############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ChemmineOB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ChemmineOB’ ... ** this is package ‘ChemmineOB’ version ‘1.45.0’ ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENBABEL... no checking for OPENBABEL... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c ChemmineOB.cpp -o ChemmineOB.o ChemmineOB.cpp:758: warning: "R_NO_REMAP" redefined 758 | # define R_NO_REMAP | : note: this is the location of the previous definition In file included from /usr/include/openbabel3/openbabel/format.h:22, from /usr/include/openbabel3/openbabel/obconversion.h:37, from ChemmineOB.cpp:1587: /usr/include/openbabel3/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/stdexcept:39, from ChemmineOB.cpp:1559: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ChemmineOB.cpp: In function ‘SEXPREC* R_swig_new_dummy()’: ChemmineOB.cpp:13728:45: warning: ‘template 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 ; | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ChemmineOB.cpp:13730:18: warning: ‘template 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 >(); | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ChemmineOB.cpp:13730:79: warning: ‘template 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 >(); | ^~~~~~~~~~~~~~~ /usr/include/c++/13/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 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 ; | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ChemmineOB.cpp:13734:72: warning: ‘template 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 ; | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ChemmineOB.cpp:13739:34: warning: ‘template 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; | ^~~~~~~~~~~~~~~ /usr/include/c++/13/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 struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 39656 | return (void *)((std::binary_function< char const *,char const *,bool > *) ((OpenBabel::CharPtrLess *) x)); | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c canonical.cpp -o canonical.o In file included from /usr/include/openbabel3/openbabel/op.h:25, from canonical.cpp:3: /usr/include/openbabel3/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/openbabel3/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o ChemmineOB.so ChemmineOB.o canonical.o -L/usr/local/lib/openbabel3 -lopenbabel -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-ChemmineOB/00new/ChemmineOB/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChemmineOB)