=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for sra-tools-3.0.6 /usr/pkg/bin/cmake -S/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -B/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/pkg/bin/cmake -E cmake_progress_start /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/CMakeFiles /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" 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cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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/shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/VByteBlob.c.o -MF CMakeFiles/ngs.dir/VByteBlob.c.o.d -o CMakeFiles/ngs.dir/VByteBlob.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs/VByteBlob.c [ 10%] Linking C static library ../../../ilib/libngs.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs && /usr/pkg/bin/cmake -P CMakeFiles/ngs.dir/cmake_clean_target.cmake cd 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CMakeFiles/ngs.dir/NGS_Pileup.c.o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o CMakeFiles/ngs.dir/NGS_Alignment.c.o CMakeFiles/ngs.dir/NGS_Reference.c.o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Read.c.o CMakeFiles/ngs.dir/NGS_Fragment.c.o CMakeFiles/ngs.dir/NGS_Cursor.c.o CMakeFiles/ngs.dir/NGS_Refcount.c.o CMakeFiles/ngs.dir/NGS_String.c.o CMakeFiles/ngs.dir/NGS_Id.c.o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o CMakeFiles/ngs.dir/VByteBlob.c.o /usr/bin/ranlib ../../../ilib/libngs.a [ 10%] Built target ngs /usr/bin/make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-c++ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-c++ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build [ 10%] Building CXX object ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-c++ && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs-c++\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -fPIC -MD -MT ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -MF CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o.d -o CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-c++/NCBI-NGS.cpp [ 11%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-c++ && /usr/pkg/bin/cmake -P CMakeFiles/ncbi-ngs-c++.dir/cmake_clean_target.cmake cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-c++ && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-c++.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libncbi-ngs-c++.a "CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" /usr/bin/ranlib ../../../lib/libncbi-ngs-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && rm -f libncbi-ngs-c++.a.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && mv libncbi-ngs-c++.a libncbi-ngs-c++.a.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs-c++.a.3.0.6 libncbi-ngs-c++.a.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs-c++.a.3 libncbi-ngs-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs-c++.a libncbi-ngs-c++-static.a [ 11%] Built target ncbi-ngs-c++ /usr/bin/make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ncbi/ngs-py /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-py /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build [ 11%] Building C object ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ncbi/ngs-py && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"ngs/ncbi/ngs-py\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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/shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/Statistics.cpp [ 16%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/StringRef.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/c++/StringRef.cpp [ 16%] Linking CXX static library ../../../../ilib/libngs-bind-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/c++ && /usr/pkg/bin/cmake -P CMakeFiles/ngs-bind-c++.dir/cmake_clean_target.cmake cd 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"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 [ 16%] Built target ngs-bind-c++ /usr/bin/make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/ErrorMsg.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/dispatch/ErrorMsg.cpp [ 21%] Linking CXX static library ../../../ilib/libngs-disp.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /usr/pkg/bin/cmake -P CMakeFiles/ngs-disp.dir/cmake_clean_target.cmake cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/dispatch && /usr/pkg/bin/cmake -E cmake_link_script 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 [ 21%] Built target ngs-disp /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build [ 21%] Linking CXX shared library ../../lib/libngs-c++.so cd /shared/pkgsrc/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 /shared/pkgsrc/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" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" -L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && rm -f libngs-c++.so.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && mv libngs-c++.so libngs-c++.so.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libngs-c++.so.3.0.6 libngs-c++.so.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libngs-c++.so.3 libngs-c++.so [ 21%] Built target ngs-c++-shared /usr/bin/make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make 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cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp [ 26%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_Refcount.cpp [ 26%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/language/python/py_StringItf.cpp [ 27%] Linking CXX static library ../../../../ilib/libngs-bind-python.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /usr/pkg/bin/cmake -P CMakeFiles/ngs-bind-python.dir/cmake_clean_target.cmake cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/language/python && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-python.dir/link.txt --verbose=1 /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" /usr/bin/ranlib ../../../../ilib/libngs-bind-python.a [ 27%] Built target ngs-bind-python /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build [ 27%] Linking CXX shared library ../../lib/libncbi-ngs.so cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-shared.dir/link.txt --verbose=1 /shared/pkgsrc/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,libncbi-ngs.so -o ../../lib/libncbi-ngs.so "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" -L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && rm -f libncbi-ngs.so.