+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb32/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb32/work.log
WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead.
=> Checksum BLAKE2s OK for openbabel-3.1.1.tar.gz
=> Checksum SHA512 OK for openbabel-3.1.1.tar.gz
===> Installing dependencies for openbabel-3.1.1nb32
==========================================================================
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-2.82.2
=> Tool dependency cmake>=3.18: found cmake-3.31.1
=> Tool dependency pkgconf-[0-9]*: found pkgconf-2.3.0
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency boost-headers-1.86.*: found boost-headers-1.86.0
=> 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-1.86.*: found boost-libs-1.86.0nb3
=> Full dependency boost-libs>=1.86.0: found boost-libs-1.86.0nb3
=> Full dependency cairo>=1.18.0nb2: found cairo-1.18.2
=> Full dependency coordgenlibs>=1.4.2nb8: found coordgenlibs-1.4.2nb8
=> Full dependency libxml2>=2.12.9nb3: found libxml2-2.12.9nb3
=> Full dependency maeparser>=1.2.4nb8: found maeparser-1.2.4nb8
=> 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-2.6.3
=> 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 glib2-2.82.2
=> Full dependency libiconv>=1.9.1: found libiconv-1.17
=> Full dependency libX11>=1.1: found libX11-1.8.10
=> 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-3.4.6
=> 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 pcre2-10.44
=> Full dependency pixman>=0.40.0: found pixman-0.44.2
=> Full dependency png>=1.2.4: found png-1.6.44
=> Full dependency xz>=5.0.0: found xz-5.6.3
===> Overriding tools for openbabel-3.1.1nb32
===> Extracting for openbabel-3.1.1nb32
/usr/bin/mkdir -p /home/pbulk/build/biology/openbabel/work/build
===> Patching for openbabel-3.1.1nb32
=> Applying pkgsrc patches for openbabel-3.1.1nb32
=> 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
===> Creating toolchain wrappers for openbabel-3.1.1nb32
===> Configuring for openbabel-3.1.1nb32
=> 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 < 3.10 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
-- 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: /opt/pkg/lib/libxml2.so (found version "2.12.9")
-- Found ZLIB: /opt/pkg/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: /opt/pkg/include (found version "1.86.0") found components: program_options iostreams regex
-- Found Eigen3: /opt/pkg/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: /opt/pkg/include (found version "1.86.0") found components: filesystem iostreams unit_test_framework regex
-- maeparser include dir set as '/opt/pkg/include'
-- maeparser libraries set as '/opt/pkg/lib/libmaeparser.so'
-- Maestro formats will be supported. Using MaeParser libraries at /opt/pkg/lib/libmaeparser.so.
-- coordgen include dir set as /opt/pkg/include
-- coordgen libraries set as '/opt/pkg/lib/libcoordgen.so'
-- Coordinate generation with Coordgen will be supported. Using Coordgen libraries at /opt/pkg/lib/libcoordgen.so.
-- Found PkgConfig: /home/pbulk/build/biology/openbabel/work/.tools/bin/pkg-config (found version "2.3.0")
-- Found RapidJSON: /opt/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 /opt/pkg/include
-- Checking for module 'cairo'
--   Found cairo, version 1.18.2
-- Found Cairo: /opt/pkg/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: /opt/pkg/include (found suitable version "1.86.0", 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: /opt/pkg/include (found version "1.86.0") 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: /opt/pkg/bin/python3.12 (found version "3.12.8")
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 <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.


-- Configuring done (39.5s)
-- Generating done (2.2s)
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