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20 hours ago •
openbabel
openbabel
<< Compilation stop in: "Built target plugin_charges" >>
Environment Information
Open Babel version: 3.1.1 Operating system and version: Ubuntu 22.04.4 LTS, GCC: v12
Expected Behavior
Compile without errors.
Command used:
cmake ../openbabel-3.1.1 -DBUILD_GUI=ON -DPYTHON_BINDINGS=ON
Actual Behavior
The compilation process stop as:
[ 35%] Linking CXX shared module ../lib/plugin_ops.so
[ 35%] Built target plugin_ops
[ 35%] Linking CXX shared module ../lib/plugin_charges.so
[ 35%] Built target plugin_charges
make: *** [Makefile:146: all] Error 2
I searched for compilation issues here. I found issue 1838, where a (different) compilation problem was solved adding -DBUILD_SHARED=OFF, I did that, and the compilation go further, but stopped in another error:
[100%] Linking CXX executable ../bin/test_runner
[100%] Built target test_runner
[100%] Linking CXX shared module ../lib/_openbabel.so
/usr/bin/ld: ../src/libopenbabel.a(phmodel.cpp.o): relocation R_X86_64_TPOFF32 against `__tls_guard' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: failed to set dynamic section sizes: bad value
collect2: error: ld returned 1 exit status
make[2]: *** [scripts/CMakeFiles/bindings_python.dir/build.make:102: lib/_openbabel.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:1095: scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
Thanks for opening your first issue here! Be sure to follow the issue template!
![welcome[bot] avatar](https://avatars.githubusercontent.com/in/4141?v=4 "Published by a pub.dev verified publisher"){kind=small}
You don't want -DBUILD_SHARED=OFF .. among other things, this is not tested by the build actions.
Can you post more of the issue from the initial compile error? It looks like you're building in parallel and the actual error is farther up in the compile log.
I check the configuration step, and realize that had some missing libraries, like boost and RapidJSON, for example. Everything if ok now at configuration step (configuration.log)
Now, when running make, I got new errors (make.log):
Consolidate compiler generated dependencies of target maeparser
[ 1%] Built target maeparser
Consolidate compiler generated dependencies of target coordgen
[ 4%] Built target coordgen
Consolidate compiler generated dependencies of target openbabel
[ 4%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/alias.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/alias.cpp:16:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/base.cpp.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.cpp.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/bond.cpp.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.cpp.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/builder.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/builder.cpp:31:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/builder.h:23,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/builder.cpp:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/canon.cpp.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/chains.cpp.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/chargemodel.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/chargemodel.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/data.cpp.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/data_utilities.cpp.o
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/descriptor.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptor.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptor.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/elements.cpp.o
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/fingerprint.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/fingerprint.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprint.cpp:27:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprint.cpp:21:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/forcefield.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/forcefield.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefield.cpp:24:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefield.cpp:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/format.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/format.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/generic.cpp.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/graphsym.cpp.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/grid.cpp.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/griddata.cpp.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/isomorphism.cpp.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/kekulize.cpp.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/locale.cpp.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/matrix.cpp.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/mcdlutil.cpp:27:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/mcdlutil.cpp:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/molchrg.cpp.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/mol.cpp.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/obconversion.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/obconversion.cpp:48:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/obconversion.cpp:37:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/oberror.cpp.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obfunctions.cpp.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obiter.cpp.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obutil.cpp.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/op.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/op.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/parsmart.cpp.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/patty.cpp.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.cpp.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/plugin.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/plugin.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/pointgroup.cpp.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/query.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/query.cpp:29:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/base.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/bond.h:31,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/query.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/query.cpp:25:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/rand.cpp.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/residue.cpp.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/ring.cpp.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/rotamer.cpp.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/rotor.cpp.o
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/spectrophore.cpp.o
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/tautomer.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/tautomer.cpp:26:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/tautomer.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/tautomer.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/tokenst.cpp.o
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/transform.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/transform.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/transform.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/typer.cpp.o
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obmolecformat.h:36,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/obmolecformat.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/conformersearch.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/forcefield.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/conformersearch.cpp:22:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/conformersearch.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/conformersearch.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/confsearch.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/forcefield.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/confsearch.cpp:24:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/atom.h:30,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/confsearch.cpp:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/confsearch.cpp: In constructor ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/confsearch.cpp:134:66: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less<double>; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