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && mv libncbi-ngs.so libncbi-ngs.so.3.0.6 cd /shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs.so.3 libncbi-ngs.so [ 27%] Built target ncbi-ngs-shared /usr/bin/make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build [ 27%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ReadCollectionItf.cpp [ 27%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ReferenceSequenceItf.cpp [ 29%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/adapter && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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-I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk/adapter/ErrBlock.cpp [ 31%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a cd /shared/pkgsrc/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 /shared/pkgsrc/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 [ 31%] Built target ngs-adapt-c++ /usr/bin/make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/depend cd 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc-parsexml.c [ 32%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/kxml && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/usr/pkg/include/libxml2 -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -fPIC -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o -MF CMakeFiles/kxml.dir/xtoc.c.o.d -o CMakeFiles/kxml.dir/xtoc.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc.c In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc.c:44: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc.c: In function 'KDirectoryOpenXTocDirReadInt': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/kfs/directory.h:599:39: warning: 'xdir' may be used uninitialized in this function [-Wmaybe-uninitialized] 599 | #define KDirectoryRelease NAME_VERS ( KDirectoryRelease, KDIRECTORY_VERS ) | ^~~~~~~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc.c:3212:30: note: 'xdir' was declared here 3212 | const KXTocDir * xdir; | ^~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc.c:840:32: warning: 'xtoc' may be used uninitialized in this function [-Wmaybe-uninitialized] 840 | switch (KRefcountDrop (&self->refcount, XTocClassname)) | ^~~~~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/kxml/xtoc.c:3193:12: note: 'xtoc' was declared here 3193 | XToc * xtoc; | ^~~~ [ 32%] Linking C static library ../../ilib/libkxml.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/kxml && /usr/pkg/bin/cmake -P CMakeFiles/kxml.dir/cmake_clean_target.cmake cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/kxml && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/kxml.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libkxml.a CMakeFiles/kxml.dir/xml.c.o "CMakeFiles/kxml.dir/xtoc-parsexml.c.o" CMakeFiles/kxml.dir/xtoc.c.o /usr/bin/ranlib ../../ilib/libkxml.a [ 32%] Built target kxml /usr/bin/make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c 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-I/shared/pkgsrc/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/common-writer.c.o -MF CMakeFiles/loader.dir/common-writer.c.o.d -o CMakeFiles/loader.dir/common-writer.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/common-writer.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/common-writer.c:31: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/common-writer.c: In function 'platform_cmp': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/common-writer.c:717:35: warning: array subscript has type 'char' [-Wchar-subscripts] 717 | int ch2 = toupper(platform[i]); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/common-writer.c: In function 'PlatformToId': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/common-writer.c:866:29: warning: array subscript has type 'char' [-Wchar-subscripts] 866 | switch (toupper(name[0])) { | ^ [ 34%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/loader && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/loader/sequence-writer.c [ 35%] Linking C static library ../../ilib/libloader.a cd /shared/pkgsrc/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 /shared/pkgsrc/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 [ 35%] Built target loader /usr/bin/make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/vdb-sqlite /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/vdb-sqlite /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/DependInfo.cmake "--color=" 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/vdb-sqlite/sqlite3.c:115649:10: warning: function may return address of local variable [-Wreturn-local-addr] 115649 | return pNew; | ^~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/vdb-sqlite/sqlite3.c:115609:10: note: declared here 115609 | Select standin; | ^~~~~~~ [ 36%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/vdb-sqlite && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/vdb-sqlite/sqlite3vdb.c [ 36%] Linking C static library ../../ilib/libvdb-sqlite.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/vdb-sqlite && /usr/pkg/bin/cmake -P CMakeFiles/vdb-sqlite.dir/cmake_clean_target.cmake cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/vdb-sqlite && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/vdb-sqlite.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libvdb-sqlite.a "CMakeFiles/vdb-sqlite.dir/sqlite3.c.o" "CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o" /usr/bin/ranlib ../../ilib/libvdb-sqlite.a [ 36%] Built target vdb-sqlite /usr/bin/make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/depend cd 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libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/ReferenceBlob.cpp [ 38%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 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libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ngs-vdb && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ngs-vdb/NGS-VDB.cpp [ 39%] Linking CXX static library ../../ilib/libngs-vdb.a cd /shared/pkgsrc/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 /shared/pkgsrc/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 [ 39%] Built target ngs-vdb /usr/bin/make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp /shared/pkgsrc/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 [ 40%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/ascp.c [ 40%] Building C object libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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 -Wno-unused-result -MD -MT libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o -MF CMakeFiles/ascp.dir/unix/connect.c.o.d -o CMakeFiles/ascp.dir/unix/connect.