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pemsley / coot

Software for macromolecular model-building
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
GNU General Public License v3.0
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GLM and other homebrew build errors #167

Open stachowskitim opened 1 day ago

stachowskitim commented 1 day ago

Just getting around to updating my Coot1 for FLEXR...

from a fresh fork on MacOS 14 using homebrew, this new bit in configure.ac makes it so it can't find glm.

If I replace it with the original PKG_CHECK_MODULES(GLM, glm >= 0.9.9) it moves along. 

# While GLM has no pkgconfig glm.pc file, we have to be a bit more hand-to-mouth
# about its configuration
# PKG_CHECK_MODULES(GLM, glm >= 0.9.9)

# Copied and adapted from how gemmi and rdkit are found below
AC_ARG_WITH([glm], AS_HELP_STRING([--with-glm location of the GLM package]), with_glm="$withval", with_glm=false)

AC_MSG_CHECKING([for GLM])
if test "x$with_glm" = xfalse ; then
   if test -x $prefix/include/glm ; then
      #echo OK, good we found glm in $prefix
      AC_MSG_RESULT(yes)
      glm_install_dir=$prefix
      AC_SUBST(GLM_CXXFLAGS, "-I$glm_install_dir/include")
      AC_SUBST(GLM_LIBS, "-L$glm_install_dir/lib -lglm")
   else
      AC_MSG_RESULT(no)
      echo Configuration error. Could not find GLM.
      exit 1
   fi
else
   AC_MSG_RESULT(yes)
   AC_SUBST(GLM_CXXFLAGS, "-I$withval/include")
   AC_SUBST(GLM_LIBS, "-L$withval/lib -lglm")
fi

Then the build crashes with: 