134 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less<double>(), (cutoff + 0.1) )), vec.end());
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_function.h:1438:
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/confsearch.cpp: In member function ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/confsearch.cpp:444:77: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = plus<double>; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
444 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(std::plus<double>(), energy_offset));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/distgeom.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/distgeom.cpp:38:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/distgeom.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/distgeom.cpp:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/depict/depict.cpp.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/math/vector3.cpp.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.cpp.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o
[ 17%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o
[ 17%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/perception.cpp: In function ‘void OpenBabel::StereoRefToImplicit(OBMol&, OBStereo::Ref)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/perception.cpp:2973:16: warning: ‘template<class _Operation> class std::binder1st’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
2973 | const std::binder1st<std::equal_to<OBStereo::Ref> > equal_to_atomId = std::bind1st (equal_to<OBStereo::Ref>(), atomId);
| ^~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_function.h:1438,
from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/base.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/stereo/stereo.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/stereo/tetranonplanar.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/stereo/tetrahedral.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/perception.cpp:26:
/usr/include/c++/12/backward/binders.h:108:11: note: declared here
108 | class binder1st
| ^~~~~~~~~
/home/icamps/Temp/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<long unsigned int>; _Tp = long unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
2973 | const std::binder1st<std::equal_to<OBStereo::Ref> > equal_to_atomId = std::bind1st (equal_to<OBStereo::Ref>(), atomId);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:136:5: note: declared here
136 | bind1st(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/perception.cpp: In function ‘void OpenBabel::ImplicitRefToStereo(OBMol&, OBStereo::Ref, OBStereo::Ref)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/perception.cpp:3005:16: warning: ‘template<class _Operation> class std::binder1st’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
3005 | const std::binder1st<std::equal_to<OBStereo::Ref> > equal_to_implicitRef = std::bind1st (equal_to<OBStereo::Ref>(), (OBStereo::Ref) OBStereo::ImplicitRef);
| ^~~~~~~~~
/usr/include/c++/12/backward/binders.h:108:11: note: declared here
108 | class binder1st
| ^~~~~~~~~
/home/icamps/Temp/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<long unsigned int>; _Tp = long unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
3005 | const std::binder1st<std::equal_to<OBStereo::Ref> > equal_to_implicitRef = std::bind1st (equal_to<OBStereo::Ref>(), (OBStereo::Ref) OBStereo::ImplicitRef);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/backward/binders.h:136:5: note: declared here
136 | bind1st(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
[ 17%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o
[ 17%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/gen3dstereohelper.cpp:29:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/gen3dstereohelper.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/stereo/gen3dstereohelper.cpp:25:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 17%] Linking CXX shared library ../lib/libopenbabel.so
[ 17%] Built target openbabel
Consolidate compiler generated dependencies of target plugin_descriptors
[ 17%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/cansmidescriptor.cpp:22:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/cansmidescriptor.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 17%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/cmpdfilter.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/cmpdfilter.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 17%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/groupcontrib.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/groupcontrib.cpp:33:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/groupcontrib.cpp:25:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 17%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/filters.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/inchidescriptor.cpp:22:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/inchidescriptor.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/inchidescriptor.cpp:24:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/inchiformat.h:134:19: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
134 | : public std::binary_function<const std::string&, const std::string&, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/descriptor.h:27,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/smartsdescriptors.cpp:22:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/descriptors/smartsdescriptors.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Linking CXX shared module ../lib/plugin_descriptors.so
[ 18%] Built target plugin_descriptors
Consolidate compiler generated dependencies of target plugin_fingerprints
[ 18%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/fingerprint.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprints/finger2.cpp:24:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprints/finger2.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/fingerprint.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprints/finger3.cpp:27:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprints/finger3.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/fingerprint.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprints/fingerecfp.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/oberror.h:26,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/fingerprints/fingerecfp.cpp:15:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 19%] Linking CXX shared module ../lib/plugin_fingerprints.so
[ 19%] Built target plugin_fingerprints
Consolidate compiler generated dependencies of target plugin_forcefields
[ 19%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/forcefield.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldgaff.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldgaff.cpp:29:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldgaff.cpp:21:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 19%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/forcefield.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldghemical.h:23,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldghemical.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldghemical.cpp:20:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 19%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefieldmmff94.cpp:31:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 19%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/forcefield.h:28,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefielduff.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefielduff.cpp:32:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/forcefields/forcefielduff.cpp:21:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 19%] Linking CXX shared module ../lib/plugin_forcefields.so
[ 19%] Built target plugin_forcefields