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/unix/connect.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/unix/connect.c:40: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/unix/connect.c: In function 'run_ascp': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/unix/connect.c:263:34: warning: array subscript has type 'char' [-Wchar-subscripts] 263 | else if (isspace(*c)) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/unix/connect.c:281:34: warning: array subscript has type 'char' [-Wchar-subscripts] 281 | else if (isspace(*c)) { | ^ [ 40%] Building C object libs/ascp/CMakeFiles/ascp.dir/bsd/ascp-path.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/ascp && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/ascp/bsd/ascp-path.c [ 40%] Linking C static library ../../ilib/libascp.a cd 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libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -MF CMakeFiles/diagnose.dir/diagnose.c.o.d -o CMakeFiles/diagnose.dir/diagnose.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose/diagnose.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose/diagnose.c:60: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose/diagnose.c: In function 'KConfig_Verbosity': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose/diagnose.c:1954:34: warning: array subscript has type 'char' [-Wchar-subscripts] 1954 | if ( isdigit ( s -> addr [ 0 ] ) ) | ^ [ 40%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/diagnose && /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/diagnose -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/libs/general-writer && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/prefetch /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch /shared/pkgsrc/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 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/prefetch/prefetch.c: In function 'KService_ProcessId': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/prefetch/prefetch.c:357:24: warning: array subscript has type 'char' [-Wchar-subscripts] 357 | if (!isdigit(id[i])) { | ^ [ 42%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/prefetch\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/prefetch && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/prefetch\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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-dump/CMakeFiles/fastq-dump.dir/factory.c.o -MF CMakeFiles/fastq-dump.dir/factory.c.o.d -o CMakeFiles/fastq-dump.dir/factory.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:37: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c: In function 'SRASplitterFiler_PushKey': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:171:25: warning: array subscript has type 'char' [-Wchar-subscripts] 171 | while( !isalnum(*key) && *key != '\0' ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c: In function 'SRASplitterFiler_GetCurrFile': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:356:55: warning: array subscript has type 'char' [-Wchar-subscripts] 356 | if( i != 0 && isalnum(g_filer->path[i][0]) ) { | ^ [ 51%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o -MF 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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-dump/CMakeFiles/fastq-dump.dir/core.c.o -MF CMakeFiles/fastq-dump.dir/core.c.o.d -o CMakeFiles/fastq-dump.dir/core.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/core.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/core.c:56: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/core.c: In function 'KMain': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/core.c:1504:46: warning: array subscript has type 'char' [-Wchar-subscripts] 1504 | if (!isdigit(*(p++))) | ^ [ 51%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/fastq.c:42: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/fastq.c: In function 'FastqDumper_AddArg': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/fastq.c:3240:44: warning: array subscript has type 'char' [-Wchar-subscripts] 3240 | if ( k < argc && isdigit( argv[ k ][ 0 ] ) ) | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/fastq.c:3306:37: warning: array subscript has type 'char' [-Wchar-subscripts] 3306 | else if ( !isdigit( *c ) ) | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/fastq.c:3357:37: warning: array subscript has type 'char' [-Wchar-subscripts] 3357 | else if ( !isdigit( *arg ) ) | ^ [ 52%] Linking C executable ../../../bin/fastq-dump cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/fastq-dump.dir/link.txt --verbose=1 /shared/pkgsrc/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 "CMakeFiles/fastq-dump.dir/factory.c.o" "CMakeFiles/fastq-dump.dir/fasta_dump.c.o" "CMakeFiles/fastq-dump.dir/core.c.o" "CMakeFiles/fastq-dump.dir/fastq.c.o" -o ../../../bin/fastq-dump -L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f fastq-dump.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv fastq-dump fastq-dump.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s fastq-dump.3.0.6 fastq-dump.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s fastq-dump.3 fastq-dump cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 fastq-dump-driver [ 52%] Built target fastq-dump /usr/bin/make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump/CMakeFiles/sff-dump.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/build [ 53%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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-dump/CMakeFiles/sff-dump.dir/factory.c.o -MF CMakeFiles/sff-dump.dir/factory.c.o.d -o CMakeFiles/sff-dump.dir/factory.