=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. 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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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o.d -o 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/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o --- [ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o --- [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT 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-I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/c++/PileupIterator.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o --- [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces 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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-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/dispatch/PileupEventItf.cpp --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o --- [ 8%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.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-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/SRA_DB_ReadCollection.c --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o --- [ 9%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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 CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/c++/PileupEventIterator.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-3.2.0/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-3.2.0/ncbi-vdb/interfaces 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ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/python/py_PileupItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o --- [ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/SRA_ReadGroup.c --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- [ 9%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o cd 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/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/c++/PileupEvent.cpp --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 10%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/dispatch/AlignmentItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o --- [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/SRA_ReadGroupInfo.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o --- [ 10%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o --- [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/SRA_ReadCollection.c --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o --- [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc 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CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp --- 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 --- [ 13%] 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-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o --- [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build/ngs/ncbi/ngs && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -MF CMakeFiles/ngs.dir/NGS_ReadCollection.c.o.d 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-I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/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/Alignment.cpp.o --- [ 13%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces 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/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/NGS_PileupEvent.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o --- [ 14%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o --- [ 14%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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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-I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/NGS_ReferenceSequence.c --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o --- --- 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 --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o --- --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && 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-I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- [ 17%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd 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-I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o -MF CMakeFiles/ngs.dir/NGS_Cursor.c.o.d -o CMakeFiles/ngs.dir/NGS_Cursor.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/NGS_Cursor.c --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/all --- --- ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o --- [ 19%] 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-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 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-I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/ngs/ngs-sdk/language/c++/Read.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o --- [ 19%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 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/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/NGS_Id.c --- 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 --- [ 20%] 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-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs-py -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o --- [ 20%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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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-I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/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/FragmentIterator.cpp.o --- [ 20%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc 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-I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ncbi/ngs/NGS_ReferenceBlob.c --- 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 --- [ 21%] 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-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc 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-I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -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-3.2.0/ngs/ngs-sdk/dispatch/Refcount.cpp --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/all --- --- ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o --- [ 21%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces 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-I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c++1z -fPIC -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk/dispatch/ErrorMsg.cpp --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o --- [ 26%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc 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/usr/bin/make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/build --- libs/kxml/CMakeFiles/kxml.dir/xml.c.o --- [ 27%] Building C object libs/kxml/CMakeFiles/kxml.dir/xml.c.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build/libs/kxml && /tmp/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 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"CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" /usr/bin/ranlib ../../../ilib/libngs-disp.a --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- /usr/bin/ar qc ../../../../ilib/libngs-bind-c++.a "CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "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" /usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a --- ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/all --- [ 27%] Built target ngs-disp --- libs/loader/CMakeFiles/loader.dir/all --- --- ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/all --- [ 27%] Built target ngs-bind-c++ --- libs/loader/CMakeFiles/loader.dir/all --- /usr/bin/make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/depend --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- /usr/bin/make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/depend --- libs/loader/CMakeFiles/loader.dir/all --- --- libs/loader/CMakeFiles/loader.dir/depend --- cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" 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ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o --- --- libs/loader/CMakeFiles/loader.dir/all --- /usr/bin/make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/build --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- /usr/bin/make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build --- libs/loader/CMakeFiles/loader.dir/all --- --- libs/loader/CMakeFiles/loader.dir/progressbar.c.o --- --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o --- --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- [ 27%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /tmp/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX 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object libs/loader/CMakeFiles/loader.dir/progressbar.c.o --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- [ 27%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o --- libs/loader/CMakeFiles/loader.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/loader/CMakeFiles/loader.dir/progressbar.c.o -MF CMakeFiles/loader.dir/progressbar.c.o.d -o CMakeFiles/loader.dir/progressbar.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/loader/progressbar.c --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- cd /tmp/biology/sra-tools/work/sra-tools-3.2.0/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-3.2.0/ncbi-vdb/interfaces -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/bsd -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/ngs/ngs-sdk -I/tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/inc -I/tmp/biology/sra-tools/work/sra-tools-3.2.0 -Wall -O2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I/usr/pkg/include/libxml2 -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -c /tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/vdb-sqlite/sqlite3.c --- libs/kxml/CMakeFiles/kxml.dir/all --- /tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/kxml/xml.c:174:52: error: expected ';', ',' or ')' before 'ATTRIBUTE_UNUSED' static void s_xmlGenericErrorDefaultFunc(void *ctx ATTRIBUTE_UNUSED, ^~~~~~~~~~~~~~~~ /tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/kxml/xml.c: In function 'KXMLMgrMakeDocReadFromMemory': /tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/kxml/xml.c:266:35: error: 's_xmlGenericErrorDefaultFunc' undeclared (first use in this function); did you mean 'initGenericErrorDefaultFunc'? { xmlSetGenericErrorFunc(0, s_xmlGenericErrorDefaultFunc); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ initGenericErrorDefaultFunc /tmp/biology/sra-tools/work/sra-tools-3.2.0/libs/kxml/xml.c:266:35: note: each undeclared identifier is reported only once for each function it appears in *** [libs/kxml/CMakeFiles/kxml.dir/xml.c.o] Error code 1 make[2]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build 1 error make[2]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build *** [libs/kxml/CMakeFiles/kxml.dir/all] Error code 2 make[1]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build --- libs/loader/CMakeFiles/loader.dir/all --- A failure has been detected in another branch of the parallel make make[2]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build *** [libs/loader/CMakeFiles/loader.dir/all] Error code 2 make[1]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build --- ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all --- A failure has been detected in another branch of the parallel make make[2]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build *** [ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/all] Error code 2 make[1]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build --- libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all --- A failure has been detected in another branch of the parallel make make[2]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build *** [libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/all] Error code 2 make[1]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build 4 errors make[1]: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build *** [all] Error code 2 make: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build 1 error make: stopped in /tmp/biology/sra-tools/work/sra-tools-3.2.0/cmake-pkgsrc-build *** Error code 2 Stop. make[1]: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/sra-tools *** Error code 1 Stop. make: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/sra-tools