+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb34/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb34/work.log => Checksum BLAKE2s OK for openbabel-3.1.1.tar.gz => Checksum SHA512 OK for openbabel-3.1.1.tar.gz ===> Installing dependencies for openbabel-3.1.1nb34 ========================================================================== The supported build options for openbabel are: wxwidgets You can select which build options to use by setting PKG_DEFAULT_OPTIONS or the following variable. Its current value is shown: PKG_OPTIONS.openbabel (not defined) ========================================================================== => Tool dependency cmake>=0: found cmake-3.31.7 => Tool dependency glib2-tools-[0-9]*: found glib2-tools-2.82.5 => Tool dependency pkgconf-[0-9]*: found pkgconf-2.4.3 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency boost-headers-1.87.*: found boost-headers-1.87.0nb3 => Build dependency eigen3>=3.1.2: found eigen3-3.4.0nb1 => Build dependency rapidjson>=1.1.0: found rapidjson-1.1.0nb2 => Full dependency boost-libs-1.87.*: found boost-libs-1.87.0nb1 => Full dependency boost-libs>=1.87.0: found boost-libs-1.87.0nb1 => Full dependency cairo>=1.18.0nb2: found cairo-1.18.4 => Full dependency coordgenlibs>=1.4.2nb9: found coordgenlibs-1.4.2nb9 => Full dependency libxml2>=2.12.9nb3: found libxml2-2.12.10 => Full dependency maeparser>=1.2.4nb9: found maeparser-1.2.4nb9 => Full dependency zlib>=1.2.3: found zlib-1.3.1 => Build dependency xcb-proto>=1.4: found xcb-proto-1.17.0nb4 => Build dependency xorgproto>=2016.1: found xorgproto-2024.1 => Full dependency brotli>=1.0.1: found brotli-1.1.0 => Full dependency bzip2>=1.0.1: found bzip2-1.0.8 => Full dependency expat>=1.95.7: found expat-2.7.1 => Full dependency fontconfig>=2.11.91: found fontconfig-2.15.0 => Full dependency freetype2>=2.13.0: found freetype2-2.13.3 => Full dependency gettext-lib>=0.22: found gettext-lib-0.22.5 => Full dependency glib2>=2.4.0: found glib2-2.82.5 => Full dependency libiconv>=1.9.1: found libiconv-1.17 => Full dependency libX11>=1.1: found libX11-1.8.12 => Full dependency libXau>=1.0: found libXau-1.0.12 => Full dependency libXdmcp>=0.99: found libXdmcp-1.1.5 => Full dependency libXext>=0.99.0: found libXext-1.3.6 => Full dependency libXrender>=0.9.2: found libXrender-0.9.12 => Full dependency libffi>=1.20: found libffi-3.4.8 => Full dependency libxcb>=1.6: found libxcb-1.17.0 => Full dependency lzo>=2.01: found lzo-2.10 => Full dependency pcre2>=10.21: found pcre2-10.45 => Full dependency pixman>=0.40.0: found pixman-0.44.2 => Full dependency png>=1.2.4: found png-1.6.47 => Full dependency xz>=5.0.0: found xz-5.8.1 ===> Overriding tools for openbabel-3.1.1nb34 ===> Extracting for openbabel-3.1.1nb34 ===> Patching for openbabel-3.1.1nb34 => Applying pkgsrc patches for openbabel-3.1.1nb34 => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel/patches/patch-CMakeLists.txt => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel/patches/patch-CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-CMakeLists.txt,v 1.1 2025/01/31 15:49:47 wiz Exp $ | |Remove obsolete variable. | |--- CMakeLists.txt.orig 2025-01-31 15:47:24.131445152 +0000 |+++ CMakeLists.txt -------------------------- Patching file CMakeLists.txt using Plan A... Hunk #1 succeeded at 344. Hunk #2 succeeded at 357. Hunk #3 succeeded at 472. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-cmake_modules_Findcoordgen.cmake,v 1.1 2020/11/04 19:54:12 bsiegert Exp $ | |coordgenlibs does not install the template file, and it is not needed. | |--- cmake/modules/Findcoordgen.cmake.orig 2020-05-08 15:38:02.000000000 +0000 |+++ cmake/modules/Findcoordgen.cmake -------------------------- Patching file cmake/modules/Findcoordgen.cmake using Plan A... Hunk #1 succeeded at 6. Hunk #2 succeeded at 27. done => Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel/patches/patch-tools_CMakeLists.txt => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel/patches/patch-tools_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-tools_CMakeLists.txt,v 1.1 2025/01/31 15:49:47 wiz Exp $ | |Remove obsolete variable. | |--- tools/CMakeLists.txt.orig 2025-01-31 15:47:10.271879998 +0000 |+++ tools/CMakeLists.txt -------------------------- Patching file tools/CMakeLists.txt using Plan A... Hunk #1 succeeded at 5. done ===> Creating toolchain wrappers for openbabel-3.1.1nb34 ===> Configuring for