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:37: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c: In function 'SRASplitterFiler_PushKey': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:171:25: warning: array subscript has type 'char' [-Wchar-subscripts] 171 | while( !isalnum(*key) && *key != '\0' ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c: In function 'SRASplitterFiler_GetCurrFile': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:356:55: warning: array subscript has type 'char' [-Wchar-subscripts] 356 | if( i != 0 && isalnum(g_filer->path[i][0]) ) { | ^ [ 53%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/core.c: In function 'KMain': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/core.c:1504:46: warning: array subscript has type 'char' [-Wchar-subscripts] 1504 | if (!isdigit(*(p++))) | ^ [ 53%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c: In function 'SRASplitterFiler_GetCurrFile': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:356:55: warning: array subscript has type 'char' [-Wchar-subscripts] 356 | if( i != 0 && isalnum(g_filer->path[i][0]) ) { | ^ [ 55%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c: In function 'SRASplitterFiler_GetCurrFile': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-dump/factory.c:356:55: warning: array subscript has type 'char' [-Wchar-subscripts] 356 | if( i != 0 && isalnum(g_filer->path[i][0]) ) { | ^ [ 55%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-dump && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/perf_log.c.o -MF CMakeFiles/sra-pileup.dir/perf_log.c.o.d -o CMakeFiles/sra-pileup.dir/perf_log.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/perf_log.c [ 57%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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 /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/reref.c [ 57%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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 CMakeFiles/sra-pileup.dir/cg_tools.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:41: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'ExplodeCIGAR': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:84:28: warning: array subscript has type 'char' [-Wchar-subscripts] 84 | if ( isdigit( cigar[ i ] ) ) { | ^ In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/rc.h:44, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.h:35, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:27: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:87:35: warning: array subscript has type 'char' [-Wchar-subscripts] 87 | assert( isalpha( cigar[ i ] ) ); | ^ In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/debug.h:30, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:30: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'print_CG_cigar': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:111:72: warning: array subscript has type 'char' [-Wchar-subscripts] 111 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, tolower( op[ i ].code ) ) ); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/debug.h:507:22: note: in definition of macro 'DBGMSG' 507 | ? KDbgMsg msg : 0) | ^~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:111:13: note: in expansion of macro 'SAM_DUMP_DBG' 111 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, tolower( op[ i ].code ) ) ); | ^~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:113:72: warning: array subscript has type 'char' [-Wchar-subscripts] 113 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, toupper( op[ i ].code ) ) ); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/debug.h:507:22: note: in definition of macro 'DBGMSG' 507 | ? KDbgMsg msg : 0) | ^~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:113:13: note: in expansion of macro 'SAM_DUMP_DBG' 113 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, toupper( op[ i ].code ) ) ); | ^~~~~~~~~~~~ In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:41: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'CIGAR_to_CG_Ops': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:149:89: warning: array subscript has type 'char' [-Wchar-subscripts] 149 | for ( n = 0; ( ( n + i ) < input->p_cigar.len ) && ( isdigit( input->p_cigar.ptr[ n + i ] ) ); n++ ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:1553:32: warning: array subscript has type 'char' [-Wchar-subscripts] 1553 | if ( isdigit( cigar[ i ] ) ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:1555:39: warning: array subscript has type 'char' [-Wchar-subscripts] 1555 | } else if ( isalpha( cigar[ i ] ) ) { | ^ [ 58%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/report_deletes.c.o -MF CMakeFiles/sra-pileup.dir/report_deletes.c.o.d -o CMakeFiles/sra-pileup.dir/report_deletes.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/report_deletes.c [ 58%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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_regions.c.o -MF CMakeFiles/sra-pileup.dir/ref_regions.c.o.d -o CMakeFiles/sra-pileup.dir/ref_regions.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/ref_regions.c [ 58%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk 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-L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sra-pileup.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sra-pileup sra-pileup.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-pileup.3.0.6 sra-pileup.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-pileup.3 sra-pileup cd 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tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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-unaligned.c.o -MF CMakeFiles/sam-dump.dir/sam-unaligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-unaligned.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-unaligned.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-unaligned.c:45: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-unaligned.c: In function 'print_sliced_read': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-unaligned.c:372:44: warning: array subscript has type 'char' [-Wchar-subscripts] 372 | c = tolower ( cmp_tbl [ toupper ( c ) - 'A' ] ); | ^ [ 64%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/md_flag.c.o -MF CMakeFiles/sam-dump.dir/md_flag.c.o.d -o CMakeFiles/sam-dump.dir/md_flag.