Last 15 lines from /Users/tstachow/Library/Logs/Homebrew/coot/09.make:
      |                                ^
1 error generated.
make[1]: *** [key-bindings.lo] Error 1
make[1]: *** Waiting for unfinished jobs....
mv -f .deps/gtk-manual.Tpo .deps/gtk-manual.Plo
libtool: compile:  clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.x-pre\" "-DPACKAGE_STRING=\"coot 1.1.x-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.x-pre\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_THREAD=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_PYTHON -I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.15.0/include -I/opt/homebrew/Cellar/pcre2/10.44/include -I/opt/homebrew/Cellar/xz/5.6.3/include -I/opt/homebrew/Cellar/glib/2.82.1/include -I/opt/homebrew/Cellar/glib/2.82.1/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.82.1/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/1.1.5/include -I/opt/homebrew/Cellar/libxcb/1.17.0/include -I/opt/homebrew/Cellar/libx11/1.8.10/include -I/opt/homebrew/Cellar/libxext/1.3.6/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/1.18.2/include/cairo -I/opt/homebrew/Cellar/jpeg-turbo/3.0.4/include -I/opt/homebrew/opt/zstd/include -I/opt/homebrew/Cellar/libtiff/4.7.0/include -I/opt/homebrew/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/opt/homebrew/Cellar/fribidi/1.0.16/include/fribidi -I/opt/homebrew/Cellar/graphite2/1.3.14/include -I/opt/homebrew/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/opt/homebrew/Cellar/pango/1.54.0/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/gtk4/4.16.3/include/gtk-4.0 -I/opt/homebrew/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/opt/homebrew/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/opt/homebrew/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_MOLECULES_TO_TRIANGLES -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -I/opt/homebrew/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/opt/homebrew/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/opt/homebrew/Cellar/libccp4/542516076_2/include -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -I/opt/homebrew/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000 -DUSE_SQLITE3 -I/opt/homebrew/opt/sqlite/include -DUSE_BACKWARD -I/opt/homebrew/opt/clipper4coot/fftw2/include -DUSE_MOLECULES_TO_TRIANGLES -DPKGDATADIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share/coot\" -DPACKAGE_LOCALE_DIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share/coot/locale\" -DPKGPYTHONDIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages/coot\" -DPYTHONDIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages\" -DXDATADIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share\" -DCOOT_SYS_BUILD_TYPE=\"Darwin-MacOSX-14.7-arm64-gtk4\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -I/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include -I/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13 -g -O2 -Wall -Wno-unused -std=c++17 -MT lbg-callbacks-outer.lo -MD -MP -MF .deps/lbg-callbacks-outer.Tpo -c lbg-callbacks-outer.cc -o lbg-callbacks-outer.o >/dev/null 2>&1
libtool: compile:  clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.x-pre\" "-DPACKAGE_STRING=\"coot 1.1.x-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.x-pre\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_THREAD=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_PYTHON -I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.15.0/include -I/opt/homebrew/Cellar/pcre2/10.44/include -I/opt/homebrew/Cellar/xz/5.6.3/include -I/opt/homebrew/Cellar/glib/2.82.1/include -I/opt/homebrew/Cellar/glib/2.82.1/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.82.1/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/1.1.5/include -I/opt/homebrew/Cellar/libxcb/1.17.0/include -I/opt/homebrew/Cellar/libx11/1.8.10/include -I/opt/homebrew/Cellar/libxext/1.3.6/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/1.18.2/include/cairo -I/opt/homebrew/Cellar/jpeg-turbo/3.0.4/include -I/opt/homebrew/opt/zstd/include -I/opt/homebrew/Cellar/libtiff/4.7.0/include -I/opt/homebrew/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/opt/homebrew/Cellar/fribidi/1.0.16/include/fribidi -I/opt/homebrew/Cellar/graphite2/1.3.14/include -I/opt/homebrew/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/opt/homebrew/Cellar/pango/1.54.0/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/gtk4/4.16.3/include/gtk-4.0 -I/opt/homebrew/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/opt/homebrew/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/opt/homebrew/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_MOLECULES_TO_TRIANGLES -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -I/opt/homebrew/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/opt/homebrew/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/opt/homebrew/Cellar/libccp4/542516076_2/include -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -I/opt/homebrew/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000 -DUSE_SQLITE3 -I/opt/homebrew/opt/sqlite/include -DUSE_BACKWARD -I/opt/homebrew/opt/clipper4coot/fftw2/include -DUSE_MOLECULES_TO_TRIANGLES -DPKGDATADIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share/coot\" -DPACKAGE_LOCALE_DIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share/coot/locale\" -DPKGPYTHONDIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages/coot\" -DPYTHONDIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages\" -DXDATADIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share\" -DCOOT_SYS_BUILD_TYPE=\"Darwin-MacOSX-14.7-arm64-gtk4\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -I/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include -I/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13 -g -O2 -Wall -Wno-unused -std=c++17 -MT LigandViewMesh.lo -MD -MP -MF .deps/LigandViewMesh.Tpo -c LigandViewMesh.cc -o LigandViewMesh.o >/dev/null 2>&1
mv -f .deps/lbg-callbacks-outer.Tpo .deps/lbg-callbacks-outer.Plo
mv -f .deps/graphics-ligand-mesh-molecule.Tpo .deps/graphics-ligand-mesh-molecule.Plo
mv -f .deps/LinesMesh.Tpo .deps/LinesMesh.Plo
mv -f .deps/LigandViewMesh.Tpo .deps/LigandViewMesh.Plo
libtool: compile:  clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.x-pre\" "-DPACKAGE_STRING=\"coot 1.1.x-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.x-pre\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_THREAD=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_PYTHON -I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/Cellar/fontconfig/2.15.0/include -I/opt/homebrew/Cellar/pcre2/10.44/include -I/opt/homebrew/Cellar/xz/5.6.3/include -I/opt/homebrew/Cellar/glib/2.82.1/include -I/opt/homebrew/Cellar/glib/2.82.1/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.82.1/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/1.1.5/include -I/opt/homebrew/Cellar/libxcb/1.17.0/include -I/opt/homebrew/Cellar/libx11/1.8.10/include -I/opt/homebrew/Cellar/libxext/1.3.6/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/1.18.2/include/cairo -I/opt/homebrew/Cellar/jpeg-turbo/3.0.4/include -I/opt/homebrew/opt/zstd/include -I/opt/homebrew/Cellar/libtiff/4.7.0/include -I/opt/homebrew/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/opt/homebrew/Cellar/fribidi/1.0.16/include/fribidi -I/opt/homebrew/Cellar/graphite2/1.3.14/include -I/opt/homebrew/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/opt/homebrew/Cellar/pango/1.54.0/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/gtk4/4.16.3/include/gtk-4.0 -I/opt/homebrew/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/opt/homebrew/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/opt/homebrew/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_MOLECULES_TO_TRIANGLES -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -I/opt/homebrew/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/opt/homebrew/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/opt/homebrew/Cellar/libccp4/542516076_2/include -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -I/opt/homebrew/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000 -DUSE_SQLITE3 -I/opt/homebrew/opt/sqlite/include -DUSE_BACKWARD -I/opt/homebrew/opt/clipper4coot/fftw2/include -DUSE_MOLECULES_TO_TRIANGLES -DPKGDATADIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share/coot\" -DPACKAGE_LOCALE_DIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share/coot/locale\" -DPKGPYTHONDIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages/coot\" -DPYTHONDIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages\" -DXDATADIR=\"/opt/homebrew/Cellar/coot/HEAD-508303a/share\" -DCOOT_SYS_BUILD_TYPE=\"Darwin-MacOSX-14.7-arm64-gtk4\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -I/opt/homebrew/Cellar/coot/HEAD-508303a/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include -I/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13 -g -O2 -Wall -Wno-unused -std=c++17 -MT init-from-gtkbuilder.lo -MD -MP -MF .deps/init-from-gtkbuilder.Tpo -c init-from-gtkbuilder.cc -o init-from-gtkbuilder.o >/dev/null 2>&1
mv -f .deps/gtk-utils.Tpo .deps/gtk-utils.Plo
mv -f .deps/init-from-gtkbuilder.Tpo .deps/init-from-gtkbuilder.Plo
make: *** [all-recursive] Error 1`
stachowskitim commented 20 hours ago

