Created
December 25, 2023 14:28
Revisions
-
tdsmith created this gist
Dec 25, 2023 .There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,2 @@ Homebrew build logs for coot on macOS 14.1 Build date: 2023-12-25 09:28:06 This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,23 @@ HOMEBREW_VERSION: 4.2.0-68-g7817518 ORIGIN: https://github.com/Homebrew/brew HEAD: 7817518992920b8dbd15e48a5e6c5ad768f4ba8b Last commit: 19 hours ago Core tap HEAD: 53c07cf94b73f3240906be827e6e19f73a037266 Core tap last commit: 13 hours ago Core tap JSON: 25 Dec 14:27 UTC Core cask tap HEAD: 31dff3eaa0bce1f55d3873fbe4c9d7f1998fcfa9 Core cask tap last commit: 15 hours ago Core cask tap JSON: 25 Dec 14:27 UTC HOMEBREW_PREFIX: /opt/homebrew HOMEBREW_CASK_OPTS: [] HOMEBREW_MAKE_JOBS: 10 HOMEBREW_SORBET_RUNTIME: set Homebrew Ruby: 3.1.4 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.1.4/bin/ruby CPU: 10-core 64-bit arm_firestorm_icestorm Clang: 15.0.0 build 1500 Git: 2.43.0 => /opt/homebrew/bin/git Curl: 8.1.2 => /usr/bin/curl macOS: 14.1.1-arm64 CLT: 15.1.0.0.1.1700200546 Xcode: N/A Rosetta 2: false This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,65 @@ Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry or file an issue; just ignore this. Thanks! Warning: Some installed casks are deprecated or disabled. You should find replacements for the following casks: kindle Warning: Some installed kegs have no formulae! This means they were either deleted or installed manually. You should find replacements for the following formulae: szip Warning: Some installed formulae are deprecated or disabled. You should find replacements for the following formulae: lua@5.3 openssl@1.1 proj@7 sdl_net sdl_sound youtube-dl Warning: /usr/bin occurs before /opt/homebrew/bin in your PATH. This means that system-provided programs will be used instead of those provided by Homebrew. Consider setting your PATH so that /opt/homebrew/bin occurs before /usr/bin. Here is a one-liner: fish_add_path /opt/homebrew/bin The following tools exist at both paths: bashbug dwarfdump git git-receive-pack git-shell git-upload-archive git-upload-pack less lessecho openssl pip3 pp python3 scp sftp slogin ssh ssh-add ssh-agent ssh-keygen ssh-keyscan tclsh vi view vim vimdiff wish Warning: Homebrew's "bin" was not found in your PATH. Consider setting your PATH for example like so: fish_add_path /opt/homebrew/bin Warning: Homebrew's "sbin" was not found in your PATH but you have installed formulae that put executables in /opt/homebrew/sbin. Consider setting your PATH for example like so: fish_add_path /opt/homebrew/sbin This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1 @@ coot This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,3 @@ Formula: coot Tap: Path: /Users/tim/upstream/coot/coot.rb This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,16 @@ 2023-12-25 14:27:51 +0000 ./autogen.sh glibtoolize --copy glibtoolize: putting auxiliary files in '.'. glibtoolize: copying file './ltmain.sh' glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'macros'. glibtoolize: copying file 'macros/libtool.m4' glibtoolize: copying file 'macros/ltversion.m4' aclocal -I macros fatal: not a git repository (or any of the parent directories): .git autoconf fatal: not a git repository (or any of the parent directories): .git automake --add-missing --copy fatal: not a git repository (or any of the parent directories): .git This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,139 @@ 2023-12-25 14:27:55 +0000 /opt/homebrew/opt/python@3.11/bin/python3.11 -c import setuptools, tokenize __file__ = 'setup.py' exec(compile(getattr(tokenize, 'open', open)(__file__).read() .replace('\r\n', '\n'), __file__, 'exec')) --no-user-cfg install --prefix=/opt/homebrew/Cellar/coot/1.1.03/libexec --install-scripts=/opt/homebrew/Cellar/coot/1.1.03/libexec/bin --install-lib=/opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages --single-version-externally-managed --record=installed.txt /opt/homebrew/lib/python3.11/site-packages/setuptools/dist.py:498: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'provides-extra' will not be supported in future versions. Please use the underscore name 'provides_extra' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /opt/homebrew/lib/python3.11/site-packages/setuptools/dist.py:498: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'requires-dist' will not be supported in future versions. Please use the underscore name 'requires_dist' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /opt/homebrew/lib/python3.11/site-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` !! ******************************************************************************** The license_file parameter is deprecated, use license_files instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! parsed = self.parsers.get(option_name, lambda x: x)(value) running install /opt/homebrew/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py creating build creating build/lib creating build/lib/requests copying requests/cookies.py -> build/lib/requests copying requests/auth.py -> build/lib/requests copying requests/sessions.py -> build/lib/requests copying requests/hooks.py -> build/lib/requests copying requests/compat.py -> build/lib/requests copying requests/models.py -> build/lib/requests copying requests/certs.py -> build/lib/requests copying requests/__init__.py -> build/lib/requests copying requests/status_codes.py -> build/lib/requests copying requests/packages.py -> build/lib/requests copying requests/__version__.py -> build/lib/requests copying requests/api.py -> build/lib/requests copying requests/_internal_utils.py -> build/lib/requests copying requests/utils.py -> build/lib/requests copying requests/exceptions.py -> build/lib/requests copying requests/structures.py -> build/lib/requests copying requests/help.py -> build/lib/requests copying requests/adapters.py -> build/lib/requests running egg_info writing requests.egg-info/PKG-INFO writing dependency_links to requests.egg-info/dependency_links.txt writing requirements to requests.egg-info/requires.txt writing top-level names to requests.egg-info/top_level.txt reading manifest file 'requests.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'pytest.ini' adding license file 'LICENSE' writing manifest file 'requests.egg-info/SOURCES.txt' warning: build_py: byte-compiling is disabled, skipping. running install_lib creating /opt/homebrew/Cellar/coot/1.1.03/libexec creating /opt/homebrew/Cellar/coot/1.1.03/libexec/lib creating /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11 creating /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages creating /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/cookies.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/auth.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/sessions.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/hooks.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/compat.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/models.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/certs.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/__init__.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/status_codes.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/packages.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/__version__.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/api.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/_internal_utils.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/utils.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/exceptions.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/structures.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/help.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests copying build/lib/requests/adapters.py -> /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests warning: install_lib: byte-compiling is disabled, skipping. running install_egg_info Copying requests.egg-info to /opt/homebrew/Cellar/coot/1.1.03/libexec/lib/python3.11/site-packages/requests-2.31.0-py3.11.egg-info running install_scripts writing list of installed files to 'installed.txt' This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,198 @@ 2023-12-25 14:27:55 +0000 ./configure --prefix=/opt/homebrew/Cellar/coot/1.1.03 --with-enhanced-ligand-tools --with-boost=/opt/homebrew/opt/boost --with-boost-libdir=/opt/homebrew/opt/boost/lib --with-rdkit-prefix=/opt/homebrew/opt/rdkit --with-fftw-prefix=/opt/homebrew/opt/clipper4coot/fftw2 --with-backward --with-libdw BOOST_PYTHON_LIB=boost_python312-mt checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... mkdir -p checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether clang++ accepts -g... yes checking for clang++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of clang++... gcc3 checking build system type... arm-apple-darwin23.1.0 checking host system type... arm-apple-darwin23.1.0 checking how to print strings... printf checking for gcc... clang checking whether the compiler supports GNU C... yes checking whether clang accepts -g... yes checking for clang option to enable C11 features... none needed checking whether clang understands -c and -o together... yes checking dependency style of clang... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by clang... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert arm-apple-darwin23.1.0 file names to arm-apple-darwin23.1.0 format... func_convert_file_noop checking how to convert arm-apple-darwin23.1.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from clang object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... ld: warning: -single_module is obsolete no checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if clang supports -fno-rtti -fno-exceptions... yes checking for clang option to produce PIC... -fno-common -DPIC checking if clang PIC flag -fno-common -DPIC works... yes checking if clang static flag -static works... no checking if clang supports -c -o file.o... yes checking if clang supports -c -o file.o... (cached) yes checking whether the clang linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin23.1.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... clang++ -E checking for ld used by clang++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the clang++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for clang++ option to produce PIC... -fno-common -DPIC checking if clang++ PIC flag -fno-common -DPIC works... yes checking if clang++ static flag -static works... no checking if clang++ supports -c -o file.o... yes checking if clang++ supports -c -o file.o... (cached) yes checking whether the clang++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin23.1.0 dyld checking how to hardcode library paths into programs... immediate checking which libtool initialization strategy to adopt... AC-PROG-LIBTOOL checking what warning flags to pass to the C compiler... -Wall -Wunused checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused checking what language compliance flags to pass to the C++ compiler... checking for sys/stdtypes.h... no checking for OpenMP flag of C compiler... unknown checking whether clang++ supports C++11 features by default... yes checking for std::thread in thread... yes checking for pkg-config... /opt/homebrew/Library/Homebrew/shims/mac/super/pkg-config checking pkg-config is at least version 0.9.0... yes checking for glib-2.0... yes checking if this is MINGW on Windows... no checking if this is msys2 windows 64... no checking for libpng >= 1.2... yes checking for cairo >= 1.14... yes checking for SQLite3... yes checking for libdwarf >= 0.7... yes checking for mmdb2... yes checking for ssm... yes checking for non-prefixed single-precision FFTW2 (fftw.h)... yes checking for Clipper... yes checking for gsl-config... /opt/homebrew/opt/gsl/bin/gsl-config checking for GSL - version >= 1.3... yes checking for glm >= 0.9.9... yes checking for gtk4 >= 4.4... yes checking for epoxy >= 1.5... yes checking for glfw3 >= 3.0... yes checking for a Python interpreter with version >= 3.7... python3 checking for python3... /opt/homebrew/opt/python@3.11/bin/python3 checking for python3 version... 3.11 checking for python3 platform... darwin checking for python3 script directory... ${prefix}/lib/python3.11/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.11/site-packages checking for python3.11... (cached) /opt/homebrew/opt/python@3.11/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11 checking for Python library path... -L/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib -lpython3.11 checking for Python site-packages path... /opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages checking python extra libraries... -ldl -framework CoreFoundation checking python extra linking flags... -Wl,-stack_size,1000000 -framework CoreFoundation /opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/Python checking consistency of all components of python development environment... yes checking python3 module: requests... no configure: error: failed to find required module requests HOMEBREW_VERSION: 4.2.0-68-g7817518 ORIGIN: https://github.com/Homebrew/brew HEAD: 7817518992920b8dbd15e48a5e6c5ad768f4ba8b Last commit: 19 hours ago Core tap HEAD: 53c07cf94b73f3240906be827e6e19f73a037266 Core tap last commit: 13 hours ago Core tap JSON: 25 Dec 14:27 UTC Core cask tap HEAD: 31dff3eaa0bce1f55d3873fbe4c9d7f1998fcfa9 Core cask tap last commit: 15 hours ago Core cask tap JSON: 25 Dec 14:27 UTC HOMEBREW_PREFIX: /opt/homebrew HOMEBREW_CASK_OPTS: [] HOMEBREW_MAKE_JOBS: 10 HOMEBREW_NO_BOOTSNAP: set HOMEBREW_SORBET_RUNTIME: set Homebrew Ruby: 3.1.4 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.1.4/bin/ruby CPU: 10-core 64-bit arm_firestorm_icestorm Clang: 15.0.0 build 1500 Git: 2.43.0 => /opt/homebrew/bin/git Curl: 8.1.2 => /usr/bin/curl macOS: 14.1.1-arm64 CLT: 15.1.0.0.1.1700200546 Xcode: N/A Rosetta 2: false HOMEBREW_CC: clang HOMEBREW_CXX: clang++ MAKEFLAGS: -j10 CMAKE_PREFIX_PATH: /opt/homebrew/opt/icu4c:/opt/homebrew/opt/readline:/opt/homebrew/opt/sqlite:/opt/homebrew/opt/libomp:/opt/homebrew/opt/m4:/opt/homebrew/opt/jpeg:/opt/homebrew/opt/openblas:/opt/homebrew/opt/krb5:/opt/homebrew/opt/postgresql@15:/opt/homebrew CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries CMAKE_FRAMEWORK_PATH: /opt/homebrew/opt/python@3.12/Frameworks:/opt/homebrew/opt/python@3.11/Frameworks PKG_CONFIG_PATH: /opt/homebrew/opt/glm/lib/pkgconfig:/opt/homebrew/opt/libpng/lib/pkgconfig:/opt/homebrew/opt/freetype/lib/pkgconfig:/opt/homebrew/opt/fontconfig/lib/pkgconfig:/opt/homebrew/opt/pcre2/lib/pkgconfig:/opt/homebrew/opt/glib/lib/pkgconfig:/opt/homebrew/opt/libxau/lib/pkgconfig:/opt/homebrew/opt/libxdmcp/lib/pkgconfig:/opt/homebrew/opt/libxcb/lib/pkgconfig:/opt/homebrew/opt/libx11/lib/pkgconfig:/opt/homebrew/opt/libxext/lib/pkgconfig:/opt/homebrew/opt/libxrender/lib/pkgconfig:/opt/homebrew/opt/lzo/lib/pkgconfig:/opt/homebrew/opt/pixman/lib/pkgconfig:/opt/homebrew/opt/cairo/lib/pkgconfig:/opt/homebrew/opt/jpeg-turbo/lib/pkgconfig:/opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/lz4/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/libtiff/lib/pkgconfig:/opt/homebrew/opt/gdk-pixbuf/lib/pkgconfig:/opt/homebrew/opt/fribidi/lib/pkgconfig:/opt/homebrew/opt/graphite2/lib/pkgconfig:/opt/homebrew/opt/icu4c/lib/pkgconfig:/opt/homebrew/opt/harfbuzz/lib/pkgconfig:/opt/homebrew/opt/pango/lib/pkgconfig:/opt/homebrew/opt/librsvg/lib/pkgconfig:/opt/homebrew/opt/openssl@3/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/python@3.12/lib/pkgconfig:/opt/homebrew/opt/libccp4/lib/pkgconfig:/opt/homebrew/opt/mmdb2/lib/pkgconfig:/opt/homebrew/opt/clipper4coot/lib/pkgconfig:/opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/brotli/lib/pkgconfig:/opt/homebrew/opt/highway/lib/pkgconfig:/opt/homebrew/opt/imath/lib/pkgconfig:/opt/homebrew/opt/little-cms2/lib/pkgconfig:/opt/homebrew/opt/openexr/lib/pkgconfig:/opt/homebrew/opt/webp/lib/pkgconfig:/opt/homebrew/opt/jpeg-xl/lib/pkgconfig:/opt/homebrew/opt/libvmaf/lib/pkgconfig:/opt/homebrew/opt/aom/lib/pkgconfig:/opt/homebrew/opt/libavif/lib/pkgconfig:/opt/homebrew/opt/gd/lib/pkgconfig:/opt/homebrew/opt/jbig2dec/lib/pkgconfig:/opt/homebrew/opt/libidn/lib/pkgconfig:/opt/homebrew/opt/openjpeg/lib/pkgconfig:/opt/homebrew/opt/libde265/lib/pkgconfig:/opt/homebrew/opt/x265/lib/pkgconfig:/opt/homebrew/opt/libheif/lib/pkgconfig:/opt/homebrew/opt/liblqr/lib/pkgconfig:/opt/homebrew/opt/jasper/lib/pkgconfig:/opt/homebrew/opt/libraw/lib/pkgconfig:/opt/homebrew/opt/imagemagick/lib/pkgconfig:/opt/homebrew/opt/jpeg/lib/pkgconfig:/opt/homebrew/opt/ssm/lib/pkgconfig:/opt/homebrew/opt/dwarfutils/lib/pkgconfig:/opt/homebrew/opt/glfw/lib/pkgconfig:/opt/homebrew/opt/gsl/lib/pkgconfig:/opt/homebrew/opt/graphene/lib/pkgconfig:/opt/homebrew/opt/libepoxy/lib/pkgconfig:/opt/homebrew/opt/gtk4/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/python@3.11/lib/pkgconfig:/opt/homebrew/opt/krb5/lib/pkgconfig:/opt/homebrew/opt/postgresql@15/lib/pkgconfig:/opt/homebrew/opt/gobject-introspection/lib/pkgconfig:/opt/homebrew/opt/pygobject3/lib/pkgconfig:/opt/homebrew/opt/xorgproto/share/pkgconfig:/opt/homebrew/opt/adwaita-icon-theme/share/pkgconfig:/opt/homebrew/opt/shared-mime-info/share/pkgconfig:/opt/homebrew/opt/eigen/share/pkgconfig PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/14 HOMEBREW_GIT: git HOMEBREW_SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk ACLOCAL_PATH: /opt/homebrew/share/aclocal PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew/opt/autoconf/bin:/opt/homebrew/opt/automake/bin:/opt/homebrew/opt/libtool/bin:/opt/homebrew/opt/pkg-config/bin:/opt/homebrew/opt/swig/bin:/opt/homebrew/opt/libpng/bin:/opt/homebrew/opt/freetype/bin:/opt/homebrew/opt/fontconfig/bin:/opt/homebrew/opt/pcre2/bin:/opt/homebrew/opt/gettext/bin:/opt/homebrew/opt/glib/bin:/opt/homebrew/opt/cairo/bin:/opt/homebrew/opt/jpeg-turbo/bin:/opt/homebrew/opt/xz/bin:/opt/homebrew/opt/lz4/bin:/opt/homebrew/opt/zstd/bin:/opt/homebrew/opt/libtiff/bin:/opt/homebrew/opt/gdk-pixbuf/bin:/opt/homebrew/opt/fribidi/bin:/opt/homebrew/opt/graphite2/bin:/opt/homebrew/opt/icu4c/bin:/opt/homebrew/opt/harfbuzz/bin:/opt/homebrew/opt/pango/bin:/opt/homebrew/opt/librsvg/bin:/opt/homebrew/opt/openssl@3/bin:/opt/homebrew/opt/sqlite/bin:/opt/homebrew/opt/python@3.12/bin:/opt/homebrew/opt/gemmi/bin:/opt/homebrew/opt/gcc/bin:/opt/homebrew/opt/brotli/bin:/opt/homebrew/opt/giflib/bin:/opt/homebrew/opt/little-cms2/bin:/opt/homebrew/opt/openexr/bin:/opt/homebrew/opt/webp/bin:/opt/homebrew/opt/jpeg-xl/bin:/opt/homebrew/opt/libvmaf/bin:/opt/homebrew/opt/aom/bin:/opt/homebrew/opt/libavif/bin:/opt/homebrew/opt/gd/bin:/opt/homebrew/opt/jbig2dec/bin:/opt/homebrew/opt/libidn/bin:/opt/homebrew/opt/openjpeg/bin:/opt/homebrew/opt/ghostscript/bin:/opt/homebrew/opt/libde265/bin:/opt/homebrew/opt/shared-mime-info/bin:/opt/homebrew/opt/x265/bin:/opt/homebrew/opt/libheif/bin:/opt/homebrew/opt/jasper/bin:/opt/homebrew/opt/libraw/bin:/opt/homebrew/opt/m4/bin:/opt/homebrew/opt/imagemagick/bin:/opt/homebrew/opt/jpeg/bin:/opt/homebrew/opt/raster3d/bin:/opt/homebrew/opt/dwarfutils/bin:/opt/homebrew/opt/gsl/bin:/opt/homebrew/opt/gtk4/bin:/opt/homebrew/opt/numpy/bin:/opt/homebrew/opt/python@3.11/bin:/opt/homebrew/opt/krb5/bin:/opt/homebrew/opt/postgresql@15/bin:/opt/homebrew/opt/gobject-introspection/bin:/opt/homebrew/opt/python@3.12/libexec/bin:/opt/homebrew/opt/python@3.11/libexec/bin:/usr/bin:/bin:/usr/sbin:/sbin This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,1603 @@ This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by coot configure 1.1.03, which was generated by GNU Autoconf 2.72. Invocation command line was $ ./configure --prefix=/opt/homebrew/Cellar/coot/1.1.03 --with-enhanced-ligand-tools --with-boost=/opt/homebrew/opt/boost --with-boost-libdir=/opt/homebrew/opt/boost/lib --with-rdkit-prefix=/opt/homebrew/opt/rdkit --with-fftw-prefix=/opt/homebrew/opt/clipper4coot/fftw2 --with-backward --with-libdw BOOST_PYTHON_LIB=boost_python312-mt ## --------- ## ## Platform. ## ## --------- ## hostname = enchiridion.local uname -m = arm64 uname -r = 23.1.0 uname -s = Darwin uname -v = Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 /usr/bin/uname -p = arm /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = Mach kernel version: Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 Kernel configured for up to 10 processors. 10 processors are physically available. 10 processors are logically available. Processor type: arm64e (ARM64E) Processors active: 0 1 2 3 4 5 6 7 8 9 Primary memory available: 32.00 gigabytes Default processor set: 818 tasks, 5178 threads, 10 processors Load average: 4.89, Mach factor: 5.10 /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /opt/homebrew/Library/Homebrew/shims/mac/super/ PATH: /opt/homebrew/opt/autoconf/bin/ PATH: /opt/homebrew/opt/automake/bin/ PATH: /opt/homebrew/opt/libtool/bin/ PATH: /opt/homebrew/opt/pkg-config/bin/ PATH: /opt/homebrew/opt/swig/bin/ PATH: /opt/homebrew/opt/libpng/bin/ PATH: /opt/homebrew/opt/freetype/bin/ PATH: /opt/homebrew/opt/fontconfig/bin/ PATH: /opt/homebrew/opt/pcre2/bin/ PATH: /opt/homebrew/opt/gettext/bin/ PATH: /opt/homebrew/opt/glib/bin/ PATH: /opt/homebrew/opt/cairo/bin/ PATH: /opt/homebrew/opt/jpeg-turbo/bin/ PATH: /opt/homebrew/opt/xz/bin/ PATH: /opt/homebrew/opt/lz4/bin/ PATH: /opt/homebrew/opt/zstd/bin/ PATH: /opt/homebrew/opt/libtiff/bin/ PATH: /opt/homebrew/opt/gdk-pixbuf/bin/ PATH: /opt/homebrew/opt/fribidi/bin/ PATH: /opt/homebrew/opt/graphite2/bin/ PATH: /opt/homebrew/opt/icu4c/bin/ PATH: /opt/homebrew/opt/harfbuzz/bin/ PATH: /opt/homebrew/opt/pango/bin/ PATH: /opt/homebrew/opt/librsvg/bin/ PATH: /opt/homebrew/opt/openssl@3/bin/ PATH: /opt/homebrew/opt/sqlite/bin/ PATH: /opt/homebrew/opt/python@3.12/bin/ PATH: /opt/homebrew/opt/gemmi/bin/ PATH: /opt/homebrew/opt/gcc/bin/ PATH: /opt/homebrew/opt/brotli/bin/ PATH: /opt/homebrew/opt/giflib/bin/ PATH: /opt/homebrew/opt/little-cms2/bin/ PATH: /opt/homebrew/opt/openexr/bin/ PATH: /opt/homebrew/opt/webp/bin/ PATH: /opt/homebrew/opt/jpeg-xl/bin/ PATH: /opt/homebrew/opt/libvmaf/bin/ PATH: /opt/homebrew/opt/aom/bin/ PATH: /opt/homebrew/opt/libavif/bin/ PATH: /opt/homebrew/opt/gd/bin/ PATH: /opt/homebrew/opt/jbig2dec/bin/ PATH: /opt/homebrew/opt/libidn/bin/ PATH: /opt/homebrew/opt/openjpeg/bin/ PATH: /opt/homebrew/opt/ghostscript/bin/ PATH: /opt/homebrew/opt/libde265/bin/ PATH: /opt/homebrew/opt/shared-mime-info/bin/ PATH: /opt/homebrew/opt/x265/bin/ PATH: /opt/homebrew/opt/libheif/bin/ PATH: /opt/homebrew/opt/jasper/bin/ PATH: /opt/homebrew/opt/libraw/bin/ PATH: /opt/homebrew/opt/m4/bin/ PATH: /opt/homebrew/opt/imagemagick/bin/ PATH: /opt/homebrew/opt/jpeg/bin/ PATH: /opt/homebrew/opt/raster3d/bin/ PATH: /opt/homebrew/opt/dwarfutils/bin/ PATH: /opt/homebrew/opt/gsl/bin/ PATH: /opt/homebrew/opt/gtk4/bin/ PATH: /opt/homebrew/opt/numpy/bin/ PATH: /opt/homebrew/opt/python@3.11/bin/ PATH: /opt/homebrew/opt/krb5/bin/ PATH: /opt/homebrew/opt/postgresql@15/bin/ PATH: /opt/homebrew/opt/gobject-introspection/bin/ PATH: /opt/homebrew/opt/python@3.12/libexec/bin/ PATH: /opt/homebrew/opt/python@3.11/libexec/bin/ PATH: /usr/bin/ PATH: /bin/ PATH: /usr/sbin/ PATH: /sbin/ ## ----------- ## ## Core tests. ## ## ----------- ## configure:3017: looking for aux files: compile config.guess config.sub ltmain.sh missing install-sh configure:3030: trying ./ configure:3059: ./compile found configure:3059: ./config.guess found configure:3059: ./config.sub found configure:3059: ./ltmain.sh found configure:3059: ./missing found configure:3041: ./install-sh found configure:3190: checking for a BSD-compatible install configure:3264: result: /usr/bin/install -c configure:3275: checking whether build environment is sane configure:3330: result: yes configure:3491: checking for a race-free mkdir -p configure:3534: result: mkdir -p configure:3541: checking for gawk configure:3577: result: no configure:3541: checking for mawk configure:3577: result: no configure:3541: checking for nawk configure:3577: result: no configure:3541: checking for awk configure:3562: found /usr/bin/awk configure:3574: result: awk configure:3585: checking whether make sets $(MAKE) configure:3609: result: yes configure:3639: checking whether make supports nested variables configure:3658: result: yes configure:3941: checking for C++ compiler version configure:3950: clang++ --version >&5 Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.1.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin configure:3961: $? = 0 configure:3950: clang++ -v >&5 Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.1.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin configure:3961: $? = 0 configure:3950: clang++ -V >&5 clang: error: unsupported option '-V -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk' configure:3961: $? = 1 configure:3950: clang++ -qversion >&5 clang: error: unknown argument '-qversion'; did you mean '--version'? configure:3961: $? = 1 configure:3981: checking whether the C++ compiler works configure:4003: clang++ conftest.cpp >&5 configure:4007: $? = 0 configure:4058: result: yes configure:4062: checking for C++ compiler default output file name configure:4064: result: a.out configure:4070: checking for suffix of executables configure:4077: clang++ -o conftest conftest.cpp >&5 configure:4081: $? = 0 configure:4105: result: configure:4129: checking whether we are cross compiling configure:4137: clang++ -o conftest conftest.cpp >&5 configure:4141: $? = 0 configure:4148: ./conftest configure:4152: $? = 0 configure:4167: result: no configure:4173: checking for suffix of object files configure:4196: clang++ -c conftest.cpp >&5 configure:4200: $? = 0 configure:4224: result: o configure:4228: checking whether the compiler supports GNU C++ configure:4248: clang++ -c conftest.cpp >&5 configure:4248: $? = 0 configure:4260: result: yes configure:4271: checking whether clang++ accepts -g configure:4292: clang++ -c -g conftest.cpp >&5 configure:4292: $? = 0 configure:4339: result: yes configure:4359: checking for clang++ option to enable C++11 features configure:4374: clang++ -c -g -O2 conftest.cpp >&5 conftest.cpp:177:25: warning: empty parentheses interpreted as a function declaration [-Wvexing-parse] cxx11test::delegate d2(); ^~ conftest.cpp:177:25: note: remove parentheses to declare a variable cxx11test::delegate d2(); ^~ 1 warning generated. configure:4374: $? = 0 configure:4393: result: none needed configure:4465: checking whether make supports the include directive configure:4480: make -f confmf.GNU && cat confinc.out this is the am__doit target configure:4483: $? = 0 configure:4502: result: yes (GNU style) configure:4528: checking dependency style of clang++ configure:4641: result: gcc3 configure:4691: checking build system type configure:4707: result: arm-apple-darwin23.1.0 configure:4727: checking host system type configure:4742: result: arm-apple-darwin23.1.0 configure:4783: checking how to print strings configure:4810: result: printf configure:4894: checking for gcc configure:4927: result: clang configure:5286: checking for C compiler version configure:5295: clang --version >&5 Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.1.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin configure:5306: $? = 0 configure:5295: clang -v >&5 Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.1.