+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb22/work.log + su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb22/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for openbabel-3.1.1.tar.gz => Checksum SHA512 OK for openbabel-3.1.1.tar.gz ===> Installing dependencies for openbabel-3.1.1nb22 ========================================================================== 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 glib2-tools-[0-9]*: found glib2-tools-2.78.1 => Tool dependency mktools-[0-9]*: found mktools-20220614 => Tool dependency cmake>=3.18: found cmake-3.28.1 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency pkgconf-[0-9]*: found pkgconf-2.0.3 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency boost-headers-1.83.*: found boost-headers-1.83.0 => Build dependency xcb-proto>=1.15.2nb3: found xcb-proto-1.16.0nb1 => Build dependency xorgproto>=2016.1: found xorgproto-2023.2 => Build dependency eigen3>=3.1.2: found eigen3-3.4.0nb1 => Build dependency rapidjson>=1.1.0: found rapidjson-1.1.0nb1 => Build dependency gcc6>=6.5.0nb9: found gcc6-6.5.0nb9 => Full dependency coordgenlibs>=1.4.2nb6: found coordgenlibs-1.4.2nb6 => Full dependency maeparser>=1.2.4nb6: found maeparser-1.2.4nb6 => Full dependency boost-libs-1.83.*: found boost-libs-1.83.0nb1 => Full dependency boost-libs>=1.83.0: found boost-libs-1.83.0nb1 => Full dependency zlib>=1.2.3: found zlib-1.2.13 => Full dependency cairo>=1.18.0: found cairo-1.18.0nb1 => Full dependency libxml2>=2.10.4nb3: found libxml2-2.10.4nb6 ===> Overriding tools for openbabel-3.1.1nb22 ===> Extracting for openbabel-3.1.1nb22 /bin/mkdir -p /home/pbulk/build/biology/openbabel/work/build ===> Patching for openbabel-3.1.1nb22 => Applying pkgsrc patches for openbabel-3.1.1nb22 => Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 ===> Creating toolchain wrappers for openbabel-3.1.1nb22 ===> Configuring for openbabel-3.1.1nb22 => Adding run-time search paths to pkg-config files. => Fixing CMAKE_MODULE_PATH in CMakeLists.txt => Checking for portability problems in extracted files CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 6.5.0 -- The CXX compiler identification is GNU 6.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/pbulk/build/biology/openbabel/work/.cwrapper/bin/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: /home/pbulk/build/biology/openbabel/work/.cwrapper/bin/c++ - 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: /usr/pkg/lib/libxml2.so (found version "2.10.4") -- Found ZLIB: /usr/pkg/lib/libz.so (found version "1.2.13") -- 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 -- Found Boost: /usr/pkg/include (found version "1.83.0") found components: program_options iostreams regex -- Found Eigen3: /usr/pkg/include/eigen3 (Required is at least version "2.91.0") -- Found Boost: /usr/pkg/include (found version "1.83.0") found components: filesystem iostreams unit_test_framework regex -- maeparser include dir set as '/usr/pkg/include' -- maeparser libraries set as '/usr/pkg/lib/libmaeparser.so' -- Maestro formats will be supported. Using MaeParser libraries at /usr/pkg/lib/libmaeparser.so. -- coordgen include dir set as /usr/pkg/include -- coordgen libraries set as '/usr/pkg/lib/libcoordgen.so' -- Coordinate generation with Coordgen will be supported. Using Coordgen libraries at /usr/pkg/lib/libcoordgen.so. -- Found PkgConfig: /home/pbulk/build/biology/openbabel/work/.tools/bin/pkg-config (found version "2.0.3") -- Found RapidJSON: /usr/pkg/include (found suitable version "1.1.0", minimum required is "1.1.0") -- JSON formats will be supported. Using RapidJSON 1.1.0 at /usr/pkg/include -- Checking for module 'cairo' -- Found cairo, version 1.18.0 -- Found Cairo: /usr/pkg/lib/libcairo.so -- Cairo found. PNG output will be supported. -- Found Boost: /usr/pkg/include (found suitable version "1.83.0", 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 -- Found Boost: /usr/pkg/include (found version "1.83.0") found components: program_options iostreams regex -- 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: /bin/python (found version "2.7.5") CMake Deprecation Warning at scripts/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (12.6s) -- Generating done (1.2s) CMake Warning: Manually-specified variables were not used by the project: LLVM_CONFIG -- Build files have been written to: /home/pbulk/build/biology/openbabel/work/build => Rewrite cmake Dependencies files