Also, if install from the brewsci/bio/ hosted formula (coot--1.1.10.arm64_sonoma.bottle.2.tar.gz), it builds (very quickly) but I get an rdkit error when I try to launch the GUI:

Library not loaded: /opt/homebrew/opt/rdkit/lib/libRDKitcoordgen.1.dylib
  Referenced from: <73CC3838-885F-32AC-B8AB-D09027406DF7> /opt/homebrew/Cellar/coot/1.1.10/libexec/MacCoot
  Reason: tried: '/opt/homebrew/opt/rdkit/lib/libRDKitcoordgen.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/rdkit/lib/libRDKitcoordgen.1.dylib' (no such file), '/opt/homebrew/opt/rdkit/lib/libRDKitcoordgen.1.dylib' (no such file), '/opt/homebrew/Cellar/rdkit/2024.09.1/lib/libRDKitcoordgen.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/Cellar/rdkit/2024.09.1/lib/libRDKitcoordgen.1.dylib' (no such file), '/opt/homebrew/Cellar/rdkit/2024.09.1/lib/libRDKitcoordgen.1.dylib' (no such file)
/opt/homebrew/bin/coot: line 7: 94856 Abort trap: 6           ${exec_prefix}/libexec/MacCoot "$@"
YoshitakaMo commented 13 hours ago

@stachowskitim and @pemsley,

At the moment, libRDKitcoordgen does not seem to be available in the latest RDKit.

