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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ChemmineOB
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'ChemmineOB' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -Ic:/openbabel3/src/x64/include -IC:/openbabel3/deps/eigen-3.4.0 -DHAVE_EIGEN -DHAVE_ISFINITE -Wno-misleading-indentation -fPIC -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChemmineOB.cpp -o ChemmineOB.o
In file included from c:/openbabel3/src/x64/include/openbabel/format.h:22,
from c:/openbabel3/src/x64/include/openbabel/obconversion.h:37,
from ChemmineOB.cpp:1587:
c:/openbabel3/src/x64/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 c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\stdexcept:39,
from ChemmineOB.cpp:1559:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'void _p_f_enum_std__ios_base__event_r_std__ios_base_int__void(std::ios_base::event, std::ios_base&, int)':
ChemmineOB.cpp:4160:7: warning: unused variable 'ecode' [-Wunused-variable]
4160 | int ecode = 0; arg1 = (std::ios_base::event) swigarg_arg1; arg2 = (std::ios_base *) &swigarg_arg2; arg3 = (int) swigarg_arg3;
| ^~~~~
ChemmineOB.cpp: In function 'SEXPREC* R_swig_new_dummy()':
ChemmineOB.cpp:13728:45: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13728 | SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13730:18: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13730 | result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13730:79: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13730 | result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'SEXPREC* R_swig_delete_dummy(SEXP)':
ChemmineOB.cpp:13734:8: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13734 | std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13734:72: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13734 | std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13739:34: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13739 | arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'void* _p_OpenBabel__CharPtrLessTo_p_std__binary_functionT_char_const_p_char_const_p_bool_t(void*, int*)':
ChemmineOB.cpp:39656:27: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
39656 | return (void *)((std::binary_function< char const *,char const *,bool > *) ((OpenBabel::CharPtrLess *) x));
| ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -Ic:/openbabel3/src/x64/include -IC:/openbabel3/deps/eigen-3.4.0 -DHAVE_EIGEN -DHAVE_ISFINITE -Wno-misleading-indentation -fPIC -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c canonical.cpp -o canonical.o
In file included from c:/openbabel3/src/x64/include/openbabel/op.h:25,
from canonical.cpp:3:
c:/openbabel3/src/x64/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 c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
from c:/openbabel3/src/x64/include/openbabel/op.h:23:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o ChemmineOB.dll tmp.def ChemmineOB.o canonical.o -Lc:/openbabel3/bin/x64/bin -lopenbabel -LF:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ChemmineOB/00new/ChemmineOB/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'copyToR' with signature '"_p_std::char_traits<(char)>"': no definition for class "_p_std::char_traits<(char)>"
in method for 'copyToR' with signature '"_p_std::pair<(unsigned int,unsigned int)>"': no definition for class "_p_std::pair<(unsigned int,unsigned int)>"
in method for 'copyToR' with signature '"_p_OpenBabel::CharPtrLess"': no definition for class "_p_OpenBabel::CharPtrLess"
in method for 'copyToR' with signature '"_p_OpenBabel::FptIndexHeader"': no definition for class "_p_OpenBabel::FptIndexHeader"
in method for 'copyToR' with signature '"_p_OpenBabel::OBStereo"': no definition for class "_p_OpenBabel::OBStereo"
in method for 'copyToR' with signature '"_p_OpenBabel::OBStereoUnit"': no definition for class "_p_OpenBabel::OBStereoUnit"
in method for 'copyToR' with signature '"_p_OpenBabel::LineSearchType"': no definition for class "_p_OpenBabel::LineSearchType"
in method for 'copyToR' with signature '"_p_OpenBabel::OBTetrahedralConfig"': no definition for class "_p_OpenBabel::OBTetrahedralConfig"
in method for 'copyToR' with signature '"_p_OpenBabel::OBCisTransConfig"': no definition for class "_p_OpenBabel::OBCisTransConfig"
in method for 'copyToR' with signature '"_p_OpenBabel::OBSquarePlanarConfig"': no definition for class "_p_OpenBabel::OBSquarePlanarConfig"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineOB)