Consolidate compiler generated dependencies of target plugin_ops
[ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addfilename.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addfilename.cpp:18:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addinindex.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/base.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addinindex.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addpolarh.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addpolarh.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addnonpolarh.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/addnonpolarh.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/canonical.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/changecell.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/changecell.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/delpolarh.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/delpolarh.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/delnonpolarh.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/delnonpolarh.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/gen2D.cpp:22:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/gen2D.cpp:21:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/fillUC.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/forcefield.cpp:31:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/forcefield.cpp:29:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/gen3d.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/largest.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/largest.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/loader.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/loader.cpp:24:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/loader.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/neutralize.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opsplit.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/optransform.h:21,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/optransform.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/parsmart.h:23,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/phmodel.h:23,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/optransform.h:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/partialcharges.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/readconformers.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/sort.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/sort.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/sort.cpp:32:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
32 | struct Order : public std::binary_function<std::pair<OBBase*,T>, std::pair<OBBase*,T>, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opisomorph.h:15,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opisomorph.cpp:17:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/parsmart.h:23,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opisomorph.cpp:15:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/ophighlight.cpp:17:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/parsmart.h:23,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/ophighlight.cpp:16:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 24%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/xout.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 24%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/conformer.cpp:32:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/conformer.cpp:29:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 24%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opalign.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opalign.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 24%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opconfab.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/opconfab.cpp:22:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 24%] Linking CXX shared module ../lib/plugin_ops.so
[ 24%] Built target plugin_ops
Consolidate compiler generated dependencies of target plugin_charges
[ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/eem.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/eem.cpp:24:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/eem.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/gasteiger.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/none.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/none.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/mmff94.cpp:20:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/fromfile.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/eqeq.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/eqeq.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/qeq.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/qeq.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/chargemodel.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/qtpie.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/charges/qtpie.cpp:21:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/dlhandler.h:24,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 26%] Linking CXX shared module ../lib/plugin_charges.so
[ 26%] Built target plugin_charges
Consolidate compiler generated dependencies of target inchi
[ 26%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.c.o
[ 26%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.c.o
[ 26%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichican2.c.o
[ 26%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichicano.c.o
[ 27%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichicans.c.o
[ 27%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiisot.c.o
[ 27%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichilnct.c.o
[ 27%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimak2.c.o
[ 27%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimake.c.o
[ 28%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimap1.c.o
[ 28%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimap2.c.o
[ 28%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimap4.c.o
[ 28%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichinorm.c.o
[ 28%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiparm.c.o
[ 28%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiprt1.c.o
[ 29%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiprt2.c.o
[ 29%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiprt3.c.o
[ 29%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiqueu.c.o
[ 29%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiread.c.o
[ 29%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichiring.c.o
[ 30%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr1.c.o
[ 30%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr2.c.o
[ 30%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr3.c.o
[ 30%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr4.c.o
[ 30%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr5.c.o
[ 30%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr6.c.o
[ 31%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichirvr7.c.o
[ 31%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichisort.c.o
[ 31%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichister.c.o
[ 31%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichitaut.c.o
[ 31%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ikey_base26.c.o
[ 32%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ikey_dll.c.o
[ 32%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/inchi_dll.c.o
[ 32%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/inchi_dll_a.c.o
[ 32%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/inchi_dll_a2.c.o
[ 32%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/inchi_dll_main.c.o
[ 32%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/runichi.c.o
[ 33%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/sha2.c.o
[ 33%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/strutil.c.o
[ 33%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/util.c.o
[ 33%] Linking C shared library ../../../lib/libinchi.so
[ 33%] Built target inchi
Consolidate compiler generated dependencies of target smilesformat