libtool: link: clang++ -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libcoot-lidia-core.0.dylib .libs/libcoot-lidia-core.0.dylib-master.o  ../geometry/.libs/libcoot-geometry.dylib -L/usr/local/Cellar/libccp4/542516076_2/lib -L/usr/local/Cellar/mmdb2/2.0.22/lib -L/usr/local/Cellar/clipper4coot/2.1.20180802_3/lib -L/usr/local/Cellar/dwarfutils/0.11.0/lib ../utils/.libs/libcoot-utils.dylib ../mini-mol/.libs/libcoot-mini-mol.dylib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/local/opt/rdkit/lib -lRDKitMolDraw2D -lRDKitForceFieldHelpers -lRDKitDescriptors -lRDKitForceField -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDistGeomHelpers -lRDKitDistGeometry -lRDKitChemReactions -lRDKitAlignment -lRDKitEigenSolvers -lRDKitDepictor -lRDKitcoordgen -lRDKitMolChemicalFeatures -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitShapeHelpers -lRDKitFingerprints -lRDKitMolAlign -lRDKitMolTransforms -lRDKitChemTransforms -lRDKitSmilesParse -lRDKitGenericGroups -lRDKitRingDecomposerLib -lRDKitFilterCatalog -lRDKitCatalogs -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitRDGeneral -lRDKitDataStructs -lboost_serialization -lboost_iostreams -L/usr/local/opt/boost/lib -L/usr/local/opt/sqlite/lib -lsqlite3  -g -O2 -Wl,-dylib_file -Wl,/usr/local/Cellar/coot/1.1.10/lib/libcoot-mini-mol.0.dylib:/private/tmp/coot-20241016-82372-tsp141/coot-1.1.10/mini-mol/.libs/libcoot-mini-mol.dylib -Wl,-dylib_file -Wl,/usr/local/Cellar/coot/1.1.10/lib/libcoot-utils.0.dylib:/private/tmp/coot-20241016-82372-tsp141/coot-1.1.10/utils/.libs/libcoot-utils.dylib -Wl,-dylib_file -Wl,/usr/local/Cellar/coot/1.1.10/lib/libcoot-compat.0.dylib:/private/tmp/coot-20241016-82372-tsp141/coot-1.1.10/compat/.libs/libcoot-compat.dylib -Wl,-dylib_file -Wl,/usr/local/Cellar/coot/1.1.10/lib/libcoot-utils.0.dylib:/private/tmp/coot-20241016-82372-tsp141/coot-1.1.10/utils/.libs/libcoot-utils.dylib   -pthread -install_name  /usr/local/Cellar/coot/1.1.10/lib/libcoot-lidia-core.0.dylib -compatibility_version 1 -current_version 1.0
ld: library 'RDKitcoordgen' not found
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [libcoot-lidia-core.la] Error 1
make: *** [all-recursive] Error 1

Probably this issue is introduced by this PR for Homebrew's rdkit. Now that -DMAEPARSER_FORCE_BUILD=ON and -DCOORDGEN_FORCE_BUILD=ON are removed (See https://github.com/Homebrew/homebrew-core/pull/192286/commits/021b9adbe4dce76bdc5180f38a3363c303cab227), I guess libRDKitcoordgen is not built.

I don't know how the library is incorporated in Coot, but if libRDKitcoordgen can be completely altered by libcoordgen of Schrodinger's coordgenlibs, the installation of Coot is not difficult with it.

brew install coordgen
sed -i -e "s/RDKitcoordgen/coordgen/g" ./configure.ac (or ./configure)

But I do not guarantee that this will work correctly. If this trick works, it would be easy to rebuild Homebrew's coot. I would like to hear your opinion.