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin configure:5306: $? = 0 configure:5295: clang -V >&5 clang: error: unsupported option '-V -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk' configure:5306: $? = 1 configure:5295: clang -qversion >&5 clang: error: unknown argument '-qversion'; did you mean '--version'? configure:5306: $? = 1 configure:5295: clang -version >&5 clang: error: unknown argument '-version'; did you mean '--version'? configure:5306: $? = 1 configure:5310: checking whether the compiler supports GNU C configure:5330: clang -c conftest.c >&5 configure:5330: $? = 0 configure:5342: result: yes configure:5353: checking whether clang accepts -g configure:5374: clang -c -g conftest.c >&5 configure:5374: $? = 0 configure:5421: result: yes configure:5441: checking for clang option to enable C11 features configure:5456: clang -c -g -O2 conftest.c >&5 configure:5456: $? = 0 configure:5475: result: none needed configure:5599: checking whether clang understands -c and -o together configure:5622: clang -c conftest.c -o conftest2.o configure:5625: $? = 0 configure:5622: clang -c conftest.c -o conftest2.o configure:5625: $? = 0 configure:5638: result: yes configure:5657: checking dependency style of clang configure:5770: result: gcc3 configure:5785: checking for a sed that does not truncate output configure:5857: result: /usr/bin/sed configure:5875: checking for grep that handles long lines and -e configure:5941: result: /usr/bin/grep configure:5946: checking for egrep configure:6016: result: /usr/bin/grep -E configure:6023: checking for fgrep configure:6093: result: /usr/bin/grep -F configure:6130: checking for ld used by clang configure:6199: result: /Library/Developer/CommandLineTools/usr/bin/ld configure:6206: checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld configure:6223: result: no configure:6235: checking for BSD- or MS-compatible name lister (nm) configure:6291: result: /usr/bin/nm -B configure:6433: checking the name lister (/usr/bin/nm -B) interface configure:6441: clang -c -g -O2 conftest.c >&5 configure:6444: /usr/bin/nm -B "conftest.o" configure:6447: output 0000000000000234 S _some_variable 0000000000000000 t ltmp0 0000000000000234 s ltmp1 configure:6455: result: BSD nm configure:6458: checking whether ln -s works configure:6462: result: yes configure:6470: checking the maximum length of command line arguments configure:6603: result: 786432 configure:6651: checking how to convert arm-apple-darwin23.1.0 file names to arm-apple-darwin23.1.0 format configure:6693: result: func_convert_file_noop configure:6700: checking how to convert arm-apple-darwin23.1.0 file names to toolchain format configure:6722: result: func_convert_file_noop configure:6729: checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files configure:6738: result: -r configure:6818: checking for file configure:6839: found /usr/bin/file configure:6851: result: file configure:6928: checking for objdump configure:6949: found /usr/bin/objdump configure:6961: result: objdump configure:6993: checking how to recognize dependent libraries configure:7195: result: pass_all configure:7286: checking for dlltool configure:7322: result: no configure:7352: checking how to associate runtime and link libraries configure:7381: result: printf %s\n configure:7448: checking for ar configure:7469: found /usr/bin/ar configure:7481: result: ar configure:7534: checking for archiver @FILE support configure:7552: clang -c -g -O2 conftest.c >&5 configure:7552: $? = 0 configure:7556: ar cr libconftest.a @conftest.lst >&5 ar: @conftest.lst: No such file or directory configure:7559: $? = 1 configure:7580: result: no configure:7644: checking for strip configure:7665: found /usr/bin/strip configure:7677: result: strip configure:7755: checking for ranlib configure:7776: found /usr/bin/ranlib configure:7788: result: ranlib configure:7890: checking command to parse /usr/bin/nm -B output from clang object configure:8044: clang -c -g -O2 conftest.c >&5 configure:8047: $? = 0 configure:8051: /usr/bin/nm -B conftest.o \| /usr/bin/sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | /usr/bin/sed '/ __gnu_lto/d' \> conftest.nm configure:8054: $? = 0 cannot find nm_test_var in conftest.nm configure:8044: clang -c -g -O2 conftest.c >&5 configure:8047: $? = 0 configure:8051: /usr/bin/nm -B conftest.o \| /usr/bin/sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p' | /usr/bin/sed '/ __gnu_lto/d' \> conftest.nm configure:8054: $? = 0 configure:8120: clang -o conftest -g -O2 conftest.c conftstm.o >&5 configure:8123: $? = 0 configure:8162: result: ok configure:8209: checking for sysroot configure:8241: result: no configure:8248: checking for a working dd configure:8293: result: /bin/dd configure:8297: checking how to truncate binary pipes configure:8314: result: /bin/dd bs=4096 count=1 configure:8654: checking for mt configure:8690: result: no configure:8710: checking if : is a manifest tool configure:8717: : '-?' configure:8726: result: no configure:8788: checking for dsymutil configure:8809: found /usr/bin/dsymutil configure:8821: result: dsymutil configure:8892: checking for nmedit configure:8913: found /usr/bin/nmedit configure:8925: result: nmedit configure:8996: checking for lipo configure:9017: found /usr/bin/lipo configure:9029: result: lipo configure:9100: checking for otool configure:9121: found /usr/bin/otool configure:9133: result: otool configure:9204: checking for otool64 configure:9240: result: no configure:9285: checking for -single_module linker flag clang -g -O2 -o libconftest.dylib -dynamiclib -Wl,-single_module conftest.c ld: warning: -single_module is obsolete configure:9320: result: no configure:9323: checking for -exported_symbols_list linker flag configure:9344: clang -o conftest -g -O2 -Wl,-exported_symbols_list,conftest.sym conftest.c >&5 configure:9344: $? = 0 configure:9357: result: yes configure:9360: checking for -force_load linker flag clang -g -O2 -c -o conftest.o conftest.c ar cr libconftest.a conftest.o ranlib libconftest.a clang -g -O2 -o conftest conftest.c -Wl,-force_load,./libconftest.a configure:9394: result: yes configure:9465: checking for stdio.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for stdlib.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for string.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for inttypes.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for stdint.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for strings.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for sys/stat.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for sys/types.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9465: checking for unistd.h configure:9465: clang -c -g -O2 conftest.c >&5 configure:9465: $? = 0 configure:9465: result: yes configure:9490: checking for dlfcn.h configure:9490: clang -c -g -O2 conftest.c >&5 configure:9490: $? = 0 configure:9490: result: yes configure:9766: checking for objdir configure:9783: result: .libs configure:10049: checking if clang supports -fno-rtti -fno-exceptions configure:10068: clang -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 configure:10072: $? = 0 configure:10086: result: yes configure:10444: checking for clang option to produce PIC configure:10453: result: -fno-common -DPIC configure:10461: checking if clang PIC flag -fno-common -DPIC works configure:10480: clang -c -g -O2 -fno-common -DPIC -DPIC conftest.c >&5 configure:10484: $? = 0 configure:10498: result: yes configure:10527: checking if clang static flag -static works configure:10557: result: no configure:10572: checking if clang supports -c -o file.o configure:10594: clang -c -g -O2 -o out/conftest2.o conftest.c >&5 configure:10598: $? = 0 configure:10621: result: yes configure:10629: checking if clang supports -c -o file.o configure:10678: result: yes configure:10711: checking whether the clang linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries configure:11984: result: yes configure:12226: checking dynamic linker characteristics configure:13048: result: darwin23.1.0 dyld configure:13170: checking how to hardcode library paths into programs configure:13195: result: immediate configure:13795: checking whether stripping libraries is possible configure:13812: result: yes configure:13846: checking if libtool supports shared libraries configure:13848: result: yes configure:13851: checking whether to build shared libraries configure:13876: result: yes configure:13879: checking whether to build static libraries configure:13883: result: yes configure:13906: checking how to run the C++ preprocessor configure:13928: clang++ -E conftest.cpp configure:13928: $? = 0 configure:13944: clang++ -E conftest.cpp conftest.cpp:23:10: fatal error: 'ac_nonexistent.h' file not found #include <ac_nonexistent.h> ^~~~~~~~~~~~~~~~~~ 1 error generated. configure:13944: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include <ac_nonexistent.h> configure:13973: result: clang++ -E configure:13987: clang++ -E conftest.cpp configure:13987: $? = 0 configure:14003: clang++ -E conftest.cpp conftest.cpp:23:10: fatal error: 'ac_nonexistent.h' file not found #include <ac_nonexistent.h> ^~~~~~~~~~~~~~~~~~ 1 error generated. configure:14003: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include <ac_nonexistent.h> configure:14171: checking for ld used by clang++ configure:14240: result: /Library/Developer/CommandLineTools/usr/bin/ld configure:14247: checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld configure:14264: result: no configure:14319: checking whether the clang++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries configure:15399: result: yes configure:15435: clang++ -c -g -O2 conftest.cpp >&5 configure:15438: $? = 0 configure:15919: checking for clang++ option to produce PIC configure:15928: result: -fno-common -DPIC configure:15936: checking if clang++ PIC flag -fno-common -DPIC works configure:15955: clang++ -c -g -O2 -fno-common -DPIC -DPIC conftest.cpp >&5 configure:15959: $? = 0 configure:15973: result: yes configure:15996: checking if clang++ static flag -static works configure:16026: result: no configure:16038: checking if clang++ supports -c -o file.o configure:16060: clang++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 configure:16064: $? = 0 configure:16087: result: yes configure:16092: checking if clang++ supports -c -o file.o configure:16141: result: yes configure:16171: checking whether the clang++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries configure:16211: result: yes configure:16354: checking dynamic linker characteristics configure:17103: result: darwin23.1.0 dyld configure:17168: checking how to hardcode library paths into programs configure:17193: result: immediate configure:17257: checking which libtool initialization strategy to adopt configure:17259: result: AC-PROG-LIBTOOL configure:17274: checking what warning flags to pass to the C compiler configure:17295: result: -Wall -Wunused configure:17308: checking what language compliance flags to pass to the C compiler configure:17324: result: configure:17343: checking what warning flags to pass to the C++ compiler configure:17363: result: -Wall -Wno-unused configure:17376: checking what language compliance flags to pass to the C++ compiler configure:17392: result: configure:17416: checking for sys/stdtypes.h configure:17416: clang -c -g -O2 -Wall -Wunused conftest.c >&5 conftest.c:51:10: fatal error: 'sys/stdtypes.h' file not found #include <sys/stdtypes.h> ^~~~~~~~~~~~~~~~ 1 error generated. configure:17416: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include <stddef.h> | #ifdef HAVE_STDIO_H | # include <stdio.h> | #endif | #ifdef HAVE_STDLIB_H | # include <stdlib.h> | #endif | #ifdef HAVE_STRING_H | # include <string.h> | #endif | #ifdef HAVE_INTTYPES_H | # include <inttypes.h> | #endif | #ifdef HAVE_STDINT_H | # include <stdint.h> | #endif | #ifdef HAVE_STRINGS_H | # include <strings.h> | #endif | #ifdef HAVE_SYS_TYPES_H | # include <sys/types.h> | #endif | #ifdef HAVE_SYS_STAT_H | # include <sys/stat.h> | #endif | #ifdef HAVE_UNISTD_H | # include <unistd.h> | #endif | #include <sys/stdtypes.h> configure:17416: result: no configure:17430: checking for OpenMP flag of C compiler configure:17476: clang -o conftest -g -O2 -Wall -Wunused -fopenmp conftest.c >&5 clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest -g -O2 -Wall -Wunused -openmp conftest.c >&5 ld: Undefined symbols: _omp_set_num_threads, referenced from: _main in conftest-729cac.o clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest -g -O2 -Wall -Wunused -qopenmp conftest.c >&5 clang: error: unknown argument '-qopenmp'; did you mean '-fopenmp'? configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest -g -O2 -Wall -Wunused -mp conftest.c >&5 clang: error: unknown argument: '-mp' configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest -g -O2 -Wall -Wunused -xopenmp conftest.c >&5 clang: error: language not recognized: 'openmp' configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest -g -O2 -Wall -Wunused -omp conftest.c >&5 ld: Undefined symbols: _omp_set_num_threads, referenced from: _main in conftest-fd1c38.o clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest -g -O2 -Wall -Wunused -qsmp=omp conftest.c >&5 clang: error: unknown argument: '-qsmp=omp' configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17476: clang -o conftest conftest.c >&5 ld: Undefined symbols: _omp_set_num_threads, referenced from: _main in conftest-4d71b1.o clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:17476: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "coot" | #define PACKAGE_TARNAME "coot" | #define PACKAGE_VERSION "1.1.03" | #define PACKAGE_STRING "coot 1.1.03" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "coot" | #define VERSION "1.1.03" | #define HAVE_STDIO_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_UNISTD_H 1 | #define STDC_HEADERS 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | | #include <omp.h> | | static void | parallel_fill(int * data, int n) | { | int i; | #pragma omp parallel for | for (i = 0; i < n; ++i) | data[i] = i; | } | | int | main() | { | int arr[100000]; | omp_set_num_threads(2); | parallel_fill(arr, 100000); | return 0; | } | configure:17487: result: unknown configure:17513: checking whether clang++ supports C++11 features by default configure:17808: clang++ -c -g -O2 -Wall -Wno-unused conftest.cpp >&5 configure:17808: $? = 0 configure:17818: result: yes configure:18503: checking for std::thread in thread configure:18531: clang++ -c -g -O2 -Wall -Wno-unused conftest.cpp >&5 configure:18531: $? = 0 configure:18548: result: yes configure:18651: checking for pkg-config configure:18674: found /opt/homebrew/Library/Homebrew/shims/mac/super/pkg-config configure:18687: result: /opt/homebrew/Library/Homebrew/shims/mac/super/pkg-config configure:18712: checking pkg-config is at least version 0.9.0 configure:18715: result: yes configure:18725: checking for glib-2.0 configure:18732: $PKG_CONFIG --exists --print-errors "glib-2.0" configure:18735: $? = 0 configure:18749: $PKG_CONFIG --exists --print-errors "glib-2.0" configure:18752: $? = 0 configure:18810: result: yes configure:18818: checking if this is MINGW on Windows configure:18845: result: no configure:18848: checking if this is msys2 windows 64 configure:18873: result: no configure:18981: checking for libpng >= 1.2 configure:18988: $PKG_CONFIG --exists --print-errors "libpng >= 1.2" configure:18991: $? = 0 configure:19005: $PKG_CONFIG --exists --print-errors "libpng >= 1.2" configure:19008: $? = 0 configure:19066: result: yes configure:19079: checking for cairo >= 1.14 configure:19086: $PKG_CONFIG --exists --print-errors "cairo >= 1.14" configure:19089: $? = 0 configure:19103: $PKG_CONFIG --exists --print-errors "cairo >= 1.14" configure:19106: $? = 0 configure:19164: result: yes configure:19182: checking for SQLite3 configure:19195: result: yes configure:19244: checking for libdwarf >= 0.7 configure:19251: $PKG_CONFIG --exists --print-errors "libdwarf >= 0.7" configure:19254: $? = 0 configure:19268: $PKG_CONFIG --exists --print-errors "libdwarf >= 0.7" configure:19271: $? = 0 configure:19329: result: yes configure:19465: checking for mmdb2 configure:19476: result: yes configure:19505: clang++ -c -g -O2 -Wall -Wno-unused -std=c++17 -I/opt/homebrew/Cellar/mmdb2/2.0.20_1/include conftest.cpp >&5 conftest.cpp:29:34: warning: variable 'l' is uninitialized when used here [-Wuninitialized] mmdb::Link *l; mmdb::realtype ll=l->dist ^ conftest.cpp:29:14: note: initialize the variable 'l' to silence this warning mmdb::Link *l; mmdb::realtype ll=l->dist ^ = nullptr 1 warning generated. configure:19505: $? = 0 configure:19534: checking for ssm configure:19547: result: yes configure:19587: checking for non-prefixed single-precision FFTW2 (fftw.h) configure:19617: clang++ -o conftest -g -O2 -Wall -Wno-unused -std=c++17 -I/opt/homebrew/opt/clipper4coot/fftw2/include conftest.cpp -L/opt/homebrew/opt/clipper4coot/fftw2/lib -lrfftw -lfftw >&5 configure:19617: $? = 0 configure:19626: result: yes configure:19677: checking for Clipper configure:19706: clang++ -c -g -O2 -Wall -Wno-unused -std=c++17 -D_THREAD_SAFE -pthread -I/opt/homebrew/Cellar/libccp4/542516076_1/include -I/opt/homebrew/Cellar/mmdb2/2.0.20_1/include -I/opt/homebrew/Cellar/clipper4coot/2.1.20180802_2/include -I/opt/homebrew/opt/clipper4coot/fftw2/include conftest.cpp >&5 configure:19706: $? = 0 configure:19739: result: yes configure:20003: checking for gsl-config configure:20026: found /opt/homebrew/opt/gsl/bin/gsl-config configure:20040: result: /opt/homebrew/opt/gsl/bin/gsl-config configure:20049: checking for GSL - version >= 1.3 configure:20144: clang -o conftest -g -O2 -Wall -Wunused -I/opt/homebrew/Cellar/gsl/2.7.1/include -I/opt/homebrew/opt/clipper4coot/fftw2/include conftest.c -L/opt/homebrew/Cellar/gsl/2.7.1/lib -lgsl -lgslcblas >&5 configure:20144: $? = 0 configure:20144: ./conftest configure:20144: $? = 0 configure:20161: result: yes configure:20229: checking for glm >= 0.9.9 configure:20236: $PKG_CONFIG --exists --print-errors "glm >= 0.9.9" configure:20239: $? = 0 configure:20253: $PKG_CONFIG --exists --print-errors "glm >= 0.9.9" configure:20256: $? = 0 configure:20314: result: yes configure:20322: checking for gtk4 >= 4.4 configure:20329: $PKG_CONFIG --exists --print-errors "gtk4 >= 4.4" configure:20332: $? = 0 configure:20346: $PKG_CONFIG --exists --print-errors "gtk4 >= 4.4" configure:20349: $? = 0 configure:20407: result: yes configure:20414: checking for epoxy >= 1.5 configure:20421: $PKG_CONFIG --exists --print-errors "epoxy >= 1.5" configure:20424: $? = 0 configure:20438: $PKG_CONFIG --exists --print-errors "epoxy >= 1.5" configure:20441: $? = 0 configure:20499: result: yes configure:20507: checking for glfw3 >= 3.0 configure:20514: $PKG_CONFIG --exists --print-errors "glfw3 >= 3.0" configure:20517: $? = 0 configure:20531: $PKG_CONFIG --exists --print-errors "glfw3 >= 3.0" configure:20534: $? = 0 configure:20592: result: yes configure:20631: checking for a Python interpreter with version >= 3.7 configure:20649: python3 -c import sys # split strings by '.' and convert to numeric. Append some zeros # because we need at least 4 digits for the hex conversion. # map returns an iterator in Python 3.0 and a list in 2.x minver = list(map(int, '3.7'.split('.'))) + [0, 0, 0] minverhex = 0 # xrange is not present in Python 3.0 and range returns an iterator for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i] sys.exit(sys.hexversion < minverhex) configure:20652: $? = 0 configure:20660: result: python3 configure:20668: checking for python3 configure:20691: found /opt/homebrew/opt/python@3.11/bin/python3 configure:20704: result: /opt/homebrew/opt/python@3.11/bin/python3 configure:20722: checking for python3 version configure:20731: result: 3.11 configure:20748: checking for python3 platform configure:20757: result: darwin configure:20764: checking for python3 script directory configure:20798: result: ${prefix}/lib/python3.11/site-packages configure:20807: checking for python3 extension module directory configure:20841: result: ${exec_prefix}/lib/python3.11/site-packages configure:20862: checking for python3.11 configure:20898: result: /opt/homebrew/opt/python@3.11/bin/python3 configure:20914: checking for a version of Python >= '2.1.0' configure:20940: result: yes configure:20971: checking for the distutils Python package configure:20975: result: yes configure:20989: checking for Python include path configure:21005: result: -I/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11 configure:21012: checking for Python library path configure:21087: result: -L/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib -lpython3.11 configure:21094: checking for Python site-packages path configure:21100: result: /opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages configure:21107: checking python extra libraries configure:21114: result: -ldl -framework CoreFoundation configure:21121: checking python extra linking flags configure:21128: result: -Wl,-stack_size,1000000 -framework CoreFoundation /opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/Python configure:21135: checking consistency of all components of python development environment configure:21163: clang -o conftest -g -O2 -Wall -Wunused -I/opt/homebrew/opt/clipper4coot/fftw2/include -I/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11 -Wl,-stack_size,1000000 -framework CoreFoundation /opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/Python conftest.c -L/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib -lpython3.11 -ldl -framework CoreFoundation -ldl -framework CoreFoundation >&5 ld: warning: ignoring duplicate libraries: '-ldl' configure:21163: $? = 0 configure:21183: result: yes configure:21220: checking python3 module: requests configure:21229: result: no configure:21235: error: failed to find required module requests ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=arm-apple-darwin23.1.0 ac_cv_build_alias= ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_ALSA_CFLAGS_set= ac_cv_env_ALSA_CFLAGS_value= ac_cv_env_ALSA_LIBS_set= ac_cv_env_ALSA_LIBS_value= ac_cv_env_CAIRO_CFLAGS_set= ac_cv_env_CAIRO_CFLAGS_value= ac_cv_env_CAIRO_LIBS_set= ac_cv_env_CAIRO_LIBS_value= ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set=set ac_cv_env_CC_value=clang ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set=set ac_cv_env_CXX_value=clang++ ac_cv_env_EPOXY_CFLAGS_set= ac_cv_env_EPOXY_CFLAGS_value= ac_cv_env_EPOXY_LIBS_set= ac_cv_env_EPOXY_LIBS_value= ac_cv_env_GLFW3_CFLAGS_set= ac_cv_env_GLFW3_CFLAGS_value= ac_cv_env_GLFW3_LIBS_set= ac_cv_env_GLFW3_LIBS_value= ac_cv_env_GLIB_CFLAGS_set= ac_cv_env_GLIB_CFLAGS_value= ac_cv_env_GLIB_LIBS_set= ac_cv_env_GLIB_LIBS_value= ac_cv_env_GLM_CFLAGS_set= ac_cv_env_GLM_CFLAGS_value= ac_cv_env_GLM_LIBS_set= ac_cv_env_GLM_LIBS_value= ac_cv_env_GTK_CFLAGS_set= ac_cv_env_GTK_CFLAGS_value= ac_cv_env_GTK_LIBS_set= ac_cv_env_GTK_LIBS_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBDW_CFLAGS_set= ac_cv_env_LIBDW_CFLAGS_value= ac_cv_env_LIBDW_LIBS_set= ac_cv_env_LIBDW_LIBS_value= ac_cv_env_LIBPNG_CFLAGS_set= ac_cv_env_LIBPNG_CFLAGS_value= ac_cv_env_LIBPNG_LIBS_set= ac_cv_env_LIBPNG_LIBS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_LT_SYS_LIBRARY_PATH_set= ac_cv_env_LT_SYS_LIBRARY_PATH_value= ac_cv_env_OpenAL_CFLAGS_set= ac_cv_env_OpenAL_CFLAGS_value= ac_cv_env_OpenAL_LIBS_set= ac_cv_env_OpenAL_LIBS_value= ac_cv_env_PKG_CONFIG_LIBDIR_set=set ac_cv_env_PKG_CONFIG_LIBDIR_value=/usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/14 ac_cv_env_PKG_CONFIG_PATH_set=set ac_cv_env_PKG_CONFIG_PATH_value=/opt/homebrew/opt/glm/lib/pkgconfig:/opt/homebrew/opt/libpng/lib/pkgconfig:/opt/homebrew/opt/freetype/lib/pkgconfig:/opt/homebrew/opt/fontconfig/lib/pkgconfig:/opt/homebrew/opt/pcre2/lib/pkgconfig:/opt/homebrew/opt/glib/lib/pkgconfig:/opt/homebrew/opt/libxau/lib/pkgconfig:/opt/homebrew/opt/libxdmcp/lib/pkgconfig:/opt/homebrew/opt/libxcb/lib/pkgconfig:/opt/homebrew/opt/libx11/lib/pkgconfig:/opt/homebrew/opt/libxext/lib/pkgconfig:/opt/homebrew/opt/libxrender/lib/pkgconfig:/opt/homebrew/opt/lzo/lib/pkgconfig:/opt/homebrew/opt/pixman/lib/pkgconfig:/opt/homebrew/opt/cairo/lib/pkgconfig:/opt/homebrew/opt/jpeg-turbo/lib/pkgconfig:/opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/lz4/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/libtiff/lib/pkgconfig:/opt/homebrew/opt/gdk-pixbuf/lib/pkgconfig:/opt/homebrew/opt/fribidi/lib/pkgconfig:/opt/homebrew/opt/graphite2/lib/pkgconfig:/opt/homebrew/opt/icu4c/lib/pkgconfig:/opt/homebrew/opt/harfbuzz/lib/pkgconfig:/opt/homebrew/opt/pango/lib/pkgconfig:/opt/homebrew/opt/librsvg/lib/pkgconfig:/opt/homebrew/opt/openssl@3/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/python@3.12/lib/pkgconfig:/opt/homebrew/opt/libccp4/lib/pkgconfig:/opt/homebrew/opt/mmdb2/lib/pkgconfig:/opt/homebrew/opt/clipper4coot/lib/pkgconfig:/opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/brotli/lib/pkgconfig:/opt/homebrew/opt/highway/lib/pkgconfig:/opt/homebrew/opt/imath/lib/pkgconfig:/opt/homebrew/opt/little-cms2/lib/pkgconfig:/opt/homebrew/opt/openexr/lib/pkgconfig:/opt/homebrew/opt/webp/lib/pkgconfig:/opt/homebrew/opt/jpeg-xl/lib/pkgconfig:/opt/homebrew/opt/libvmaf/lib/pkgconfig:/opt/homebrew/opt/aom/lib/pkgconfig:/opt/homebrew/opt/libavif/lib/pkgconfig:/opt/homebrew/opt/gd/lib/pkgconfig:/opt/homebrew/opt/jbig2dec/lib/pkgconfig:/opt/homebrew/opt/libidn/lib/pkgconfig:/opt/homebrew/opt/openjpeg/lib/pkgconfig:/opt/homebrew/opt/libde265/lib/pkgconfig:/opt/homebrew/opt/x265/lib/pkgconfig:/opt/homebrew/opt/libheif/lib/pkgconfig:/opt/homebrew/opt/liblqr/lib/pkgconfig:/opt/homebrew/opt/jasper/lib/pkgconfig:/opt/homebrew/opt/libraw/lib/pkgconfig:/opt/homebrew/opt/imagemagick/lib/pkgconfig:/opt/homebrew/opt/jpeg/lib/pkgconfig:/opt/homebrew/opt/ssm/lib/pkgconfig:/opt/homebrew/opt/dwarfutils/lib/pkgconfig:/opt/homebrew/opt/glfw/lib/pkgconfig:/opt/homebrew/opt/gsl/lib/pkgconfig:/opt/homebrew/opt/graphene/lib/pkgconfig:/opt/homebrew/opt/libepoxy/lib/pkgconfig:/opt/homebrew/opt/gtk4/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/python@3.11/lib/pkgconfig:/opt/homebrew/opt/krb5/lib/pkgconfig:/opt/homebrew/opt/postgresql@15/lib/pkgconfig:/opt/homebrew/opt/gobject-introspection/lib/pkgconfig:/opt/homebrew/opt/pygobject3/lib/pkgconfig:/opt/homebrew/opt/xorgproto/share/pkgconfig:/opt/homebrew/opt/adwaita-icon-theme/share/pkgconfig:/opt/homebrew/opt/shared-mime-info/share/pkgconfig:/opt/homebrew/opt/eigen/share/pkgconfig ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_value= ac_cv_env_PYTHON_VERSION_set= ac_cv_env_PYTHON_VERSION_value= ac_cv_env_PyGObject_CFLAGS_set= ac_cv_env_PyGObject_CFLAGS_value= ac_cv_env_PyGObject_LIBS_set= ac_cv_env_PyGObject_LIBS_value= ac_cv_env_VORBISFILE_CFLAGS_set= ac_cv_env_VORBISFILE_CFLAGS_value= ac_cv_env_VORBISFILE_LIBS_set= ac_cv_env_VORBISFILE_LIBS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_header_dlfcn_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_stdint_h=yes ac_cv_header_stdio_h=yes ac_cv_header_stdlib_h=yes ac_cv_header_string_h=yes ac_cv_header_strings_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_stdtypes_h=no ac_cv_header_sys_types_h=yes ac_cv_header_unistd_h=yes ac_cv_host=arm-apple-darwin23.1.0 ac_cv_objext=o ac_cv_path_EGREP='/usr/bin/grep -E' ac_cv_path_EGREP_TRADITIONAL='/usr/bin/grep -E' ac_cv_path_FGREP='/usr/bin/grep -F' ac_cv_path_GREP=/usr/bin/grep ac_cv_path_GSL_CONFIG=/opt/homebrew/opt/gsl/bin/gsl-config ac_cv_path_PYTHON=/opt/homebrew/opt/python@3.11/bin/python3 ac_cv_path_SED=/usr/bin/sed ac_cv_path_ac_pt_PKG_CONFIG=/opt/homebrew/Library/Homebrew/shims/mac/super/pkg-config ac_cv_path_install='/usr/bin/install -c' ac_cv_path_lt_DD=/bin/dd ac_cv_prog_AWK=awk ac_cv_prog_CXXCPP='clang++ -E' ac_cv_prog_ac_ct_AR=ar ac_cv_prog_ac_ct_CC=clang ac_cv_prog_ac_ct_DSYMUTIL=dsymutil ac_cv_prog_ac_ct_FILECMD=file ac_cv_prog_ac_ct_LIPO=lipo ac_cv_prog_ac_ct_NMEDIT=nmedit ac_cv_prog_ac_ct_OBJDUMP=objdump ac_cv_prog_ac_ct_OTOOL=otool ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_ac_ct_STRIP=strip ac_cv_prog_cc_c11= ac_cv_prog_cc_g=yes