+ 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-3.31.1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency doxygen-[0-9]*: found doxygen-1.12.0nb3
=> Build dependency boost-headers-1.86.*: found boost-headers-1.86.0
=> Build dependency gcc13>=13.1.0: found gcc13-13.3.0
=> Full dependency boost-libs-1.86.*: found boost-libs-1.86.0nb3
=> Full dependency boost-libs>=1.86.0: found boost-libs-1.86.0nb3
=> 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-2024Q4-x86_64/joyent/cgatools/patches/patch-CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_cgdata_GenomeMetadata.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_command_Evidence2Sam.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_command_JunctionCmp.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_command_JunctionDiff.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_core.hpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_mapping_LaneBatchCache.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_util_Files.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_variants_AlleleDiffSegment.hpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_variants_calib_CalibratedScorer.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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-2024Q4-x86_64/joyent/cgatools/patches/patch-cgatools_variants_calib_CalibratedScorer.hpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-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 <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> 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.
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found Boost: /home/pbulk/build/joyent/cgatools/work/.buildlink/include (found suitable version "1.86.0", minimum required is "1.35.0") found components: regex iostreams filesystem program_options date_time system thread chrono atomic
-- Found Doxygen: /opt/local/bin/doxygen (found version "1.12.0") found components: doxygen dot
-- Configuring done (3.9s)
-- Generating done (0.1s)
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