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/md_flag.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/md_flag.c:33: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/md_flag.c: In function 'parse_cigar_t': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/md_flag.c:92:31: warning: array subscript has type 'char' [-Wchar-subscripts] 92 | if ( isdigit( *cigar_str ) ) { | ^ [ 64%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/cg_tools.c.o -MF CMakeFiles/sam-dump.dir/cg_tools.c.o.d -o CMakeFiles/sam-dump.dir/cg_tools.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:41: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'ExplodeCIGAR': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:84:28: warning: array subscript has type 'char' [-Wchar-subscripts] 84 | if ( isdigit( cigar[ i ] ) ) { | ^ In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/rc.h:44, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.h:35, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:27: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:87:35: warning: array subscript has type 'char' [-Wchar-subscripts] 87 | assert( isalpha( cigar[ i ] ) ); | ^ In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/debug.h:30, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:30: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'print_CG_cigar': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:111:72: warning: array subscript has type 'char' [-Wchar-subscripts] 111 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, tolower( op[ i ].code ) ) ); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/debug.h:507:22: note: in definition of macro 'DBGMSG' 507 | ? KDbgMsg msg : 0) | ^~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:111:13: note: in expansion of macro 'SAM_DUMP_DBG' 111 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, tolower( op[ i ].code ) ) ); | ^~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:113:72: warning: array subscript has type 'char' [-Wchar-subscripts] 113 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, toupper( op[ i ].code ) ) ); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/debug.h:507:22: note: in definition of macro 'DBGMSG' 507 | ? KDbgMsg msg : 0) | ^~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:113:13: note: in expansion of macro 'SAM_DUMP_DBG' 113 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, toupper( op[ i ].code ) ) ); | ^~~~~~~~~~~~ In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:41: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'CIGAR_to_CG_Ops': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:149:89: warning: array subscript has type 'char' [-Wchar-subscripts] 149 | for ( n = 0; ( ( n + i ) < input->p_cigar.len ) && ( isdigit( input->p_cigar.ptr[ n + i ] ) ); n++ ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:1553:32: warning: array subscript has type 'char' [-Wchar-subscripts] 1553 | if ( isdigit( cigar[ i ] ) ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/cg_tools.c:1555:39: warning: array subscript has type 'char' [-Wchar-subscripts] 1555 | } else if ( isalpha( cigar[ i ] ) ) { | ^ [ 65%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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.c.o -MF CMakeFiles/sam-dump.dir/sam-dump.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/debug.h:30, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:128: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c: In function 'print_CG_cigar': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:1682:72: warning: array subscript has type 'char' [-Wchar-subscripts] 1682 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, tolower( op[ i ].code ) ) ); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/debug.h:507:22: note: in definition of macro 'DBGMSG' 507 | ? KDbgMsg msg : 0) | ^~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:1682:13: note: in expansion of macro 'SAM_DUMP_DBG' 1682 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, tolower( op[ i ].code ) ) ); | ^~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:1684:72: warning: array subscript has type 'char' [-Wchar-subscripts] 1684 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, toupper( op[ i ].code ) ) ); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/debug.h:507:22: note: in definition of macro 'DBGMSG' 507 | ? KDbgMsg msg : 0) | ^~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:1684:13: note: in expansion of macro 'SAM_DUMP_DBG' 1684 | SAM_DUMP_DBG( 3, ( "%u%c", op[ i ].length, toupper( op[ i ].code ) ) ); | ^~~~~~~~~~~~ In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:134: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c: In function 'CIGAR_to_CG_Ops': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:1717:53: warning: array subscript has type 'char' [-Wchar-subscripts] 1717 | for( n = 0; n + i < ciglen && isdigit( cigar[ n + i ] ); n++ ) { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c: In function 'ExplodeCIGAR': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:2347:28: warning: array subscript has type 'char' [-Wchar-subscripts] 2347 | if ( isdigit( cigar[ i ] ) ) { | ^ In file included from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/klib/rc.h:44, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/vdb/dependencies.h:37, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:108: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump.c:2350:35: warning: array subscript has type 'char' [-Wchar-subscripts] 2350 | assert( isalpha( cigar[ i ] ) ); | ^ [ 65%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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-dump3.c.o -MF CMakeFiles/sam-dump.dir/sam-dump3.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump3.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/sam-dump3.c [ 65%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/dyn_string.c.o -MF CMakeFiles/sam-dump.dir/dyn_string.c.o.d -o CMakeFiles/sam-dump.dir/dyn_string.