+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb15/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/openbabel-3.1.1nb15/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for openbabel-3.1.1nb15 [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/alias.cpp:19: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /opt/tools/gcc12/include/c++/12.2.0/bits/locale_classes.h:40, from /opt/tools/gcc12/include/c++/12.2.0/bits/ios_base.h:41, from /opt/tools/gcc12/include/c++/12.2.0/ios:42, from /opt/tools/gcc12/include/c++/12.2.0/istream:38, from /opt/tools/gcc12/include/c++/12.2.0/sstream:38, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/alias.cpp:16: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/base.cpp.o [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.cpp.o [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/bond.cpp.o [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.cpp.o [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/builder.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/builder.cpp:31: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/builder.h:23, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/builder.cpp:22: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/canon.cpp.o [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/chains.cpp.o [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/chargemodel.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/chargemodel.cpp:21: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/data.cpp.o [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/data_utilities.cpp.o [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/descriptor.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/descriptor.cpp:23: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /opt/tools/gcc12/include/c++/12.2.0/bits/locale_classes.h:40, from /opt/tools/gcc12/include/c++/12.2.0/bits/ios_base.h:41, from /opt/tools/gcc12/include/c++/12.2.0/ios:42, from /opt/tools/gcc12/include/c++/12.2.0/istream:38, from /opt/tools/gcc12/include/c++/12.2.0/sstream:38, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/descriptor.cpp:20: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/elements.cpp.o [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/fingerprint.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/fingerprint.h:28, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/fingerprint.cpp:27: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/fingerprint.cpp:21: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/forcefield.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/forcefield.cpp:24: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/stl_tree.h:65, from /opt/tools/gcc12/include/c++/12.2.0/set:60, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/forcefield.cpp:22: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/format.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/format.cpp:20: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/generic.cpp.o [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/graphsym.cpp.o [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/grid.cpp.o [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/griddata.cpp.o [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/isomorphism.cpp.o [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/kekulize.cpp.o [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/locale.cpp.o [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/matrix.cpp.o [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:27: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:22: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/molchrg.cpp.o [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/mol.cpp.o [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/obconversion.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/obconversion.cpp:48: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /opt/tools/gcc12/include/c++/12.2.0/bits/locale_classes.h:40, from /opt/tools/gcc12/include/c++/12.2.0/bits/ios_base.h:41, from /opt/tools/gcc12/include/c++/12.2.0/ios:42, from /opt/tools/gcc12/include/c++/12.2.0/istream:38, from /opt/tools/gcc12/include/c++/12.2.0/fstream:38, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/obconversion.cpp:37: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/oberror.cpp.o [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/obfunctions.cpp.o [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/obiter.cpp.o [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/obutil.cpp.o [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/op.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/op.cpp:20: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/parsmart.cpp.o [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/patty.cpp.o [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.cpp.o [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/plugin.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/plugin.cpp:20: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/pointgroup.cpp.o [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/query.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/query.cpp:29: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/base.h:25, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/bond.h:31, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/query.h:27, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/query.cpp:25: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/rand.cpp.o [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/residue.cpp.o [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/ring.cpp.o [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/rotamer.cpp.o [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/rotor.cpp.o [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/spectrophore.cpp.o [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/tautomer.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/tautomer.cpp:26: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/tautomer.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/tautomer.cpp:19: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/tokenst.cpp.o [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/transform.