=> "/opt/pkg/bin/bmake" ["-C", "/Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools", "configure", "PYTHON_VERSION_REQD=313", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] => Checksum BLAKE2s OK for ncbi-ncbi-vdb-3.2.0.tar.gz => Checksum SHA512 OK for ncbi-ncbi-vdb-3.2.0.tar.gz => Checksum BLAKE2s OK for sra-tools-3.2.0.tar.gz => Checksum SHA512 OK for sra-tools-3.2.0.tar.gz ===> Installing dependencies for sra-tools-3.2.0nb2 ========================================================================== The following variables will affect the build process of this package, sra-tools-3.2.0nb2. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 313 Based on these variables, the following variables have been set: * PYPACKAGE = python313 You may want to abort the process now with CTRL-C and change the value of variables in the first group before continuing. Be sure to run `/opt/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency cmake>=3.18: found cmake-4.4.4 => Tool dependency bash-[0-9]*: found bash-5.3.20 => 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 hdf5>=1.8.11: found hdf5-1.14.6 => Full dependency libepoll-shim>=0.0.20210418: found libepoll-shim-0.0.20240608 => Full dependency libxml2>=2.14.6nb2: found libxml2-2.15.4 => Full dependency python313>=3.13: found python313-3.13.16 => Full dependency zstd>=1.3.6: found zstd-1.5.7 => Full dependency gettext-lib>=0.22: found gettext-lib-1.0 => Full dependency libiconv>=1.9.1: found libiconv-1.19 => Full dependency libaec>=1.0.4: found libaec-1.1.3 => Full dependency zlib>=1.1.4: found zlib-1.3.1 ===> Overriding tools for sra-tools-3.2.0nb2 ===> Extracting for sra-tools-3.2.0nb2 ===> Patching for sra-tools-3.2.0nb2 => Applying pkgsrc patches for sra-tools-3.2.0nb2 => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-build_env.cmake => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-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 1.3 2025/02/02 14:25:34 bacon Exp $ | |# static standard libs are not standard nor easy to install on Alma Linux | |--- build/env.cmake.orig 2025-01-29 20:24:37.167226512 +0000 |+++ build/env.cmake -------------------------- Patching file build/env.cmake using Plan A... Hunk #1 succeeded at 574. Hunk #2 succeeded at 582. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-libs_kxml_xml.c => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-libs_kxml_xml.c Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-libs_kxml_xml.c,v 1.1 2025/04/25 07:37:15 wiz Exp $ | |libxml2 2.14 compatibility. | |--- libs/kxml/xml.c.orig 2025-04-25 07:35:01.143677606 +0000 |+++ libs/kxml/xml.c -------------------------- Patching file libs/kxml/xml.c using Plan A... Hunk #1 succeeded at 171. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-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 1.3 2025/02/02 14:25:34 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-macos-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-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 1.3 2025/02/02 14:25:34 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-macos-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ngs_ngs-python_examples_CMakeLists.txt,v 1.2 2025/02/02 14:25:34 bacon Exp $ | |# Canonicalize python examples dir | |--- ngs/ngs-python/examples/CMakeLists.txt.orig 2024-11-18 12:08:54.646596198 +0000 |+++ ngs/ngs-python/examples/CMakeLists.txt -------------------------- Patching file ngs/ngs-python/examples/CMakeLists.txt using Plan A... Hunk #1 succeeded at 53 (offset -1 lines). done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ngs_ngs-sdk_examples_CMakeLists.txt,v 1.2 2025/02/02 14:25:35 bacon Exp $ | |# Canonicalize examples dir | |--- ngs/ngs-sdk/examples/CMakeLists.txt.orig 2024-11-18 12:10:46.495627136 +0000 |+++ ngs/ngs-sdk/examples/CMakeLists.txt -------------------------- Patching file ngs/ngs-sdk/examples/CMakeLists.txt using Plan A... Hunk #1 succeeded at 62. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-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 1.3 2025/02/02 14:25:35 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 580 (offset 2 lines). done ===> Creating toolchain wrappers for sra-tools-3.2.0nb2 ===> Configuring for sra-tools-3.2.0nb2 => 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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON .. -- The C compiler identification is AppleClang 17.0.0.17000013 -- The CXX compiler identification is AppleClang 17.0.0.17000013 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /var/tmp/work/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: /var/tmp/work/biology/sra-tools/work/.cwrapper/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (deprecated) at build/env.cmake:32 (cmake_policy): The OLD behavior for policy CMP0115 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. Call Stack (most recent call first): CMakeLists.txt:78 (include) This warning is for project developers. Use -Wno-author or -Wno-deprecated to suppress it. VERSION=3.2.0 -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /var/tmp/work/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 (3.8s) -- Generating done (0.7s) -- Build files have been written to: /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build && /opt/pkg/bin/bmake /opt/pkg/bin/cmake -S/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb -B/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build --check-build-system CMakeFiles/Makefile.cmake 0 /opt/pkg/bin/cmake -E cmake_progress_start /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/CMakeFiles /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/ktst /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst/CMakeFiles/ktst.dir/DependInfo.cmake "--color=" ktst /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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst && /var/tmp/work/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Darm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang/arm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/mac -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/../ngs/ngs-sdk -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -Wno-c++17-compat-mangling -g -std=c++11 -arch arm64 -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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/ktst/testenv.cpp [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testcase.cpp.o cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst && /var/tmp/work/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Darm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang/arm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/mac -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/../ngs/ngs-sdk -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -Wno-c++17-compat-mangling -g -std=c++11 -arch arm64 -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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/ktst/testcase.cpp [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testrunner.cpp.o cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst && /var/tmp/work/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Darm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang/arm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/mac -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/../ngs/ngs-sdk -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -Wno-c++17-compat-mangling -g -std=c++11 -arch arm64 -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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/ktst/testrunner.cpp [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/unix/systestenv.cpp.o cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst && /var/tmp/work/biology/sra-tools/work/.cwrapper/bin/c++ -DBSD -DDEBUG -DHAVE_Z128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/ktst\" -Darm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang/arm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/mac -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/../ngs/ngs-sdk -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -Wno-c++17-compat-mangling -g -std=c++11 -arch arm64 -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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/ktst/unix/systestenv.cpp [ 0%] Linking CXX static library ../../lib/libktst.a cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/ktst && /opt/pkg/bin/cmake -P CMakeFiles/ktst.dir/cmake_clean_target.cmake cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/lib && rm -f libktst.a.3.2.0 cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/lib && mv libktst.a libktst.a.3.2.0 cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/lib && ln -f -s libktst.a.3.2.0 libktst.a.3 cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/lib && ln -f -s libktst.a.3 libktst.a cd /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/align /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/align /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/align/CMakeFiles/ncbi-bam.dir/DependInfo.cmake "--color=" ncbi-bam /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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build/libs/align && /var/tmp/work/biology/sra-tools/work/.cwrapper/bin/cc -DBSD -DDEBUG -DHAVE_Z128 -DMAC -DPKGNAME=mac64 -DUNIX -D_ARCH_BITS=64 -D_DEBUGGING -D_LIBRARY -D__mod__=\"libs/align\" -Darm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/cc/clang/arm64 -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/mac -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/unix -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/../ngs/ngs-sdk -I/var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/ext/mbedtls -Wall -Wno-unused-function -g -std=gnu11 -arch arm64 -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 /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/align/bam.c In file included from /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/align/bam.c:65: /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/interfaces/os/mac/os-native.h:73:7: error: static declaration of 'strchrnul' follows non-static declaration 73 | char *strchrnul ( const char *str, int c ) | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_string.h:198:9: note: previous declaration is here 198 | strchrnul(const char *__s, int __c); | ^ /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/libs/align/bam.c:3665:30: warning: variable 'B' set but not used [-Wunused-but-set-variable] 3665 | unsigned B = i + 2; | ^ 1 warning and 1 error generated. *** Error code 1 Stop. bmake[4]: stopped making "libs/align/CMakeFiles/ncbi-bam.dir/build" in /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build *** Error code 1 Stop. bmake[3]: stopped making "all" in /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build *** Error code 1 Stop. bmake[2]: stopped making "default_target" in /var/tmp/work/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build *** Error code 1 Stop. bmake[1]: stopped making "configure" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools *** Error code 1 Stop. bmake: stopped making "configure" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/sra-tools