=> Bootstrap dependency digest>=20010302: found digest-20180917 => Checksum SHA1 OK for openbabel-2.3.2.tar.gz => Checksum RMD160 OK for openbabel-2.3.2.tar.gz => Checksum SHA512 OK for openbabel-2.3.2.tar.gz ===> Installing dependencies for openbabel-2.3.2nb8 ========================================================================== The supported build options for openbabel are: wx-gui 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>=2.8.1nb1: found cmake-3.13.2 => Tool dependency pkgconf-[0-9]*: found pkgconf-1.4.1nb1 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency eigen>=2.0beta3: found eigen-2.0.17 => Build dependency cwrappers>=20150314: found cwrappers-20180325 => Full dependency libxml2>=2.8.0nb2: found libxml2-2.9.8nb4 ===> Overriding tools for openbabel-2.3.2nb8 ===> Extracting for openbabel-2.3.2nb8 ===> Patching for openbabel-2.3.2nb8 => Applying pkgsrc patches for openbabel-2.3.2nb8 => Verifying /usr/pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt => Applying pkgsrc patch /usr/pkgsrc/biology/openbabel/patches/patch-doc_CMakeLists.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-doc_CMakeLists.txt,v 1.4 2014/11/20 09:05:56 mef Exp $ | |Fix man path. | |--- doc/CMakeLists.txt.orig 2012-10-04 04:08:55.000000000 +0900 |+++ doc/CMakeLists.txt 2014-11-20 17:53:33.000000000 +0900 -------------------------- Patching file doc/CMakeLists.txt using Plan A... Hunk #1 succeeded at 1. done => Verifying /usr/pkgsrc/biology/openbabel/patches/patch-include_openbabel_obmolecformat.h => Applying pkgsrc patch /usr/pkgsrc/biology/openbabel/patches/patch-include_openbabel_obmolecformat.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-include_openbabel_obmolecformat.h,v 1.1 2013/05/06 14:22:42 joerg Exp $ | |--- include/openbabel/obmolecformat.h.orig 2013-05-05 20:25:43.000000000 +0000 |+++ include/openbabel/obmolecformat.h -------------------------- Patching file include/openbabel/obmolecformat.h using Plan A... Hunk #1 succeeded at 23. Hunk #2 succeeded at 144. done => Verifying /usr/pkgsrc/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h => Applying pkgsrc patch /usr/pkgsrc/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-include_openbabel_shared__ptr.h,v 1.2 2014/11/20 09:05:56 mef Exp $ | |--- include/openbabel/shared_ptr.h.orig 2011-10-13 05:24:02.000000000 +0900 |+++ include/openbabel/shared_ptr.h 2014-11-20 17:51:30.000000000 +0900 -------------------------- Patching file include/openbabel/shared_ptr.h using Plan A... Hunk #1 succeeded at 21. done => Verifying /usr/pkgsrc/biology/openbabel/patches/patch-src_ops_unique.cpp => Applying pkgsrc patch /usr/pkgsrc/biology/openbabel/patches/patch-src_ops_unique.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_ops_unique.cpp,v 1.2 2014/11/24 00:47:48 joerg Exp $ | |--- src/ops/unique.cpp.orig 2014-11-23 16:04:26.000000000 +0000 |+++ src/ops/unique.cpp -------------------------- Patching file src/ops/unique.cpp using Plan A... Hunk #1 succeeded at 21. Hunk #2 succeeded at 37. done ===> Creating toolchain wrappers for openbabel-2.3.2nb8 ===> Configuring for openbabel-2.3.2nb8 => Generating pkg-config files for builtin xz package. => Fixing CMAKE_MODULE_PATH in CMakeLists.txt => Checking for portability problems in extracted files -- The C compiler identification is GNU 5.5.0 -- The CXX compiler identification is GNU 5.5.0 CMake Warning (dev) at /usr/pkg/share/cmake-3.13/Modules/Platform/NetBSD.cmake:13 (include): File /usr/pkg/share/cmake-3.13/Modules/Platform/NetBSD.cmake includes /tmp/pkgbuild/biology/openbabel/work/.buildlink/cmake-Modules/Platform/UnixPaths.cmake (found via CMAKE_MODULE_PATH) which shadows /usr/pkg/share/cmake-3.13/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): /usr/pkg/share/cmake-3.13/Modules/CMakeSystemSpecificInformation.cmake:26 (include) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /usr/pkg/share/cmake-3.13/Modules/Platform/NetBSD.cmake:13 (include): File /usr/pkg/share/cmake-3.13/Modules/Platform/NetBSD.cmake includes /tmp/pkgbuild/biology/openbabel/work/.buildlink/cmake-Modules/Platform/UnixPaths.cmake (found via CMAKE_MODULE_PATH) which shadows /usr/pkg/share/cmake-3.13/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): /usr/pkg/share/cmake-3.13/Modules/CMakeCInformation.cmake:66 (include) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- Check for working C compiler: /tmp/pkgbuild/biology/openbabel/work/.cwrapper/bin/gcc -- Check for working C compiler: /tmp/pkgbuild/biology/openbabel/work/.cwrapper/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done CMake Warning (dev) at /usr/pkg/share/cmake-3.13/Modules/Platform/NetBSD.cmake:13 (include): File /usr/pkg/share/cmake-3.13/Modules/Platform/NetBSD.cmake includes /tmp/pkgbuild/biology/openbabel/work/.buildlink/cmake-Modules/Platform/UnixPaths.cmake (found via CMAKE_MODULE_PATH) which shadows /usr/pkg/share/cmake-3.13/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): /usr/pkg/share/cmake-3.13/Modules/CMakeCXXInformation.cmake:65 (include) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- Check for working CXX compiler: /tmp/pkgbuild/biology/openbabel/work/.cwrapper/bin/c++ -- Check for working CXX compiler: /tmp/pkgbuild/biology/openbabel/work/.cwrapper/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_policy): The OLD behavior for policy CMP0005 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 "2.9.8") -- Found ZLIB: /lib/libz.so (found version "1.2.10") -- 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 - not 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 - not 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 -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") -- Found Eigen2: /tmp/pkgbuild/biology/openbabel/work/.buildlink/include/eigen2 (Required is at least version "2.0.0") -- Found PkgConfig: /tmp/pkgbuild/biology/openbabel/work/.tools/bin/pkg-config (found version "1.4.1") -- Checking for module 'cairo' -- Package 'cairo', required by 'virtual:world', not found -- Could NOT find Cairo. PNG output will NOT be supported. -- Looking for getopt -- Looking for getopt - found -- GUI will not be built CMake Warning (dev) at cmake/modules/UsePythonTest.cmake:54: Syntax Warning in cmake code at column 14 Argument not separated from preceding token by whitespace. Call Stack (most recent call first): test/CMakeLists.txt:171 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/modules/UsePythonTest.cmake:54: Syntax Warning in cmake code at column 31 Argument not separated from preceding token by whitespace. Call Stack (most recent call first): test/CMakeLists.txt:171 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/modules/UsePythonTest.cmake:57: Syntax Warning in cmake code at column 25 Argument not separated from preceding token by whitespace. Call Stack (most recent call first): test/CMakeLists.txt:171 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/modules/UsePythonTest.cmake:57: Syntax Warning in cmake code at column 39 Argument not separated from preceding token by whitespace. Call Stack (most recent call first): test/CMakeLists.txt:171 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_LIBDIR -- Build files have been written to: /tmp/pkgbuild/biology/openbabel/work/openbabel-2.3.2 => Rewrite cmake Dependencies files