CMakeFiles/sratools.dir/file-path.posix.cpp.o.d -o CMakeFiles/sratools.dir/file-path.posix.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/file-path.posix.cpp --- tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o --- [100%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -MF CMakeFiles/sratools.dir/proc.posix.cpp.o.d -o CMakeFiles/sratools.dir/proc.posix.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/proc.posix.cpp --- bin/sratools --- [100%] Linking CXX executable ../../../bin/sratools cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib CMakeFiles/sratools.dir/sratools.cpp.o CMakeFiles/sratools.dir/config.cpp.o "CMakeFiles/sratools.dir/command-line.cpp.o" "CMakeFiles/sratools.dir/run-source.cpp.o" CMakeFiles/sratools.dir/proc.cpp.o CMakeFiles/sratools.dir/uuid.cpp.o CMakeFiles/sratools.dir/accession.cpp.o CMakeFiles/sratools.dir/service.cpp.o "CMakeFiles/sratools.dir/json-parse.cpp.o" "CMakeFiles/sratools.dir/SDL-response.cpp.o" "CMakeFiles/sratools.dir/tool-args.cpp.o" "CMakeFiles/sratools.dir/build-version.cpp.o" "CMakeFiles/sratools.dir/file-path.posix.cpp.o" CMakeFiles/sratools.dir/proc.posix.cpp.o -o ../../../bin/sratools -L/tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sratools.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sratools sratools.3.0.6 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 sratools.3 cd /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3 sratools [100%] Built target sratools /usr/pkg/bin/cmake -E cmake_progress_start /tmp/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/CMakeFiles 0