[ 33%] Building CXX object src/formats/CMakeFiles/smilesformat.dir/smilesformat.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obmolecformat.h:36,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp: In member function ‘bool OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector<OpenBabel::OBAtom*>&, std::vector<unsigned int>&, std::string&)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp:2865:35: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=]
2865 | snprintf(tcount, 10, "%d", hcount);
| ^
In file included from /usr/include/stdio.h:894,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3968,
from /usr/include/c++/12/string:53:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘bool OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector<OpenBabel::OBAtom*>&, std::vector<unsigned int>&, std::string&)’ at /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp:2865:19:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 10
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp: In member function ‘bool OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector<OpenBabel::OBAtom*>&, std::vector<unsigned int>&, std::string&)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp:2857:35: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=]
2857 | snprintf(tcount, 10, "%d", i);
| ^
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘bool OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector<OpenBabel::OBAtom*>&, std::vector<unsigned int>&, std::string&)’ at /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/smilesformat.cpp:2857:19:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 10
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 33%] Linking CXX shared module ../../lib/smilesformat.so
[ 33%] Built target smilesformat
Consolidate compiler generated dependencies of target mdlformat
[ 33%] Building CXX object src/formats/CMakeFiles/mdlformat.dir/mdlformat.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obmolecformat.h:36,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp:35:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp:26:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp: In member function ‘std::string OpenBabel::MDLFormat::GetTimeDate()’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp:1709:27: warning: ‘%02d’ directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 9 [-Wformat-truncation=]
1709 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday,
| ^~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp:1709:22: note: directive argument in the range [-2147483648, 2147483547]
1709 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday,
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:894,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3968,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/iomanip:40,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp:27:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘std::string OpenBabel::MDLFormat::GetTimeDate()’ at /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mdlformat.cpp:1709:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 56 bytes into a destination of size 11
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 33%] Linking CXX shared module ../../lib/mdlformat.so
[ 33%] Built target mdlformat
Consolidate compiler generated dependencies of target mol2format
[ 33%] Building CXX object src/formats/CMakeFiles/mol2format.dir/mol2format.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obmolecformat.h:36,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/mol2format.cpp:17:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 33%] Linking CXX shared module ../../lib/mol2format.so
[ 33%] Built target mol2format
Consolidate compiler generated dependencies of target pdbformat
[ 33%] Building CXX object src/formats/CMakeFiles/pdbformat.dir/pdbformat.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obmolecformat.h:36,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:17:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:684:58: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=]
684 | snprintf(type_name, sizeof(type_name), " %-3s", tmp);
| ^
In file included from /usr/include/stdio.h:894,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3968,
from /usr/include/c++/12/string:53:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:684:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 10
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:702:70: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=]
702 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp);
| ^
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:702:29:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 5 and 11 bytes into a destination of size 10
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:739:35: warning: ‘%+d’ directive output may be truncated writing between 2 and 6 bytes into a region of size 3 [-Wformat-truncation=]
739 | snprintf(scharge, 3, "%+d", charge);
| ^~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:739:34: note: directive argument in the range [-32768, 32767]
739 | snprintf(scharge, 3, "%+d", charge);
| ^~~~~
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/pdbformat.cpp:739:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 3 and 7 bytes into a destination of size 3
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 34%] Linking CXX shared module ../../lib/pdbformat.so
[ 34%] Built target pdbformat
Consolidate compiler generated dependencies of target inchiformat
[ 34%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/inchiformat.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/inchiformat.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/mol.h:44,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/inchiformat.cpp:19:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/inchiformat.cpp:32:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/inchiformat.h:134:19: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
134 | : public std::binary_function<const std::string&, const std::string&, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 34%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o
[ 35%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/unique.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/op.h:23:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/ops/unique.cpp:23:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/inchiformat.h:134:19: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
134 | : public std::binary_function<const std::string&, const std::string&, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 35%] Linking CXX shared module ../../lib/inchiformat.so
[ 35%] Built target inchiformat
Consolidate compiler generated dependencies of target asciiformat
[ 35%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/format.h:22,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:37,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obmolecformat.h:36,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/formats/asciiformat.cpp:19:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obconversion.h:24:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 35%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o
In file included from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/depict/asciipainter.cpp:18:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h: In member function ‘void OpenBabel::OBStopwatch::Start()’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope
65 | start= clock();
| ^~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h:40:1: note: ‘clock’ is defined in header ‘<ctime>’; did you forget to ‘#include <ctime>’?
39 | #include <math.h>
+++ |+#include <ctime>
40 |
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h: In member function ‘double OpenBabel::OBStopwatch::Lap()’:
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h:70:13: error: ‘clock’ was not declared in this scope
70 | stop= clock();
| ^~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h:70:13: note: ‘clock’ is defined in header ‘<ctime>’; did you forget to ‘#include <ctime>’?