YoshitakaMo commented 13 hours ago

Unfortunately, the trick failed after a long compilation process:

libtool: compile:  clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.10\" "-DPACKAGE_STRING=\"coot 1.1.10\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.10\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_THREAD=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_PYTHON -mfpmath=sse -msse -msse2 -I/usr/local/opt/libpng/include/libpng16 -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.15.0/include -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/xz/5.6.3/include -I/usr/local/Cellar/glib/2.82.1/include -I/usr/local/Cellar/glib/2.82.1/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/libxau/1.0.11/include -I/usr/local/Cellar/libxdmcp/1.1.5/include -I/usr/local/Cellar/libxcb/1.17.0/include -I/usr/local/Cellar/libx11/1.8.10/include -I/usr/local/Cellar/libxext/1.3.6/include -I/usr/local/Cellar/libxrender/0.9.11/include -I/usr/local/Cellar/pixman/0.42.2/include/pixman-1 -I/usr/local/Cellar/cairo/1.18.2/include/cairo -I/usr/local/Cellar/jpeg-turbo/3.0.4/include -I/usr/local/opt/zstd/include -I/usr/local/Cellar/libtiff/4.7.0/include -I/usr/local/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/fribidi/1.0.16/include/fribidi -I/usr/local/Cellar/graphite2/1.3.14/include -I/usr/local/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/usr/local/Cellar/pango/1.54.0/include/pango-1.0 -I/usr/local/Cellar/graphene/1.10.8/include/graphene-1.0 -I/usr/local/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/usr/local/Cellar/gtk4/4.16.3/include/gtk-4.0 -I/usr/local/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/usr/local/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/usr/local/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_MOLECULES_TO_TRIANGLES -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/usr/local/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/usr/local/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/usr/local/Cellar/libccp4/542516076_2/include -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000 -DUSE_SQLITE3 -I/usr/local/opt/sqlite/include -DUSE_BACKWARD -I/usr/local/opt/clipper4coot/fftw2/include -DUSE_MOLECULES_TO_TRIANGLES -DPKGDATADIR=\"/usr/local/Cellar/coot/1.1.10/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/local/Cellar/coot/1.1.10/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/coot\" -DPYTHONDIR=\"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages\" -DXDATADIR=\"/usr/local/Cellar/coot/1.1.10/share\" -DCOOT_SYS_BUILD_TYPE=\"Darwin-MacOSX-14.7-x86_64-gtk4\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -I/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include -I/usr/local/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13 -g -O2 -Wall -Wno-unused -std=c++17 -MT LinesMesh.lo -MD -MP -MF .deps/LinesMesh.Tpo -c LinesMesh.cc  -fno-common -DPIC -o .libs/LinesMesh.o
/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.10\" -DPACKAGE_STRING=\"coot\ 1.1.10\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.10\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -DUSE_PYTHON -mfpmath=sse -msse -msse2 -I/usr/local/opt/libpng/include/libpng16 -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.15.0/include -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/xz/5.6.3/include -I/usr/local/Cellar/glib/2.82.1/include -I/usr/local/Cellar/glib/2.82.1/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/libxau/1.0.11/include -I/usr/local/Cellar/libxdmcp/1.1.5/include -I/usr/local/Cellar/libxcb/1.17.0/include -I/usr/local/Cellar/libx11/1.8.10/include -I/usr/local/Cellar/libxext/1.3.6/include -I/usr/local/Cellar/libxrender/0.9.11/include -I/usr/local/Cellar/pixman/0.42.2/include/pixman-1 -I/usr/local/Cellar/cairo/1.18.2/include/cairo -I/usr/local/Cellar/jpeg-turbo/3.0.4/include -I/usr/local/opt/zstd/include -I/usr/local/Cellar/libtiff/4.7.0/include -I/usr/local/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/fribidi/1.0.16/include/fribidi -I/usr/local/Cellar/graphite2/1.3.14/include -I/usr/local/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/usr/local/Cellar/pango/1.54.0/include/pango-1.0 -I/usr/local/Cellar/graphene/1.10.8/include/graphene-1.0 -I/usr/local/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/usr/local/Cellar/gtk4/4.16.3/include/gtk-4.0 -I/usr/local/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/usr/local/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/usr/local/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS  -DHAVE_SYS_STDTYPES_H=0   -DUSE_MOLECULES_TO_TRIANGLES -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/usr/local/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE  -I/usr/local/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/usr/local/Cellar/libccp4/542516076_2/include -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000       -DUSE_SQLITE3 -I/usr/local/opt/sqlite/include  -DUSE_BACKWARD  -I/usr/local/opt/clipper4coot/fftw2/include  -DUSE_MOLECULES_TO_TRIANGLES  -DPKGDATADIR='"/usr/local/Cellar/coot/1.1.10/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/local/Cellar/coot/1.1.10/share/coot/locale"' -DPKGPYTHONDIR='"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/coot"' -DPYTHONDIR='"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages"' -DXDATADIR='"/usr/local/Cellar/coot/1.1.10/share"' -DCOOT_SYS_BUILD_TYPE='"Darwin-MacOSX-14.7-x86_64-gtk4"' -DCOOT_BUILD_INFO_STRING='""'  -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0   -I/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include  -I/usr/local/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13    -g -O2 -Wall -Wno-unused  -std=c++17 -MT lbg-interface.lo -MD -MP -MF .deps/lbg-interface.Tpo -c -o lbg-interface.lo lbg-interface.cc
mv -f .deps/graphics-info-modelling.Tpo .deps/graphics-info-modelling.Plo