openbabel-3.1.1nb34 => Adding run-time search paths to pkg-config files. => Checking for portability problems in extracted files CMake Deprecation Warning at CMakeLists.txt:3 (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/openbabel/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/openbabel/work/.cwrapper/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:14 (cmake_policy): The OLD behavior for policy CMP0042 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. -- Using included inchi library. -- Found LibXml2: /home/pbulk/build/biology/openbabel/work/.buildlink/lib/libxml2.so (found version "2.12.10") -- Found ZLIB: /home/pbulk/build/biology/openbabel/work/.buildlink/lib/libz.so (found version "1.3.1") -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES wxWidgets_INCLUDE_DIRS) -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - not found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success CMake Warning (dev) at CMakeLists.txt:299 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Checking available shared pointer... -- Performing Test HAVE_STD_SHARED_PTR -- Performing Test HAVE_STD_SHARED_PTR - Success -- Performing Test HAVE_STD_TR1_SHARED_PTR -- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success -- Use std::shared_ptr in memory CMake Warning (dev) at CMakeLists.txt:358 (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/biology/openbabel/work/.buildlink/lib/cmake/Boost-1.87.0/BoostConfig.cmake (found version "1.87.0") found components: program_options iostreams -- Found Eigen3: /home/pbulk/build/biology/openbabel/work/.buildlink/include/eigen3 (Required is at least version "2.91.0") CMake Warning (dev) at CMakeLists.txt:473 (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/biology/openbabel/work/.buildlink/lib/cmake/Boost-1.87.0/BoostConfig.cmake (found version "1.87.0") found components: filesystem iostreams unit_test_framework -- maeparser include dir set as '/home/pbulk/build/biology/openbabel/work/.buildlink/include' -- maeparser libraries set as '/home/pbulk/build/biology/openbabel/work/.buildlink/lib/libmaeparser.so' -- Maestro formats will be supported. Using MaeParser libraries at /home/pbulk/build/biology/openbabel/work/.buildlink/lib/libmaeparser.so. -- coordgen include dir set as /home/pbulk/build/biology/openbabel/work/.buildlink/include -- coordgen libraries set as '/home/pbulk/build/biology/openbabel/work/.buildlink/lib/libcoordgen.so' -- Coordinate generation with Coordgen will be supported. Using Coordgen libraries at /home/pbulk/build/biology/openbabel/work/.buildlink/lib/libcoordgen.so. -- Found PkgConfig: /home/pbulk/build/biology/openbabel/work/.tools/bin/pkg-config (found version "2.4.3") -- Found RapidJSON: /home/pbulk/build/biology/openbabel/work/.buildlink/include (found suitable version "1.1.0", minimum required is "1.1.0") -- JSON formats will be supported. Using RapidJSON 1.1.0 at /home/pbulk/build/biology/openbabel/work/.buildlink/include -- Checking for module 'cairo' -- Found cairo, version 1.18.4 -- Found Cairo: /home/pbulk/build/biology/openbabel/work/.buildlink/lib/libcairo.so -- Cairo found. PNG output will be supported. CMake Warning (dev) at src/CMakeLists.txt:6 (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/biology/openbabel/work/.buildlink/lib/cmake/Boost-1.87.0/BoostConfig.cmake (found suitable version "1.87.0", minimum required is "1.45.0") found components: system -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE CMake Warning (dev) at tools/CMakeLists.txt:6 (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/biology/openbabel/work/.buildlink/lib/cmake/Boost-1.87.0/BoostConfig.cmake (found version "1.87.0") found components: program_options iostreams -- Looking for getopt -- Looking for getopt - found -- GUI will not be built CMake Warning (dev) at cmake/modules/UsePythonTest.cmake:29 (FIND_PACKAGE): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): test/CMakeLists.txt:226 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /opt/pkg/bin/python3.12 (found version "3.12.10") CMake Deprecation Warning at scripts/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. -- Configuring done (44.1s) -- Generating done (1.2s) CMake Warning: Manually-specified variables were not used by the project: FETCHCONTENT_FULLY_DISCONNECTED LLVM_CONFIG -- Build files have been written to: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/cmake-pkgsrc-build