+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/cgatools-1.8.0.1/work.log + su pbulk -c '"$@"' make /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/cgatools-1.8.0.1/work.log WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead. => Checksum SHA1 OK for cgatools-1.8.0.1-source.tar.gz => Checksum RMD160 OK for cgatools-1.8.0.1-source.tar.gz ===> Installing dependencies for cgatools-1.8.0.1 => Tool dependency cmake>=3.18: found cmake-3.31.7nb2 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency doxygen-[0-9]*: found doxygen-1.13.2nb2 => Build dependency boost-headers-1.87.*: found boost-headers-1.87.0nb3 => Build dependency gcc13>=13.1.0: found gcc13-13.3.0 => Full dependency boost-libs-1.87.*: found boost-libs-1.87.0nb2 => Full dependency boost-libs>=1.87.0: found boost-libs-1.87.0nb2 => Full dependency gcc13-libs>=13.2.0: found gcc13-libs-13.3.0 ===> Overriding tools for cgatools-1.8.0.1 ===> Extracting for cgatools-1.8.0.1 ===> Patching for cgatools-1.8.0.1 => Applying pkgsrc patches for cgatools-1.8.0.1 => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-CMakeLists.txt => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Disable HTML generation, it doesn't work due to LD_LIBRARY_PATH and |people can read docs online anyway. | |--- CMakeLists.txt.orig 2013-08-28 22:35:15.000000000 +0000 |+++ CMakeLists.txt -------------------------- Patching file CMakeLists.txt using Plan A... Hunk #1 succeeded at 127. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_cgdata_GenomeMetadata.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_cgdata_GenomeMetadata.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/cgdata/GenomeMetadata.cpp.orig 2013-08-28 22:35:17.000000000 +0000 |+++ cgatools/cgdata/GenomeMetadata.cpp -------------------------- Patching file cgatools/cgdata/GenomeMetadata.cpp using Plan A... Hunk #1 succeeded at 215. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_command_Evidence2Sam.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_command_Evidence2Sam.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/command/Evidence2Sam.cpp.orig 2013-08-28 22:35:19.000000000 +0000 |+++ cgatools/command/Evidence2Sam.cpp -------------------------- Patching file cgatools/command/Evidence2Sam.cpp using Plan A... Hunk #1 succeeded at 522. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_command_JunctionCmp.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_command_JunctionCmp.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/command/JunctionCmp.cpp.orig 2013-08-28 22:35:19.000000000 +0000 |+++ cgatools/command/JunctionCmp.cpp -------------------------- Patching file cgatools/command/JunctionCmp.cpp using Plan A... Hunk #1 succeeded at 41. Hunk #2 succeeded at 60. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_command_JunctionDiff.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_command_JunctionDiff.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/command/JunctionDiff.cpp.orig 2013-08-28 22:35:19.000000000 +0000 |+++ cgatools/command/JunctionDiff.cpp -------------------------- Patching file cgatools/command/JunctionDiff.cpp using Plan A... Hunk #1 succeeded at 58. Hunk #2 succeeded at 90. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_core.hpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_core.hpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/core.hpp.orig 2013-08-28 22:35:18.000000000 +0000 |+++ cgatools/core.hpp -------------------------- Patching file cgatools/core.hpp using Plan A... Hunk #1 succeeded at 43. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_mapping_LaneBatchCache.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_mapping_LaneBatchCache.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/mapping/LaneBatchCache.cpp.orig 2013-08-28 22:35:17.000000000 +0000 |+++ cgatools/mapping/LaneBatchCache.cpp -------------------------- Patching file cgatools/mapping/LaneBatchCache.cpp using Plan A... Hunk #1 succeeded at 83. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_util_Files.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_util_Files.