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-pileup/dyn_string.c [ 65%] Linking C executable ../../../bin/sam-dump cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-pileup && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/sam-dump.dir/link.txt --verbose=1 /shared/pkgsrc/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 "CMakeFiles/sam-dump.dir/inputfiles.c.o" "CMakeFiles/sam-dump.dir/perf_log.c.o" "CMakeFiles/sam-dump.dir/rna_splice_log.c.o" "CMakeFiles/sam-dump.dir/sam-dump-opts.c.o" "CMakeFiles/sam-dump.dir/out_redir.c.o" "CMakeFiles/sam-dump.dir/sam-hdr.c.o" "CMakeFiles/sam-dump.dir/sam-hdr1.c.o" "CMakeFiles/sam-dump.dir/matecache.c.o" "CMakeFiles/sam-dump.dir/read_fkt.c.o" "CMakeFiles/sam-dump.dir/sam-aligned.c.o" "CMakeFiles/sam-dump.dir/sam-unaligned.c.o" "CMakeFiles/sam-dump.dir/md_flag.c.o" "CMakeFiles/sam-dump.dir/cg_tools.c.o" "CMakeFiles/sam-dump.dir/sam-dump.c.o" "CMakeFiles/sam-dump.dir/sam-dump3.c.o" "CMakeFiles/sam-dump.dir/dyn_string.c.o" -o ../../../bin/sam-dump -L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sam-dump.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sam-dump sam-dump.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sam-dump.3.0.6 sam-dump.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sam-dump.3 sam-dump cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 sam-dump-driver [ 65%] Built target sam-dump /usr/bin/make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/fasterq-dump /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build [ 66%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o cd 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"CMakeFiles/fasterq-dump.dir/cleanup_task.c.o" "CMakeFiles/fasterq-dump.dir/index.c.o" "CMakeFiles/fasterq-dump.dir/lookup_writer.c.o" "CMakeFiles/fasterq-dump.dir/lookup_reader.c.o" "CMakeFiles/fasterq-dump.dir/locked_file_list.c.o" "CMakeFiles/fasterq-dump.dir/locked_value.c.o" "CMakeFiles/fasterq-dump.dir/file_printer.c.o" "CMakeFiles/fasterq-dump.dir/merge_sorter.c.o" "CMakeFiles/fasterq-dump.dir/sorter.c.o" "CMakeFiles/fasterq-dump.dir/cmn_iter.c.o" "CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o" "CMakeFiles/fasterq-dump.dir/special_iter.c.o" "CMakeFiles/fasterq-dump.dir/fq_seq_ua_iter.c.o" "CMakeFiles/fasterq-dump.dir/fq_seq_csra_iter.c.o" "CMakeFiles/fasterq-dump.dir/align_iter.c.o" "CMakeFiles/fasterq-dump.dir/simple_fasta_iter.c.o" "CMakeFiles/fasterq-dump.dir/db_join.c.o" "CMakeFiles/fasterq-dump.dir/tbl_join.c.o" "CMakeFiles/fasterq-dump.dir/temp_registry.c.o" "CMakeFiles/fasterq-dump.dir/copy_machine.c.o" "CMakeFiles/fasterq-dump.dir/multi_writer.c.o" 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fasterq-dump.3.0.6 fasterq-dump.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s fasterq-dump.3 fasterq-dump cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 fasterq-dump-driver [ 75%] Built target fasterq-dump /usr/bin/make -f tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build.make tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-dump /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build 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../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f vdb-decrypt.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv vdb-decrypt vdb-decrypt.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s vdb-decrypt.3.0.6 vdb-decrypt.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s vdb-decrypt.3 vdb-decrypt [ 81%] Built target vdb-decrypt /usr/bin/make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/depend cd 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../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f vdb-encrypt.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv vdb-encrypt vdb-encrypt.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s vdb-encrypt.3.0.6 vdb-encrypt.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s vdb-encrypt.3 vdb-encrypt [ 82%] Built target vdb-encrypt /usr/bin/make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/depend cd 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/srapath/cgi_request.c:341:14: warning: 'clone' may be used uninitialized in this function [-Wmaybe-uninitialized] 341 | rc = VectorAppend( &list->v, NULL, clone ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/srapath/cgi_request.c:338:17: note: 'clone' was declared here 338 | reply_obj * clone; | ^~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/srapath/cgi_request.c: In function 'names_request_to_list': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/srapath/cgi_request.c:638:14: warning: 'l' may be used uninitialized in this function [-Wmaybe-uninitialized] 638 | rc = parsed_names_request( request, add_reply_to_list_cb, rslt_code, l ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/srapath/cgi_request.c: In function 'search_request_to_list': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/srapath/cgi_request.c:873:14: warning: 'l' may be used uninitialized in this function [-Wmaybe-uninitialized] 873 | rc = parsed_search_request( request, add_reply_to_list_cb, rslt_code, l ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 84%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/srapath.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/srapath && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/srapath\" -Dx86_64 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sratools.3.0.6 srapath-driver [ 84%] Built target srapath /usr/bin/make -f tools/external/sra-stat/CMakeFiles/sra-stat.dir/build.make tools/external/sra-stat/CMakeFiles/sra-stat.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-stat /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-stat /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-stat/CMakeFiles/sra-stat.dir/DependInfo.cmake "--color=" /usr/bin/make -f 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&& /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/kdbmeta /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build [ 87%] Building C object tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o cd 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-I/shared/pkgsrc/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/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o -MF CMakeFiles/kdbmeta.dir/kdbmeta.c.o.d -o CMakeFiles/kdbmeta.dir/kdbmeta.