+ local run_cmd + run_cmd=run_su + shift + run_su /usr/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/sra-tools-3.0.6/work.log + su pbulk -c '"$@"' make /usr/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/sra-tools-3.0.6/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 ===> Installing for sra-tools-3.0.6 => Generating pre-install file lists /usr/pkg/bin/cmake -S/home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c -B/home/pbulk/build/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 /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/CMakeFiles /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build//CMakeFiles/progress.marks /usr/pkg/bin/bmake -f CMakeFiles/Makefile2 all /usr/pkg/bin/bmake -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/shared /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/shared 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&& /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ref-variation /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation/CMakeFiles/ref-variation.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/build [ 90%] Built target ref-variation /usr/pkg/bin/bmake -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/ref-variation /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/ref-variation/CMakeFiles/var-expand.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/build [ 91%] Built target var-expand /usr/pkg/bin/bmake -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-search /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-search/CMakeFiles/sra-search.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/build [ 93%] Built target sra-search /usr/pkg/bin/bmake -f tools/external/test-sra/CMakeFiles/test-sra.dir/build.make tools/external/test-sra/CMakeFiles/test-sra.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/test-sra /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/test-sra /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/test-sra/CMakeFiles/test-sra.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/test-sra/CMakeFiles/test-sra.dir/build.make tools/external/test-sra/CMakeFiles/test-sra.dir/build [ 94%] Built target test-sra /usr/pkg/bin/bmake -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/cache-mgr /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/cache-mgr /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build [ 95%] Built target cache-mgr /usr/pkg/bin/bmake -f tools/external/driver-tool/CMakeFiles/tool-arguments-header.dir/build.make tools/external/driver-tool/CMakeFiles/tool-arguments-header.dir/depend cd 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/home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool && sh generate-args-info.sh /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin [ 95%] Built target tool-arguments-header /usr/pkg/bin/bmake -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool/CMakeFiles/sratools.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/build [ 95%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /home/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces 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/home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/driver-tool/tool-args.cpp [ 95%] Linking CXX executable ../../../bin/sratools cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/driver-tool && /usr/pkg/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 /home/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ -Wall -pipe -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/home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && rm -f sratools.3.0.6 cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && mv sratools sratools.3.0.6 cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3.0.6 sratools.3 cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/bin && ln -f -s sratools.3 sratools [ 99%] Built target sratools /usr/pkg/bin/bmake -f tools/external/sra-info/CMakeFiles/sra-info.dir/build.make tools/external/sra-info/CMakeFiles/sra-info.dir/depend cd /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/tools/external/sra-info /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-info /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/tools/external/sra-info/CMakeFiles/sra-info.dir/DependInfo.cmake "--color=" /usr/pkg/bin/bmake -f tools/external/sra-info/CMakeFiles/sra-info.dir/build.make tools/external/sra-info/CMakeFiles/sra-info.dir/build [100%] Built target sra-info /usr/pkg/bin/cmake -E cmake_progress_start /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/cmake-pkgsrc-build/CMakeFiles 0 /usr/pkg/bin/bmake -f CMakeFiles/Makefile2 preinstall Installing the project stripped... /usr/pkg/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Debug" mkdir: /usr/pkg/bin/ncbi: Permission denied cp: /usr/pkg/bin/ncbi/default.kfg: No such file or directory mkdir: /usr/pkg/bin/ncbi: Permission denied cp: /usr/pkg/bin/ncbi/certs.kfg: No such file or directory mkdir: /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/shared/kfgsums: Not a directory cp: /home/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/shared/kfgsums/vdb-copy.kfg: Not a directory -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/lib/libncbi-ngs-c++.a.3.0.6 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/lib/libncbi-ngs-c++.a.3 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/lib/libncbi-ngs-c++.a -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/lib/libncbi-ngs-c++-static.a -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/include/ncbi-vdb/NGS.hpp -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples/FragTest.cpp -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples/AlignTest.cpp -- Installing: 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Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/test-sra.3.0.6 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/test-sra.3 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/test-sra -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/cache-mgr.3.0.6 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/cache-mgr.3 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/cache-mgr -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/sratools.3.0.6 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/sratools.3 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/sratools -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/sra-info.3.0.6 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/sra-info.3 -- Installing: /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/sra-info strip /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/bin/*.3.0.6 /bin/mv /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples-sratools /bin/mkdir -p /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples/sra-tools /bin/mv /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples-sratools/* /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples/sra-tools /bin/rmdir /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples-sratools /bin/mv /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples-python /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples/sra-tools/python mv: rename /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples-python to /home/pbulk/build/biology/sra-tools/work/.destdir/usr/pkg/share/examples/sra-tools/python: No such file or directory *** Error code 1 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-netbsd-trunk-x86_64/biology/sra-tools *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-netbsd-trunk-x86_64/biology/sra-tools