+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.51.1/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.51.1/work.log WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead. => Checksum BLAKE2s OK for kallisto-0.51.1.tar.gz => Checksum SHA512 OK for kallisto-0.51.1.tar.gz ===> Installing dependencies for kallisto-0.51.1 => Tool dependency autoconf>=2.50: found autoconf-2.72 => Tool dependency cmake>=3.18: found cmake-3.31.6 => Tool dependency gmake>=3.81: found gmake-4.4.1 => Tool dependency pax>=20040802: found pax-20210219 => 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 htslib>=1.21: found htslib-1.21nb3 => Full dependency libaec>=1.0.4: found libaec-1.1.3 => Full dependency zlib>=1.2.3: found zlib-1.3.1 ===> Overriding tools for kallisto-0.51.1 ===> Extracting for kallisto-0.51.1 /bin/cp /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/files/kallisto-test /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 /usr/bin/rm -rf /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/htslib ===> Patching for kallisto-0.51.1 => Applying pkgsrc patches for kallisto-0.51.1 => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-CMakeLists.txt => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-CMakeLists.txt,v 1.6 2024/09/20 00:03:15 bacon Exp $ | |# Use external htslib | |--- CMakeLists.txt.orig 2024-07-20 19:07:27.000000000 +0000 |+++ CMakeLists.txt -------------------------- Patching file CMakeLists.txt using Plan A... Hunk #1 succeeded at 23. Hunk #2 succeeded at 69. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# Respect pkgsrc build flags | |--- ext/bifrost/CMakeLists.txt.orig 2024-07-23 11:56:13.172038229 +0000 |+++ ext/bifrost/CMakeLists.txt -------------------------- Patching file ext/bifrost/CMakeLists.txt using Plan A... Hunk #1 succeeded at 6. Hunk #2 succeeded at 19. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# vfscanf() not found on NetBSD 9 | |--- ext/bifrost/src/BitContainer.cpp.orig 2023-11-01 12:46:19.000000000 +0000 |+++ ext/bifrost/src/BitContainer.cpp -------------------------- Patching file ext/bifrost/src/BitContainer.cpp using Plan A... Hunk #1 succeeded at 1. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# vfscanf() not found on NetBSD 9 | |--- ext/bifrost/src/ColorSet.cpp.orig 2023-11-03 12:48:11.435933052 +0000 |+++ ext/bifrost/src/ColorSet.cpp -------------------------- Patching file ext/bifrost/src/ColorSet.cpp using Plan A... Hunk #1 succeeded at 1. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# Use native popcnt | |--- ext/bifrost/src/libpopcnt.h.orig 2023-07-24 12:34:08.037669065 +0000 |+++ ext/bifrost/src/libpopcnt.h -------------------------- Patching file ext/bifrost/src/libpopcnt.h using Plan A... Hunk #1 succeeded at 32. Hunk #2 succeeded at 586. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# Portability | |--- ext/bifrost/src/strict_fstream.hpp.orig 2023-06-27 10:45:00.000000000 +0000 |+++ ext/bifrost/src/strict_fstream.hpp -------------------------- Patching file ext/bifrost/src/strict_fstream.hpp using Plan A... Hunk #1 succeeded at 64. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_Bootstrap.h => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_Bootstrap.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_Bootstrap.h,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# Portability | |--- src/Bootstrap.h.orig 2020-04-01 16:56:42 UTC |+++ src/Bootstrap.h -------------------------- Patching file src/Bootstrap.h using Plan A... Hunk #1 succeeded at 1. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_CMakeLists.txt => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_CMakeLists.txt,v 1.6 2024/09/20 00:03:15 bacon Exp $ | |# Use external htslib | |--- src/CMakeLists.txt.orig 2024-07-23 11:52:01.089699466 +0000 |+++ src/CMakeLists.txt -------------------------- Patching file src/CMakeLists.txt using Plan A... Hunk #1 succeeded at 3. Hunk #2 succeeded at 17. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_kseq.h => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_kseq.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_kseq.h,v 1.4 2024/09/20 00:03:15 bacon Exp $ | |# Portability | |--- src/kseq.h.orig 2019-11-04 16:28:52 UTC |+++ src/kseq.h -------------------------- Patching file src/kseq.h using Plan A... Hunk #1 succeeded at 28 (offset -4 lines). done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_main.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_main.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_main.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $ | |# Portability | |--- src/main.cpp.orig 2023-11-01 12:46:19.000000000 +0000 |+++ src/main.cpp -------------------------- Patching file src/main.cpp using Plan A... Hunk #1 succeeded at 11. done ===> Creating toolchain wrappers for kallisto-0.51.1 ===> Configuring for kallisto-0.51.1 => Substituting "test" in kallisto-test => Fixing CMAKE_MODULE_PATH in CMakeLists.txt INFO: [subst.mk:cmake] Nothing changed in "CMakeLists.txt". => Checking for portability problems in extracted files CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 13.3.0 -- The CXX compiler identification is GNU 13.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/gcc - 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: /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS_CXX17 -- Performing Test COMPILER_SUPPORTS_CXX17 - Success shared build -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found HDF5: hdf5-shared (found version "1.14.6") -- Found ZLIB: /opt/pkg/lib/libz.so (found version "1.3.1") -- Configuring done (6.9s) -- Generating done (0.0s) -- Build files have been written to: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 => Rewrite cmake Dependencies files