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:76: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c: In function 'value_select': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:225:36: warning: array subscript has type 'char' [-Wchar-subscripts] 225 | if ( ! isprint ( value [ i ] ) ) | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c: In function 'md_update_expr': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:571:37: warning: array subscript has type 'char' [-Wchar-subscripts] 571 | if ( tolower ( expr [ i + 1 ] ) == 'x' && | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:572:38: warning: array subscript has type 'char' [-Wchar-subscripts] 572 | isxdigit ( expr [ i + 2 ] ) && | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:573:38: warning: array subscript has type 'char' [-Wchar-subscripts] 573 | isxdigit ( expr [ i + 3 ] ) ) | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:575:46: warning: array subscript has type 'char' [-Wchar-subscripts] 575 | int msn = toupper ( expr [ i + 2 ] ) - '0'; | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/kdbmeta/kdbmeta.c:576:46: warning: array subscript has type 'char' [-Wchar-subscripts] 576 | int lsn = toupper ( expr [ i + 3 ] ) - '0'; | ^ [ 87%] Linking C executable ../../../bin/kdbmeta cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/kdbmeta && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/kdbmeta.dir/link.txt --verbose=1 /shared/pkgsrc/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 CMakeFiles/kdbmeta.dir/kdbmeta.c.o -o ../../../bin/kdbmeta -L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib 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87%] Building C object tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/align-info && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/align-info\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-info/main.cpp [ 89%] Building CXX object tools/external/sra-info/CMakeFiles/sra-info.dir/sra-info.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-info && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-info\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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-D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-info\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/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/sra-info/CMakeFiles/sra-info.dir/formatter.cpp.o -MF CMakeFiles/sra-info.dir/formatter.cpp.o.d -o CMakeFiles/sra-info.dir/formatter.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-info/formatter.cpp [ 90%] Linking CXX executable ../../../bin/sra-info cd /shared/pkgsrc/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 /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sra-info.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sra-info sra-info.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-info.3.0.6 sra-info.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-info.3 sra-info [ 90%] Built target sra-info /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/DependInfo.cmake "--color=" /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build [ 90%] Linking CXX static library ../../lib/libngs-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk && /usr/pkg/bin/cmake -P CMakeFiles/ngs-c++.dir/cmake_clean_target.cmake cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libngs-c++.a "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" 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"dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" /usr/bin/ranlib ../../lib/libngs-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && rm -f libngs-c++.a.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && mv libngs-c++.a libngs-c++.a.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libngs-c++.a.3.0.6 libngs-c++.a.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libngs-c++.a.3 libngs-c++.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libngs-c++.a libngs-c++-static.a [ 90%] Built target ngs-c++ /usr/bin/make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/ngs/ngs-sdk /shared/pkgsrc/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 [ 90%] Linking CXX static library ../../lib/libncbi-ngs.a cd /shared/pkgsrc/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 cd /shared/pkgsrc/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 /usr/bin/ar qc ../../lib/libncbi-ngs.a "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" 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"language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" /usr/bin/ranlib ../../lib/libncbi-ngs.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && rm -f libncbi-ngs.a.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && mv libncbi-ngs.a libncbi-ngs.a.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/lib && ln -f -s libncbi-ngs.a.3.0.6 libncbi-ngs.a.3 cd 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tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/gcc -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o -MF CMakeFiles/vdb-config.dir/vdb-config.c.o.d -o CMakeFiles/vdb-config.dir/vdb-config.c.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c In file included from /usr/include/ctype.h:100, from /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c:62: /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c: In function 'KConfigNodePrintChildNames': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c:434:45: warning: array subscript has type 'char' [-Wchar-subscripts] 434 | beginsWithNumberinXml = isdigit(name[0]); | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c: In function 'ParamsConstruct': /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c:686:34: warning: array subscript has type 'char' [-Wchar-subscripts] 686 | if (tolower(dummy[0]) == 'y') { | ^ /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config.c:689:39: warning: array subscript has type 'char' [-Wchar-subscripts] 689 | else if (tolower(dummy[0]) == 'n') { | ^ [ 91%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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-I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -MF CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o.d -o CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/vdb-config/vdb-config-model.cpp [ 91%] Linking CXX executable ../../../bin/vdb-config cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/vdb-config.dir/link.txt --verbose=1 /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../ilib/libtui_cpp.a ../../../ilib/libtui.