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 | |--- cgatools/util/Files.cpp.orig 2013-08-28 22:35:16.000000000 +0000 |+++ cgatools/util/Files.cpp -------------------------- Patching file cgatools/util/Files.cpp using Plan A... Hunk #1 succeeded at 47. Hunk #2 succeeded at 59. Hunk #3 succeeded at 95. Hunk #4 succeeded at 122. Hunk #5 succeeded at 138. Hunk #6 succeeded at 161. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_variants_AlleleDiffSegment.hpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_variants_AlleleDiffSegment.hpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Need utility.h for std::pair | |--- cgatools/variants/AlleleDiffSegment.hpp.orig 2013-08-28 22:35:19.000000000 +0000 |+++ cgatools/variants/AlleleDiffSegment.hpp -------------------------- Patching file cgatools/variants/AlleleDiffSegment.hpp using Plan A... Hunk #1 succeeded at 18. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_variants_calib_CalibratedScorer.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_variants_calib_CalibratedScorer.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Support BOOST_FILESYSTEM_VERSION=3 |Avoid "SS" define on SunOS. | |--- cgatools/variants/calib/CalibratedScorer.cpp.orig 2013-08-28 22:35:19.000000000 +0000 |+++ cgatools/variants/calib/CalibratedScorer.cpp -------------------------- Patching file cgatools/variants/calib/CalibratedScorer.cpp using Plan A... Hunk #1 succeeded at 191. Hunk #2 succeeded at 214. Hunk #3 succeeded at 227. Hunk #4 succeeded at 251. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_variants_calib_CalibratedScorer.hpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools/patches/patch-cgatools_variants_calib_CalibratedScorer.hpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD$ | |Avoid "SS" define on SunOS. | |--- cgatools/variants/calib/CalibratedScorer.hpp.orig 2013-08-28 22:35:19.000000000 +0000 |+++ cgatools/variants/calib/CalibratedScorer.hpp -------------------------- Patching file cgatools/variants/calib/CalibratedScorer.hpp using Plan A... Hunk #1 succeeded at 152. done ===> Creating toolchain wrappers for cgatools-1.8.0.1 /usr/bin/sed -e '/^#/d' -e 's,@LINK_ARCH_DEFAULT@,link_arch64,g' -e 's,@LINK_LIBGCC_DEFAULT@,link_libgcc_arch64,g' -e 's,@LIBGCC_PREFIX@,/opt/local/gcc13/x86_64-sun-solaris2.11,g' < ../../extra/gcc13-libs/files/specs.pkgsrc > /home/pbulk/build/joyent/cgatools/work/.cwrapper/specs.pkgsrc ===> Configuring for cgatools-1.8.0.1 /usr/bin/mkdir -p /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build => Fixing CMAKE_MODULE_PATH in CMakeLists.txt INFO: [subst.mk:cmake] Nothing changed in "CMakeLists.txt". CMake Deprecation Warning at CMakeLists.txt:17 (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 CMake Warning (dev) at /opt/local/share/cmake-3.31/Modules/Platform/SunOS.cmake:20 (include): File /opt/local/share/cmake-3.31/Modules/Platform/SunOS.cmake includes /home/pbulk/build/joyent/cgatools/work/.buildlink/cmake-Modules/Platform/UnixPaths.cmake (found via CMAKE_MODULE_PATH) which shadows /opt/local/share/cmake-3.31/Modules/Platform/UnixPaths.cmake. This may cause errors later on . Policy CMP0017 is not set: Prefer files from the CMake module directory when including from there. Run "cmake --help-policy CMP0017" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /opt/local/share/cmake-3.31/Modules/CMakeSystemSpecificInformation.cmake:32 (include) CMakeLists.txt:18 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/pbulk/build/joyent/cgatools/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/joyent/cgatools/work/.cwrapper/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:74 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /home/pbulk/build/joyent/cgatools/work/.buildlink/lib/cmake/Boost-1.87.0/BoostConfig.cmake (found suitable version "1.87.0", minimum required is "1.35.0") found components: regex iostreams filesystem program_options date_time system thread -- Found Doxygen: /opt/local/bin/doxygen (found version "1.13.2") found components: doxygen dot -- Configuring done (3.9s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_MANDIR -- Build files have been written to: /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build => Rewrite cmake Dependencies files