=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for outpaddling-ncbi-vdb-38972fc.tar.gz => Checksum SHA512 OK for outpaddling-ncbi-vdb-38972fc.tar.gz => Checksum BLAKE2s OK for sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz => Checksum SHA512 OK for sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz ===> Installing dependencies for sra-tools-3.0.6 => Tool dependency cmake>=3.18: found cmake-3.27.7 => Tool dependency mktools-[0-9]*: found mktools-20220614 => Tool dependency bison>=1.0: found bison-3.8.2nb1 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency libepoll-shim>=0.0.20210418: found libepoll-shim-0.0.20230411 => Full dependency libxml2>=2.10.4nb2: found libxml2-2.10.4nb2 => Full dependency hdf5>=1.8.11: found hdf5-1.12.2 => Full dependency zstd>=1.3.6: found zstd-1.5.5 ===> Overriding tools for sra-tools-3.0.6 ===> Extracting for sra-tools-3.0.6 ===> Patching for sra-tools-3.0.6 => Applying pkgsrc patches for sra-tools-3.0.6 => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-build_env.cmake => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-build_env.cmake Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-build_env.cmake,v 1.1 2023/08/29 00:00:25 bacon Exp $ | |# static standard libs are not standard nor easy to install on Alma Linux | |--- build/env.cmake.orig 2023-08-13 18:06:02.445968665 +0000 |+++ build/env.cmake -------------------------- Patching file build/env.cmake using Plan A... Hunk #1 succeeded at 555. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.1 2023/08/29 00:00:25 bacon Exp $ | |# Add NetBSD pthread_main_np() stand-in | |--- ncbi-vdb/libs/kproc/bsd/sysmgr.c.orig 2023-08-15 12:41:59.000000000 +0000 |+++ ncbi-vdb/libs/kproc/bsd/sysmgr.c -------------------------- Patching file ncbi-vdb/libs/kproc/bsd/sysmgr.c using Plan A... Hunk #1 succeeded at 30. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.1 2023/08/29 00:00:25 bacon Exp $ | |# Disable java | |--- ngs/ngs-java/CMakeLists.txt.orig 2023-08-13 21:46:05.343038455 +0000 |+++ ngs/ngs-java/CMakeLists.txt -------------------------- Patching file ngs/ngs-java/CMakeLists.txt using Plan A... Hunk #1 succeeded at 99. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.1 2023/08/29 00:00:25 bacon Exp $ | |# Add NetBSD pthread_main_np() stand-in | |--- tools/external/driver-tool/sratools.cpp.orig 2023-08-15 12:51:29.845642918 +0000 |+++ tools/external/driver-tool/sratools.cpp -------------------------- Patching file tools/external/driver-tool/sratools.cpp using Plan A... Hunk #1 succeeded at 578. done ===> Creating toolchain wrappers for sra-tools-3.0.6 ===> Configuring for sra-tools-3.0.6 => Substituting "binpath" in tools/external/driver-tool/file-path.posix.cpp => Substituting "etcdir" in ncbi-vdb/libs/kfg/config.c => Substituting "submoddir" in CMakeLists.txt cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON .. -- The C compiler identification is AppleClang 15.0.0.15000040 -- The CXX compiler identification is AppleClang 15.0.0.15000040 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done VERSION=3.0.6 -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /Users/pbulk/build/biology/sra-tools/work/.tools/bin/bison (found suitable version "3.8.2", minimum required is "3") -- Found Python3: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3.10 (found version "3.10.7") found components: Interpreter -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) RUN_SANITIZER_TESTS: OFF Using local mbedtls headers from interfaces/ext/mbedtls Building local copy ext/mbedtls... -- Looking for gnu/libc-version.h -- Looking for gnu/libc-version.h - not found No mbedtls libs found installed in the system, using local copy... -- Configuring done (2.8s) -- Generating done (0.3s) -- Build files have been written to: /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build for f in /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ncbi-vdb/CMakeFiles/*/link.txt; do /opt/pkg/bin/nbsed -e 's|@rpath|/opt/pkg/lib|g' ${f} > ${f}.tmp && /bin/mv -f ${f}.tmp ${f}; done cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build && /opt/pkg/bin/bmake /opt/pkg/bin/cmake -S/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb -B/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build --check-build-system CMakeFiles/Makefile.cmake 0 /opt/pkg/bin/cmake -E cmake_progress_start /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/CMakeFiles /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build//CMakeFiles/progress.marks /opt/pkg/bin/bmake -f CMakeFiles/Makefile2 all /opt/pkg/bin/bmake -f libs/ktst/CMakeFiles/ktst.dir/build.make libs/ktst/CMakeFiles/ktst.dir/depend cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/ktst /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst/CMakeFiles/ktst.dir/DependInfo.cmake "--color=" /opt/pkg/bin/bmake -f libs/ktst/CMakeFiles/ktst.dir/build.make libs/ktst/CMakeFiles/ktst.dir/build [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testenv.cpp.o cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst && /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DLONG_DOUBLE_IS_NOT_R128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Dx86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/mac -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/../ngs/ngs-sdk -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -g -std=c++11 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -MD -MT libs/ktst/CMakeFiles/ktst.dir/testenv.cpp.o -MF CMakeFiles/ktst.dir/testenv.cpp.o.d -o CMakeFiles/ktst.dir/testenv.cpp.o -c /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/ktst/testenv.cpp [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testcase.cpp.o cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst && /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DLONG_DOUBLE_IS_NOT_R128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Dx86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/mac -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/../ngs/ngs-sdk -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -g -std=c++11 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -MD -MT libs/ktst/CMakeFiles/ktst.dir/testcase.cpp.o -MF CMakeFiles/ktst.dir/testcase.cpp.o.d -o CMakeFiles/ktst.dir/testcase.cpp.o -c /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/ktst/testcase.cpp [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testrunner.cpp.o cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst && /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DLONG_DOUBLE_IS_NOT_R128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Dx86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/mac -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/../ngs/ngs-sdk -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -g -std=c++11 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -MD -MT libs/ktst/CMakeFiles/ktst.dir/testrunner.cpp.o -MF CMakeFiles/ktst.dir/testrunner.cpp.o.d -o CMakeFiles/ktst.dir/testrunner.cpp.o -c /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/ktst/testrunner.cpp [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/unix/systestenv.cpp.o cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst && /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DLONG_DOUBLE_IS_NOT_R128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Dx86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/mac -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/../ngs/ngs-sdk -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -g -std=c++11 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -MD -MT libs/ktst/CMakeFiles/ktst.dir/unix/systestenv.cpp.o -MF CMakeFiles/ktst.dir/unix/systestenv.cpp.o.d -o CMakeFiles/ktst.dir/unix/systestenv.cpp.o -c /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/ktst/unix/systestenv.cpp [ 0%] Linking CXX static library ../../lib/libktst.a cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst && /opt/pkg/bin/cmake -P CMakeFiles/ktst.dir/cmake_clean_target.cmake cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/ktst && /opt/pkg/bin/cmake -E cmake_link_script CMakeFiles/ktst.dir/link.txt --verbose=1 /usr/bin/ar Scr ../../lib/libktst.a CMakeFiles/ktst.dir/testenv.cpp.o CMakeFiles/ktst.dir/testcase.cpp.o CMakeFiles/ktst.dir/testrunner.cpp.o CMakeFiles/ktst.dir/unix/systestenv.cpp.o /usr/bin/ranlib -no_warning_for_no_symbols -c ../../lib/libktst.a cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib && rm -f libktst.a.3.0.6 cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib && mv libktst.a libktst.a.3.0.6 cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib && ln -f -s libktst.a.3.0.6 libktst.a.3 cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib && ln -f -s libktst.a.3 libktst.a cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/lib && ln -f -s libktst.a libktst-static.a [ 0%] Built target ktst /opt/pkg/bin/bmake -f libs/align/CMakeFiles/ncbi-bam.dir/build.make libs/align/CMakeFiles/ncbi-bam.dir/depend cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/align /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/align /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/align/CMakeFiles/ncbi-bam.dir/DependInfo.cmake "--color=" /opt/pkg/bin/bmake -f libs/align/CMakeFiles/ncbi-bam.dir/build.make libs/align/CMakeFiles/ncbi-bam.dir/build [ 0%] Building C object libs/align/CMakeFiles/ncbi-bam.dir/bam.c.o cd /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build/libs/align && /Users/pbulk/build/biology/sra-tools/work/.cwrapper/bin/cc -DBSD -DDEBUG -DHAVE_Z128 -DLONG_DOUBLE_IS_NOT_R128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/align\" -Dx86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64 -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/mac -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/os/unix -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/../ngs/ngs-sdk -I/Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -g -std=c11 -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -MD -MT libs/align/CMakeFiles/ncbi-bam.dir/bam.c.o -MF CMakeFiles/ncbi-bam.dir/bam.c.o.d -o CMakeFiles/ncbi-bam.dir/bam.c.o -c /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/align/bam.c /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/align/bam.c:3652:30: warning: variable 'B' set but not used [-Wunused-but-set-variable] unsigned B = i + 2; ^ 1 warning generated. In file included from /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/align/bam.c:32: In file included from /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/kfs/file.h:39: In file included from /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/kfs/file-v2.h:35: In file included from /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/kfc/refcount.h:39: /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:66:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:89:11: error: invalid output constraint '=&a' in asm : "=&a" ( cmp ), "=&r" ( rtn ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:127:18: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=r" ( c ), "=m" ( v -> counter ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:126:15: note: use constraint modifier "w" "sete %0" ^~ %w0 /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:143:18: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=r" ( c ), "=m" ( v -> counter ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:142:15: note: use constraint modifier "w" "sete %0" ^~ %w0 /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:160:11: error: invalid output constraint '=a' in asm : "=a" ( rtn ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:183:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:208:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:233:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:258:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:283:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:308:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:333:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/interfaces/cc/clang/x86_64/atomic32.h:355:11: error: invalid output constraint '=&a' in asm : "=&a" ( rtn ), "=&r" ( sum ) ^ /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/libs/align/bam.c:3652:30: warning: variable 'B' set but not used [-Wunused-but-set-variable] unsigned B = i + 2; ^ 3 warnings and 11 errors generated. *** Error code 1 Stop. bmake[4]: stopped in /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build *** Error code 1 Stop. bmake[3]: stopped in /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build *** Error code 1 Stop. bmake[2]: stopped in /Users/pbulk/build/biology/sra-tools/work/sra-tools-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build *** Error code 1 Stop. bmake[1]: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools *** Error code 1 Stop. bmake: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/sra-tools