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h:71:40: error: ‘CLOCKS_PER_SEC’ was not declared in this scope
71 | return((stop - start) / (double) CLOCKS_PER_SEC);
| ^~~~~~~~~~~~~~
/home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/obutil.h:71:40: note: the macro ‘CLOCKS_PER_SEC’ had not yet been defined
In file included from /usr/include/time.h:33,
from /usr/include/pthread.h:23,
from /usr/include/x86_64-linux-gnu/c++/12/bits/gthr-default.h:35,
from /usr/include/x86_64-linux-gnu/c++/12/bits/gthr.h:148,
from /usr/include/c++/12/ext/atomicity.h:35,
from /usr/include/c++/12/bits/ios_base.h:39,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/depict/painter.h:25,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/include/openbabel/depict/asciipainter.h:21,
from /home/icamps/Temp/openbabel/openbabel-3.1.1/src/depict/asciipainter.cpp:19:
/usr/include/x86_64-linux-gnu/bits/time.h:34: note: it was later defined here
34 | #define CLOCKS_PER_SEC ((__clock_t) 1000000)
|
make[2]: *** [src/formats/CMakeFiles/asciiformat.dir/build.make:90: src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1736: src/formats/CMakeFiles/asciiformat.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
I have the ame problem. And my gcc is in version 10(gcc-10 (Debian 10.2.1-6) 10.2.1 20210110)
I had the same problem. But adding the following statement, as suggested in the error message, solved the problem for me.
—————
openbabel-3.1.1/include/openbabel/obutil.h:40:1: note: ‘clock’ is defined in header ‘
39 | #include <math.h>
+++ |+#include
I met same problem today, and I found the key was in file obutil.h. According to error log, clock and CLOCKS_PER_SEC was not declared in this scope.
In file included from /data/openbabel-3.1.1/src/depict/asciipainter.cpp:18:
/data/openbabel-3.1.1/include/openbabel/obutil.h: In member function ‘void OpenBabel::OBStopwatch::Start()’:
/data/openbabel-3.1.1/include/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope
65 | start= clock();
| ^~~~~
/data/openbabel-3.1.1/include/openbabel/obutil.h:40:1: note: ‘clock’ is defined in header ‘<ctime>’; did you forget to ‘#include <ctime>’?
39 | #include <math.h>
+++ |+#include <ctime>
40 |
/data/openbabel-3.1.1/include/openbabel/obutil.h: In member function ‘double OpenBabel::OBStopwatch::Lap()’:
/data/openbabel-3.1.1/include/openbabel/obutil.h:70:13: error: ‘clock’ was not declared in this scope
70 | stop= clock();
| ^~~~~
/data/openbabel-3.1.1/include/openbabel/obutil.h:70:13: note: ‘clock’ is defined in header ‘<ctime>’; did you forget to ‘#include <ctime>’?
/data/openbabel-3.1.1/include/openbabel/obutil.h:71:40: error: ‘CLOCKS_PER_SEC’ was not declared in this scope
71 | return((stop - start) / (double) CLOCKS_PER_SEC);
| ^~~~~~~~~~~~~~
/data/openbabel-3.1.1/include/openbabel/obutil.h:71:40: note: the macro ‘CLOCKS_PER_SEC’ had not yet been defined
Then I had a look in this file finding them were in a if condition.
#if HAVE_CLOCK_T //!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< HERE
clock_t start; //!< the start of timing
clock_t stop; //!< the current time
#else
timeval start; //!< the start of timing
timeval stop; //!< the current time
#endif
public:
#if HAVE_CLOCK_T //!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< HERE
//! Mark the start of "stopwatch" timing
void Start()
{
start= clock(); //!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< HERE
}
//! \return The time since calling OBStopwatch::Start() in seconds.
double Lap()
{
stop= clock(); //!<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< HERE
return((stop - start) / (double) CLOCKS_PER_SEC); //!<<<<<<<<<<<<<<<<< AND HERE
}
#else
//! Mark the start of "stopwatch" timing
void Start()
{
gettimeofday(&start, nullptr);
}
//! \return The time since calling OBStopwatch::Start() in seconds.
double Lap()
{
gettimeofday(&stop, nullptr);
return((stop.tv_sec - start.tv_sec)
+ (stop.tv_usec - start.tv_usec)/1000000.0);
}
#endif
I am not familiar with C language but when I changed two HAVE_CLOCK_T to false to forcely skip the first condition, the compilation finished sucessfully. Wish developer would notice this and fix this bug.
I am not very confident with C++ either but if you add #include
For the sake of posterity, I am leaving my notes here.
I was having the same issue described above on an Ubuntu 24.04 system. I had installed these packages:
cmake libboost-all-dev libeigen3-dev libxml2-dev libghc-zlib-dev wx-common
Although I am not entirely sure that all of those were necessary. I did not have to add:
#include
to my obutil.h file, but I did have to add:
#include <ctime>
# BEFORE
#include <math.h>
# AFTER
#include <math.h>
#include <ctime>