/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.10\" -DPACKAGE_STRING=\"coot\ 1.1.10\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.10\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -DUSE_PYTHON -mfpmath=sse -msse -msse2 -I/usr/local/opt/libpng/include/libpng16 -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.15.0/include -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/xz/5.6.3/include -I/usr/local/Cellar/glib/2.82.1/include -I/usr/local/Cellar/glib/2.82.1/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/libxau/1.0.11/include -I/usr/local/Cellar/libxdmcp/1.1.5/include -I/usr/local/Cellar/libxcb/1.17.0/include -I/usr/local/Cellar/libx11/1.8.10/include -I/usr/local/Cellar/libxext/1.3.6/include -I/usr/local/Cellar/libxrender/0.9.11/include -I/usr/local/Cellar/pixman/0.42.2/include/pixman-1 -I/usr/local/Cellar/cairo/1.18.2/include/cairo -I/usr/local/Cellar/jpeg-turbo/3.0.4/include -I/usr/local/opt/zstd/include -I/usr/local/Cellar/libtiff/4.7.0/include -I/usr/local/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/fribidi/1.0.16/include/fribidi -I/usr/local/Cellar/graphite2/1.3.14/include -I/usr/local/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/usr/local/Cellar/pango/1.54.0/include/pango-1.0 -I/usr/local/Cellar/graphene/1.10.8/include/graphene-1.0 -I/usr/local/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/usr/local/Cellar/gtk4/4.16.3/include/gtk-4.0 -I/usr/local/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/usr/local/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/usr/local/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS  -DHAVE_SYS_STDTYPES_H=0   -DUSE_MOLECULES_TO_TRIANGLES -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/usr/local/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE  -I/usr/local/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/usr/local/Cellar/libccp4/542516076_2/include -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000       -DUSE_SQLITE3 -I/usr/local/opt/sqlite/include  -DUSE_BACKWARD  -I/usr/local/opt/clipper4coot/fftw2/include  -DUSE_MOLECULES_TO_TRIANGLES  -DPKGDATADIR='"/usr/local/Cellar/coot/1.1.10/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/local/Cellar/coot/1.1.10/share/coot/locale"' -DPKGPYTHONDIR='"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/coot"' -DPYTHONDIR='"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages"' -DXDATADIR='"/usr/local/Cellar/coot/1.1.10/share"' -DCOOT_SYS_BUILD_TYPE='"Darwin-MacOSX-14.7-x86_64-gtk4"' -DCOOT_BUILD_INFO_STRING='""'  -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0   -I/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include  -I/usr/local/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13    -g -O2 -Wall -Wno-unused  -std=c++17 -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c -o Model.lo Model.cc
libtool: compile:  clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.1.10\" "-DPACKAGE_STRING=\"coot 1.1.10\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.1.10\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.13\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_THREAD=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_PYTHON -mfpmath=sse -msse -msse2 -I/usr/local/opt/libpng/include/libpng16 -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.15.0/include -I/usr/local/Cellar/pcre2/10.44/include -I/usr/local/Cellar/xz/5.6.3/include -I/usr/local/Cellar/glib/2.82.1/include -I/usr/local/Cellar/glib/2.82.1/include/glib-2.0 -I/usr/local/Cellar/glib/2.82.1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/libxau/1.0.11/include -I/usr/local/Cellar/libxdmcp/1.1.5/include -I/usr/local/Cellar/libxcb/1.17.0/include -I/usr/local/Cellar/libx11/1.8.10/include -I/usr/local/Cellar/libxext/1.3.6/include -I/usr/local/Cellar/libxrender/0.9.11/include -I/usr/local/Cellar/pixman/0.42.2/include/pixman-1 -I/usr/local/Cellar/cairo/1.18.2/include/cairo -I/usr/local/Cellar/jpeg-turbo/3.0.4/include -I/usr/local/opt/zstd/include -I/usr/local/Cellar/libtiff/4.7.0/include -I/usr/local/Cellar/gdk-pixbuf/2.42.12/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/fribidi/1.0.16/include/fribidi -I/usr/local/Cellar/graphite2/1.3.14/include -I/usr/local/Cellar/harfbuzz/10.0.1_1/include/harfbuzz -I/usr/local/Cellar/pango/1.54.0/include/pango-1.0 -I/usr/local/Cellar/graphene/1.10.8/include/graphene-1.0 -I/usr/local/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/usr/local/Cellar/gtk4/4.16.3/include/gtk-4.0 -I/usr/local/Cellar/xorgproto/2024.1/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I.. -I/usr/local/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -pthread -I/usr/local/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_MOLECULES_TO_TRIANGLES -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/ssm/1.4_2/include -DHAVE_SSMLIB -I/usr/local/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/usr/local/Cellar/gsl/2.8/include -D_THREAD_SAFE -pthread -I/usr/local/Cellar/libccp4/542516076_2/include -I/usr/local/Cellar/mmdb2/2.0.22/include -I/usr/local/Cellar/clipper4coot/2.1.20180802_3/include -DCLIPPER_HAS_TOP8000 -DUSE_SQLITE3 -I/usr/local/opt/sqlite/include -DUSE_BACKWARD -I/usr/local/opt/clipper4coot/fftw2/include -DUSE_MOLECULES_TO_TRIANGLES -DPKGDATADIR=\"/usr/local/Cellar/coot/1.1.10/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/local/Cellar/coot/1.1.10/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/coot\" -DPYTHONDIR=\"/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages\" -DXDATADIR=\"/usr/local/Cellar/coot/1.1.10/share\" -DCOOT_SYS_BUILD_TYPE=\"Darwin-MacOSX-14.7-x86_64-gtk4\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -I/usr/local/Cellar/coot/1.1.10/lib/python3.13/site-packages/PyGObject-3.42.2-py3.9-linux-x86_64.egg/include -I/usr/local/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13 -g -O2 -Wall -Wno-unused -std=c++17 -MT LigandViewMesh.lo -MD -MP -MF .deps/LigandViewMesh.Tpo -c LigandViewMesh.cc  -fno-common -DPIC -o .libs/LigandViewMesh.o
key-bindings.cc:55:32: error: use of undeclared identifier 'PyEval_CallObject'
   55 |          PyObject *result_py = PyEval_CallObject(function_py, arg_list);
      |                                ^
1 error generated.
make[1]: *** [key-bindings.lo] Error 1
make[1]: *** Waiting for unfinished jobs....