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f vdb-config.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv vdb-config vdb-config.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s vdb-config.3.0.6 vdb-config.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s vdb-config.3 vdb-config cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/vdb-config && /usr/pkg/bin/cmake -E copy /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/kfg/ncbi/default.kfg /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin/ncbi/default.kfg [ 91%] Built target vdb-config /usr/bin/make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make 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/shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sratools.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sratools sratools.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 sratools.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3 sratools [ 95%] Built target sratools /usr/bin/make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/depend cd 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tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ngs-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ngs-pileup && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -I/shared/pkgsrc/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/main.cpp.o -MF CMakeFiles/ngs-pileup.dir/main.cpp.o.d -o CMakeFiles/ngs-pileup.dir/main.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ngs-pileup/main.cpp [ 96%] Linking CXX executable ../../../bin/ngs-pileup cd /shared/pkgsrc/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 /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f ngs-pileup.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv ngs-pileup ngs-pileup.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s ngs-pileup.3.0.6 ngs-pileup.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s ngs-pileup.3 ngs-pileup [ 96%] Built target ngs-pileup /usr/bin/make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ref-variation /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build 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../../../ilib/libloader.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f ref-variation.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv ref-variation ref-variation.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s ref-variation.3.0.6 ref-variation.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s ref-variation.3 ref-variation [ 97%] Built target ref-variation /usr/bin/make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ref-variation /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation/CMakeFiles/var-expand.dir/DependInfo.cmake "--color=" /usr/bin/make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/build [ 97%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/var-expand\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd 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-D_DEBUGGING -D__mod__=\"tools/var-expand\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -MF CMakeFiles/var-expand.dir/var-expand.cpp.o.d -o CMakeFiles/var-expand.dir/var-expand.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ref-variation/var-expand.cpp [ 98%] Linking CXX executable ../../../bin/var-expand cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/var-expand.dir/link.txt --verbose=1 /shared/pkgsrc/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/var-expand.dir/common.cpp.o" "CMakeFiles/var-expand.dir/helper.cpp.o" "CMakeFiles/var-expand.dir/var-expand.cpp.o" -o ../../../bin/var-expand -L/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f var-expand.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv var-expand var-expand.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s var-expand.3.0.6 var-expand.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s var-expand.3 var-expand [ 98%] Built target var-expand /usr/bin/make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/depend cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-search /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build 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tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-search\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix 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tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -MF CMakeFiles/sra-search.dir/referencematchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-search/referencematchiterator.cpp [100%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search && /shared/pkgsrc/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/sra-search\" -Dx86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/gcc/x86_64 -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/bsd -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs/ngs-sdk -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/libs/inc -I/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ngs -Wall -O2 -I/usr/pkg/include -I/usr/include -Wno-unused-function -g -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -MF CMakeFiles/sra-search.dir/vdb-search.cpp.o.d -o CMakeFiles/sra-search.dir/vdb-search.cpp.o -c /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-search/vdb-search.cpp [100%] Linking CXX executable ../../../bin/sra-search cd /shared/pkgsrc/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 /shared/pkgsrc/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/shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libtk-version.a -lkapp /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libkapp.a ../../../ilib/libtk-version.a cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sra-search.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sra-search sra-search.3.0.6 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-search.3.0.6 sra-search.3 cd /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sra-search.3 sra-search [100%] Built target sra-search /usr/pkg/bin/cmake -E cmake_progress_start /shared/pkgsrc/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/CMakeFiles 0