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/transform.cpp:23: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /opt/tools/gcc12/include/c++/12.2.0/bits/locale_classes.h:40, from /opt/tools/gcc12/include/c++/12.2.0/bits/ios_base.h:41, from /opt/tools/gcc12/include/c++/12.2.0/ios:42, from /opt/tools/gcc12/include/c++/12.2.0/istream:38, from /opt/tools/gcc12/include/c++/12.2.0/sstream:38, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/transform.cpp:19: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/typer.cpp.o [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/obmolecformat.cpp:19: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /opt/tools/gcc12/include/c++/12.2.0/bits/locale_classes.h:40, from /opt/tools/gcc12/include/c++/12.2.0/bits/ios_base.h:41, from /opt/tools/gcc12/include/c++/12.2.0/ios:42, from /opt/tools/gcc12/include/c++/12.2.0/ostream:38, from /opt/tools/gcc12/include/c++/12.2.0/iostream:39, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/conformersearch.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/conformersearch.cpp:22: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/conformersearch.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/conformersearch.cpp:20: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/confsearch.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/confsearch.cpp:24: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/atom.h:30, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/confsearch.cpp:22: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/confsearch.cpp: In constructor 'OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)': /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/confsearch.cpp:134:66: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 134 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less(), (cutoff + 0.1) )), vec.end()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:1438: /opt/tools/gcc12/include/c++/12.2.0/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/confsearch.cpp: In member function 'int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)': /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/confsearch.cpp:444:77: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = plus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 444 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(std::plus(), energy_offset)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/tools/gcc12/include/c++/12.2.0/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/distgeom.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/distgeom.cpp:38: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/distgeom.h:24, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/distgeom.cpp:22: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/depict/depict.cpp.o [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/vector3.cpp.o [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.cpp.o [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp: In function 'void OpenBabel::StereoRefToImplicit(OBMol&, OBStereo::Ref)': /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:2973:16: warning: 'template class std::binder1st' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2973 | const std::binder1st > equal_to_atomId = std::bind1st (equal_to(), atomId); | ^~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:1438, from /opt/tools/gcc12/include/c++/12.2.0/bits/refwrap.h:39, from /opt/tools/gcc12/include/c++/12.2.0/vector:66, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/base.h:25, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/stereo/stereo.h:27, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/stereo/tetranonplanar.h:27, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/stereo/tetrahedral.h:27, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:26: /opt/tools/gcc12/include/c++/12.2.0/backward/binders.h:108:11: note: declared here 108 | class binder1st | ^~~~~~~~~ /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:2973:88: warning: 'std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2973 | const std::binder1st > equal_to_atomId = std::bind1st (equal_to(), atomId); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/tools/gcc12/include/c++/12.2.0/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp: In function 'void OpenBabel::ImplicitRefToStereo(OBMol&, OBStereo::Ref, OBStereo::Ref)': /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:3005:16: warning: 'template class std::binder1st' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 3005 | const std::binder1st > equal_to_implicitRef = std::bind1st (equal_to(), (OBStereo::Ref) OBStereo::ImplicitRef); | ^~~~~~~~~ /opt/tools/gcc12/include/c++/12.2.0/backward/binders.h:108:11: note: declared here 108 | class binder1st | ^~~~~~~~~ /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:3005:93: warning: 'std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 3005 | const std::binder1st > equal_to_implicitRef = std::bind1st (equal_to(), (OBStereo::Ref) OBStereo::ImplicitRef); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/tools/gcc12/include/c++/12.2.0/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o In file included from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.cpp:29: /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /opt/tools/gcc12/include/c++/12.2.0/string:48, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.h:28, from /home/pbulk/build/biology/openbabel/work/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.cpp:25: /opt/tools/gcc12/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] Linking CXX shared library ../lib/libopenbabel.so ld: fatal: file CMakeFiles/openbabel.dir/base.cpp.o: open failed: No such file or directory ld: fatal: file processing errors. No output written to ../lib/libopenbabel.so.7.0.0 collect2: error: ld returned 1 exit status *** [lib/libopenbabel.so.7.0.0] Error code 1 bmake[2]: stopped in /home/pbulk/build/biology/openbabel/work/build 1 error bmake[2]: stopped in /home/pbulk/build/biology/openbabel/work/build *** [src/CMakeFiles/openbabel.dir/all] Error code 2 bmake[1]: stopped in /home/pbulk/build/biology/openbabel/work/build 1 error bmake[1]: stopped in /home/pbulk/build/biology/openbabel/work/build *** [all] Error code 2 bmake: stopped in /home/pbulk/build/biology/openbabel/work/build 1 error bmake: stopped in /home/pbulk/build/biology/openbabel/work/build *** Error code 2 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/openbabel