ac_cv_prog_cc_stdc= ac_cv_prog_cxx_cxx11= ac_cv_prog_cxx_g=yes ac_cv_prog_cxx_stdcxx= ac_cv_prog_make_make_set=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 am_cv_func_iconv_works=yes am_cv_make_support_nested_variables=yes am_cv_pathless_PYTHON=python3 am_cv_prog_cc_c_o=yes am_cv_python_platform=darwin am_cv_python_pyexecdir='${exec_prefix}/lib/python3.11/site-packages' am_cv_python_pythondir='${prefix}/lib/python3.11/site-packages' am_cv_python_version=3.11 ax_cv_c_openmp=unknown ax_cv_cxx_compile_cxx11=yes ax_cv_cxx_have_thread=yes lt_cv_apple_cc_single_mod=no lt_cv_ar_at_file=no lt_cv_deplibs_check_method=pass_all lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_ld_exported_symbols_list=yes lt_cv_ld_force_load=yes lt_cv_ld_reload_flag=-r lt_cv_nm_interface='BSD nm' lt_cv_objdir=.libs lt_cv_path_LD=/Library/Developer/CommandLineTools/usr/bin/ld lt_cv_path_LDCXX=/Library/Developer/CommandLineTools/usr/bin/ld lt_cv_path_NM='/usr/bin/nm -B' lt_cv_path_mainfest_tool=no lt_cv_prog_compiler_c_o=yes lt_cv_prog_compiler_c_o_CXX=yes lt_cv_prog_compiler_pic='-fno-common -DPIC' lt_cv_prog_compiler_pic_CXX='-fno-common -DPIC' lt_cv_prog_compiler_pic_works=yes lt_cv_prog_compiler_pic_works_CXX=yes lt_cv_prog_compiler_rtti_exceptions=yes lt_cv_prog_compiler_static_works=no lt_cv_prog_compiler_static_works_CXX=no lt_cv_prog_gnu_ld=no lt_cv_prog_gnu_ldcxx=no lt_cv_sharedlib_from_linklib_cmd='printf %s\n' lt_cv_sys_global_symbol_pipe='/usr/bin/sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'' | /usr/bin/sed '\''/ __gnu_lto/d'\''' lt_cv_sys_global_symbol_to_c_name_address='/usr/bin/sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/ {"\1", (void *) \&\1},/p'\''' lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='/usr/bin/sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(lib.*\)$/ {"\1", (void *) \&\1},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/ {"lib\1", (void *) \&\1},/p'\''' lt_cv_sys_global_symbol_to_cdecl='/usr/bin/sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' lt_cv_sys_global_symbol_to_import= lt_cv_sys_max_cmd_len=786432 lt_cv_to_host_file_cmd=func_convert_file_noop lt_cv_to_tool_file_cmd=func_convert_file_noop lt_cv_truncate_bin='/bin/dd bs=4096 count=1' pkg_cv_CAIRO_CFLAGS='-I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.14.2/include -I/opt/homebrew/Cellar/libxau/1.0.11/include -I/opt/homebrew/Cellar/libxdmcp/1.1.4/include -I/opt/homebrew/Cellar/libxcb/1.16/include -I/opt/homebrew/Cellar/libx11/1.8.7/include -I/opt/homebrew/Cellar/libxext/1.3.5/include -I/opt/homebrew/Cellar/libxrender/0.9.11/include -I/opt/homebrew/Cellar/pixman/0.42.2/include/pixman-1 -I/opt/homebrew/Cellar/cairo/1.18.0/include/cairo -I/opt/homebrew/Cellar/xorgproto/2023.2/include' pkg_cv_CAIRO_LIBS='-L/opt/homebrew/Cellar/cairo/1.18.0/lib -lcairo' pkg_cv_EPOXY_CFLAGS=-I/opt/homebrew/Cellar/libepoxy/1.5.10/include pkg_cv_EPOXY_LIBS='-L/opt/homebrew/Cellar/libepoxy/1.5.10/lib -lepoxy' pkg_cv_GLFW3_CFLAGS=-I/opt/homebrew/Cellar/glfw/3.3.9/include pkg_cv_GLFW3_LIBS='-L/opt/homebrew/Cellar/glfw/3.3.9/lib -lglfw' pkg_cv_GLIB_CFLAGS='-I/opt/homebrew/Cellar/pcre2/10.42/include -I/opt/homebrew/Cellar/glib/2.78.3/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.78.3/lib/glib-2.0/include -I/opt/homebrew/opt/gettext/include' pkg_cv_GLIB_LIBS='-L/opt/homebrew/Cellar/glib/2.78.3/lib -L/opt/homebrew/opt/gettext/lib -lglib-2.0 -lintl' pkg_cv_GLM_CFLAGS=-I/opt/homebrew/Cellar/glm/0.9.9.8/include pkg_cv_GLM_LIBS= pkg_cv_GTK_CFLAGS='-I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.14.2/include -I/opt/homebrew/Cellar/pcre2/10.42/include -I/opt/homebrew/Cellar/glib/2.78.3/include -I/opt/homebrew/Cellar/glib/2.78.3/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.78.3/lib/glib-2.0/include -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/Cellar/libxau/1.0.11/include -I/opt/homebrew/Cellar/libxdmcp/1.1.4/include -I/opt/homebrew/Cellar/libxcb/1.16/include -I/opt/homebrew/Cellar/libx11/1.8.7/include -I/opt/homebrew/Cellar/libxext/1.3.5/include -I/opt/homebrew/Cellar/libxrender/0.9.11/include -I/opt/homebrew/Cellar/pixman/0.42.2/include/pixman-1 -I/opt/homebrew/Cellar/cairo/1.18.0/include/cairo -I/opt/homebrew/Cellar/jpeg-turbo/3.0.0/include -I/opt/homebrew/Cellar/xz/5.4.5/include -I/opt/homebrew/Cellar/zstd/1.5.5/include -I/opt/homebrew/Cellar/libtiff/4.6.0/include -I/opt/homebrew/Cellar/gdk-pixbuf/2.42.10_1/include/gdk-pixbuf-2.0 -I/opt/homebrew/Cellar/fribidi/1.0.13/include/fribidi -I/opt/homebrew/Cellar/graphite2/1.3.14/include -I/opt/homebrew/Cellar/harfbuzz/8.3.0/include/harfbuzz -I/opt/homebrew/Cellar/pango/1.50.14/include/pango-1.0 -I/opt/homebrew/Cellar/graphene/1.10.8/include/graphene-1.0 -I/opt/homebrew/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/opt/homebrew/Cellar/gtk4/4.12.4/include/gtk-4.0 -I/opt/homebrew/Cellar/xorgproto/2023.2/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi' pkg_cv_GTK_LIBS='-L/opt/homebrew/Cellar/glib/2.78.3/lib -L/opt/homebrew/opt/gettext/lib -L/opt/homebrew/Cellar/cairo/1.18.0/lib -L/opt/homebrew/Cellar/gdk-pixbuf/2.42.10_1/lib -L/opt/homebrew/Cellar/harfbuzz/8.3.0/lib -L/opt/homebrew/Cellar/pango/1.50.14/lib -L/opt/homebrew/Cellar/graphene/1.10.8/lib -L/opt/homebrew/Cellar/gtk4/4.12.4/lib -lgtk-4 -lpangocairo-1.0 -lpango-1.0 -lharfbuzz -lgdk_pixbuf-2.0 -lcairo-gobject -lcairo -lgraphene-1.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lintl' pkg_cv_LIBDW_CFLAGS=-I/opt/homebrew/Cellar/dwarfutils/0.9.0/include/libdwarf-0 pkg_cv_LIBDW_LIBS='-L/opt/homebrew/Cellar/dwarfutils/0.9.0/lib -ldwarf' pkg_cv_LIBPNG_CFLAGS=-I/opt/homebrew/opt/libpng/include/libpng16 pkg_cv_LIBPNG_LIBS='-L/opt/homebrew/opt/libpng/lib -lpng16' ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} '\''/private/tmp/coot-20231225-86280-buolj3/coot-1.1.03/missing'\'' aclocal-1.16 -I macros' ALSA_CFLAGS='' ALSA_LIBS='' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AR='ar' AUTOCONF='${SHELL} '\''/private/tmp/coot-20231225-86280-buolj3/coot-1.1.03/missing'\'' autoconf' AUTOHEADER='${SHELL} '\''/private/tmp/coot-20231225-86280-buolj3/coot-1.1.03/missing'\'' autoheader' AUTOMAKE='${SHELL} '\''/private/tmp/coot-20231225-86280-buolj3/coot-1.1.03/missing'\'' automake-1.16' AWK='awk' BACKWARD_HAS_DW_FALSE='#' BACKWARD_HAS_DW_TRUE='' BOOST_CPPFLAGS='' BOOST_LDFLAGS='' BOOST_PYTHON_LIB='boost_python312-mt' BOOST_THREAD_LIB='' CAIRO_CFLAGS='-I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.14.2/include -I/opt/homebrew/Cellar/libxau/1.0.11/include -I/opt/homebrew/Cellar/libxdmcp/1.1.4/include -I/opt/homebrew/Cellar/libxcb/1.16/include -I/opt/homebrew/Cellar/libx11/1.8.7/include -I/opt/homebrew/Cellar/libxext/1.3.5/include -I/opt/homebrew/Cellar/libxrender/0.9.11/include -I/opt/homebrew/Cellar/pixman/0.42.2/include/pixman-1 -I/opt/homebrew/Cellar/cairo/1.18.0/include/cairo -I/opt/homebrew/Cellar/xorgproto/2023.2/include' CAIRO_LIBS='-L/opt/homebrew/Cellar/cairo/1.18.0/lib -lcairo' CC='clang' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2 -Wall -Wunused ' CLIPPER_CXXFLAGS='-D_THREAD_SAFE -pthread -I/opt/homebrew/Cellar/libccp4/542516076_1/include -I/opt/homebrew/Cellar/mmdb2/2.0.20_1/include -I/opt/homebrew/Cellar/clipper4coot/2.1.20180802_2/include -DCLIPPER_HAS_TOP8000' CLIPPER_LIBS='-L/opt/homebrew/Cellar/libccp4/542516076_1/lib -L/opt/homebrew/Cellar/mmdb2/2.0.20_1/lib -L/opt/homebrew/Cellar/clipper4coot/2.1.20180802_2/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2' CLIPPER_TOP8000_FALSE='#' CLIPPER_TOP8000_TRUE='' COND_LIBCOOTAPI_ONLY_FALSE='' COND_LIBCOOTAPI_ONLY_TRUE='' COND_LIDIA_ONLY_FALSE='' COND_LIDIA_ONLY_TRUE='' COOT_BUILD_INFO_STRING='' COOT_GSL_FLAGS='-DHAVE_GSL' COOT_STDTYPES='-DHAVE_SYS_STDTYPES_H=0' COOT_SYS_BUILD_TYPE='' COOT_USE_GUILE='' COOT_WINDOWS_CFLAGS='' COOT_WINDOWS_LDFLAGS='' CPPFLAGS='-I/opt/homebrew/opt/clipper4coot/fftw2/include ' CSCOPE='cscope' CTAGS='ctags' CURL_CFLAGS='' CURL_LIBS='' CXX='clang++' CXXCPP='clang++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2 -Wall -Wno-unused -std=c++17' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' DLLTOOL='false' DSYMUTIL='dsymutil' DUMPBIN='' ECHO_C='\c' ECHO_N='' ECHO_T='' EGREP='/usr/bin/grep -E' ENHANCED_LIGAND_TOOLS_CPPFLAGS='' EPOXY_CFLAGS='-I/opt/homebrew/Cellar/libepoxy/1.5.10/include' EPOXY_LIBS='-L/opt/homebrew/Cellar/libepoxy/1.5.10/lib -lepoxy' ETAGS='etags' EXEEXT='' EXPORT_DYNAMIC_FLAG_SPEC='' FFTW2_CPPFLAGS='-I/opt/homebrew/opt/clipper4coot/fftw2/include' FFTW2_LIBS='-L/opt/homebrew/opt/clipper4coot/fftw2/lib -lrfftw -lfftw' FGREP='/usr/bin/grep -F' FILECMD='file' GEMMI_CXXFLAGS='' GEMMI_LIBS='' GLFW3_CFLAGS='-I/opt/homebrew/Cellar/glfw/3.3.9/include' GLFW3_LIBS='-L/opt/homebrew/Cellar/glfw/3.3.9/lib -lglfw' GLIB_CFLAGS='-I/opt/homebrew/Cellar/pcre2/10.42/include -I/opt/homebrew/Cellar/glib/2.78.3/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.78.3/lib/glib-2.0/include -I/opt/homebrew/opt/gettext/include' GLIB_LIBS='-L/opt/homebrew/Cellar/glib/2.78.3/lib -L/opt/homebrew/opt/gettext/lib -lglib-2.0 -lintl' GLM_CFLAGS='-I/opt/homebrew/Cellar/glm/0.9.9.8/include' GLM_LIBS='' GLOB_CFLAGS='' GLOB_LIBS='' GREP='/usr/bin/grep' GSL_CFLAGS='-I/opt/homebrew/Cellar/gsl/2.7.1/include' GSL_CONFIG='/opt/homebrew/opt/gsl/bin/gsl-config' GSL_LIBS='-L/opt/homebrew/Cellar/gsl/2.7.1/lib -lgsl -lgslcblas' GTK_CFLAGS='-I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.14.2/include -I/opt/homebrew/Cellar/pcre2/10.42/include -I/opt/homebrew/Cellar/glib/2.78.3/include -I/opt/homebrew/Cellar/glib/2.78.3/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.78.3/lib/glib-2.0/include -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/Cellar/libxau/1.0.11/include -I/opt/homebrew/Cellar/libxdmcp/1.1.4/include -I/opt/homebrew/Cellar/libxcb/1.16/include -I/opt/homebrew/Cellar/libx11/1.8.7/include -I/opt/homebrew/Cellar/libxext/1.3.5/include -I/opt/homebrew/Cellar/libxrender/0.9.11/include -I/opt/homebrew/Cellar/pixman/0.42.2/include/pixman-1 -I/opt/homebrew/Cellar/cairo/1.18.0/include/cairo -I/opt/homebrew/Cellar/jpeg-turbo/3.0.0/include -I/opt/homebrew/Cellar/xz/5.4.5/include -I/opt/homebrew/Cellar/zstd/1.5.5/include -I/opt/homebrew/Cellar/libtiff/4.6.0/include -I/opt/homebrew/Cellar/gdk-pixbuf/2.42.10_1/include/gdk-pixbuf-2.0 -I/opt/homebrew/Cellar/fribidi/1.0.13/include/fribidi -I/opt/homebrew/Cellar/graphite2/1.3.14/include -I/opt/homebrew/Cellar/harfbuzz/8.3.0/include/harfbuzz -I/opt/homebrew/Cellar/pango/1.50.14/include/pango-1.0 -I/opt/homebrew/Cellar/graphene/1.10.8/include/graphene-1.0 -I/opt/homebrew/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/opt/homebrew/Cellar/gtk4/4.12.4/include/gtk-4.0 -I/opt/homebrew/Cellar/xorgproto/2023.2/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi' GTK_LIBS='-L/opt/homebrew/Cellar/glib/2.78.3/lib -L/opt/homebrew/opt/gettext/lib -L/opt/homebrew/Cellar/cairo/1.18.0/lib -L/opt/homebrew/Cellar/gdk-pixbuf/2.42.10_1/lib -L/opt/homebrew/Cellar/harfbuzz/8.3.0/lib -L/opt/homebrew/Cellar/pango/1.50.14/lib -L/opt/homebrew/Cellar/graphene/1.10.8/lib -L/opt/homebrew/Cellar/gtk4/4.12.4/lib -lgtk-4 -lpangocairo-1.0 -lpango-1.0 -lharfbuzz -lgdk_pixbuf-2.0 -lcairo-gobject -lcairo -lgraphene-1.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lintl' GUILE='' GUILE_CFLAGS='' GUILE_CONFIG='' GUILE_LDFLAGS='' GUILE_TOOLS='' HAVE_CXX11='1' INSIDE_GNOME_COMMON_FALSE='' INSIDE_GNOME_COMMON_TRUE='#' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LD='/Library/Developer/CommandLineTools/usr/bin/ld' LDFLAGS='' LIBDW_CFLAGS='-I/opt/homebrew/Cellar/dwarfutils/0.9.0/include/libdwarf-0' LIBDW_LIBS='-L/opt/homebrew/Cellar/dwarfutils/0.9.0/lib -ldwarf' LIBOBJS='' LIBPNG_CFLAGS='-DUSE_LIBPNG=1 -I/opt/homebrew/opt/libpng/include/libpng16' LIBPNG_LIBS='-L/opt/homebrew/opt/libpng/lib -lpng16' LIBS='' LIBSSM_CXXFLAGS='-I/opt/homebrew/Cellar/mmdb2/2.0.20_1/include -I/opt/homebrew/Cellar/ssm/1.4_1/include -DHAVE_SSMLIB' LIBSSM_LIBS='-L/opt/homebrew/Cellar/mmdb2/2.0.20_1/lib -L/opt/homebrew/Cellar/ssm/1.4_1/lib -lssm -lmmdb2' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIPO='lipo' LN_S='ln -s' LTLIBOBJS='' LT_SYS_LIBRARY_PATH='' L_BOOST_PYTHON='' MAKEINFO='${SHELL} '\''/private/tmp/coot-20231225-86280-buolj3/coot-1.1.03/missing'\'' makeinfo' MAKE_ENHANCED_LIGAND_TOOLS_FALSE='' MAKE_ENHANCED_LIGAND_TOOLS_TRUE='' MANIFEST_TOOL=':' MKDIR_P='mkdir -p' MMDB_CXXFLAGS='-I/opt/homebrew/Cellar/mmdb2/2.0.20_1/include -DMMDB_HAS_LINK_DISTANCE' MMDB_LIBS='-L/opt/homebrew/Cellar/mmdb2/2.0.20_1/lib -lmmdb2' MOLTRIANGLES_CPPFLAGS='' MOLTRIANGLES_LIBS='' MYSQL_CFLAGS='' MYSQL_LIBS='' NM='/usr/bin/nm -B' NMEDIT='nmedit' OBJDUMP='objdump' OBJEXT='o' OPENMP_CFLAGS='' OPENMP_CXXFLAGS='' OS_WIN32_FALSE='' OS_WIN32_TRUE='#' OS_WIN64_FALSE='' OS_WIN64_TRUE='#' OTOOL64=':' OTOOL='otool' OpenAL_CFLAGS='' OpenAL_LIBS='' PACKAGE='coot' PACKAGE_BUGREPORT='' PACKAGE_NAME='coot' PACKAGE_STRING='coot 1.1.03' PACKAGE_TARNAME='coot' PACKAGE_URL='' PACKAGE_VERSION='1.1.03' PATH_SEPARATOR=':' PKG_CONFIG='/opt/homebrew/Library/Homebrew/shims/mac/super/pkg-config' PKG_CONFIG_LIBDIR='/usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/14' PKG_CONFIG_PATH='/opt/homebrew/opt/glm/lib/pkgconfig:/opt/homebrew/opt/libpng/lib/pkgconfig:/opt/homebrew/opt/freetype/lib/pkgconfig:/opt/homebrew/opt/fontconfig/lib/pkgconfig:/opt/homebrew/opt/pcre2/lib/pkgconfig:/opt/homebrew/opt/glib/lib/pkgconfig:/opt/homebrew/opt/libxau/lib/pkgconfig:/opt/homebrew/opt/libxdmcp/lib/pkgconfig:/opt/homebrew/opt/libxcb/lib/pkgconfig:/opt/homebrew/opt/libx11/lib/pkgconfig:/opt/homebrew/opt/libxext/lib/pkgconfig:/opt/homebrew/opt/libxrender/lib/pkgconfig:/opt/homebrew/opt/lzo/lib/pkgconfig:/opt/homebrew/opt/pixman/lib/pkgconfig:/opt/homebrew/opt/cairo/lib/pkgconfig:/opt/homebrew/opt/jpeg-turbo/lib/pkgconfig:/opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/lz4/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/libtiff/lib/pkgconfig:/opt/homebrew/opt/gdk-pixbuf/lib/pkgconfig:/opt/homebrew/opt/fribidi/lib/pkgconfig:/opt/homebrew/opt/graphite2/lib/pkgconfig:/opt/homebrew/opt/icu4c/lib/pkgconfig:/opt/homebrew/opt/harfbuzz/lib/pkgconfig:/opt/homebrew/opt/pango/lib/pkgconfig:/opt/homebrew/opt/librsvg/lib/pkgconfig:/opt/homebrew/opt/openssl@3/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/python@3.12/lib/pkgconfig:/opt/homebrew/opt/libccp4/lib/pkgconfig:/opt/homebrew/opt/mmdb2/lib/pkgconfig:/opt/homebrew/opt/clipper4coot/lib/pkgconfig:/opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/brotli/lib/pkgconfig:/opt/homebrew/opt/highway/lib/pkgconfig:/opt/homebrew/opt/imath/lib/pkgconfig:/opt/homebrew/opt/little-cms2/lib/pkgconfig:/opt/homebrew/opt/openexr/lib/pkgconfig:/opt/homebrew/opt/webp/lib/pkgconfig:/opt/homebrew/opt/jpeg-xl/lib/pkgconfig:/opt/homebrew/opt/libvmaf/lib/pkgconfig:/opt/homebrew/opt/aom/lib/pkgconfig:/opt/homebrew/opt/libavif/lib/pkgconfig:/opt/homebrew/opt/gd/lib/pkgconfig:/opt/homebrew/opt/jbig2dec/lib/pkgconfig:/opt/homebrew/opt/libidn/lib/pkgconfig:/opt/homebrew/opt/openjpeg/lib/pkgconfig:/opt/homebrew/opt/libde265/lib/pkgconfig:/opt/homebrew/opt/x265/lib/pkgconfig:/opt/homebrew/opt/libheif/lib/pkgconfig:/opt/homebrew/opt/liblqr/lib/pkgconfig:/opt/homebrew/opt/jasper/lib/pkgconfig:/opt/homebrew/opt/libraw/lib/pkgconfig:/opt/homebrew/opt/imagemagick/lib/pkgconfig:/opt/homebrew/opt/jpeg/lib/pkgconfig:/opt/homebrew/opt/ssm/lib/pkgconfig:/opt/homebrew/opt/dwarfutils/lib/pkgconfig:/opt/homebrew/opt/glfw/lib/pkgconfig:/opt/homebrew/opt/gsl/lib/pkgconfig:/opt/homebrew/opt/graphene/lib/pkgconfig:/opt/homebrew/opt/libepoxy/lib/pkgconfig:/opt/homebrew/opt/gtk4/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/python@3.11/lib/pkgconfig:/opt/homebrew/opt/krb5/lib/pkgconfig:/opt/homebrew/opt/postgresql@15/lib/pkgconfig:/opt/homebrew/opt/gobject-introspection/lib/pkgconfig:/opt/homebrew/opt/pygobject3/lib/pkgconfig:/opt/homebrew/opt/xorgproto/share/pkgconfig:/opt/homebrew/opt/adwaita-icon-theme/share/pkgconfig:/opt/homebrew/opt/shared-mime-info/share/pkgconfig:/opt/homebrew/opt/eigen/share/pkgconfig' PYTHON='/opt/homebrew/opt/python@3.11/bin/python3' PYTHON_CPPFLAGS='-I/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11' PYTHON_EXEC_PREFIX='${exec_prefix}' PYTHON_EXTRA_LDFLAGS='-Wl,-stack_size,1000000 -framework CoreFoundation /opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/Python' PYTHON_EXTRA_LIBS='-ldl -framework CoreFoundation ' PYTHON_LIBS='-L/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib -lpython3.11' PYTHON_PLATFORM='darwin' PYTHON_PREFIX='${prefix}' PYTHON_SITE_PKG='/opt/homebrew/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages' PYTHON_VERSION='3.11' PyGObject_CFLAGS='' PyGObject_LIBS='' RANLIB='ranlib' RDKIT_CXXFLAGS='' RDKIT_LIBS='' SED='/usr/bin/sed' SET_MAKE='' SHARED_LDFLAGS='' SHELL='/bin/sh' SOUND_FLAGS='' SQLITE3_CFLAGS='-DUSE_SQLITE3 -I/opt/homebrew/opt/sqlite/include' SQLITE3_LIBS='-L/opt/homebrew/opt/sqlite/lib -lsqlite3' STRIP='strip' USE_BACKWARD_FALSE='#' USE_BACKWARD_TRUE='' USE_GUILE_FALSE='' USE_GUILE_TRUE='#' USE_LIBCURL='' VERSION='1.1.03' VORBISFILE_CFLAGS='' VORBISFILE_LIBS='' ac_ct_AR='ar' ac_ct_CC='clang' ac_ct_CXX='' ac_ct_DUMPBIN='' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='_no' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build='arm-apple-darwin23.1.0' build_alias='' build_cpu='arm' build_os='darwin23.1.0' build_vendor='apple' cflags_set='yes' cxxflags_set='yes' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='arm-apple-darwin23.1.0' host_alias='' host_cpu='arm' host_os='darwin23.1.0' host_vendor='apple' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /private/tmp/coot-20231225-86280-buolj3/coot-1.1.03/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' pkgpyexecdir='${pyexecdir}/coot' pkgpythondir='${pythondir}/coot' prefix='/opt/homebrew/Cellar/coot/1.1.03' program_transform_name='s,x,x,' psdir='${docdir}' pyexecdir='${exec_prefix}/lib/python3.11/site-packages' pythondir='${prefix}/lib/python3.11/site-packages' runstatedir='${localstatedir}/run' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "coot" #define PACKAGE_TARNAME "coot" #define PACKAGE_VERSION "1.1.03" #define PACKAGE_STRING "coot 1.1.03" #define PACKAGE_BUGREPORT "" #define PACKAGE_URL "" #define PACKAGE "coot" #define VERSION "1.1.03" #define HAVE_STDIO_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_STRINGS_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_UNISTD_H 1 #define STDC_HEADERS 1 #define HAVE_DLFCN_H 1 #define LT_OBJDIR ".libs/" #define HAVE_CXX11 1 #define HAVE_CXX_THREAD 1 #define HAVE_PYTHON "3.11" configure: exit 1