* installing *source* package ‘ChemmineOB’ ... ** 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 g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'/usr/lib/R/library/BH/include' -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/zlibbioc/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -ffat-lto-objects -c ChemmineOB.cpp -o ChemmineOB.o g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'/usr/lib/R/library/BH/include' -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/zlibbioc/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -ffat-lto-objects -c canonical.cpp -o canonical.o In file included from ChemmineOB.cpp:1569: /usr/include/openbabel3/openbabel/obutil.h: In member function ‘void OpenBabel::OBStopwatch::Start()’: /usr/include/openbabel3/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope 65 | start= clock(); | ^~~~~ /usr/include/openbabel3/openbabel/obutil.h:40:1: note: ‘clock’ is defined in header ‘’; did you forget to ‘#include ’? 39 | #include +++ |+#include 40 | /usr/include/openbabel3/openbabel/obutil.h: In member function ‘double OpenBabel::OBStopwatch::Lap()’: /usr/include/openbabel3/openbabel/obutil.h:70:13: error: ‘clock’ was not declared in this scope 70 | stop= clock(); | ^~~~~ /usr/include/openbabel3/openbabel/obutil.h:70:13: note: ‘clock’ is defined in header ‘’; did you forget to ‘#include ’? /usr/include/openbabel3/openbabel/obutil.h:71:40: error: ‘CLOCKS_PER_SEC’ was not declared in this scope 71 | return((stop - start) / (double) CLOCKS_PER_SEC); | ^~~~~~~~~~~~~~ /usr/include/openbabel3/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/c++/12.1.1/x86_64-pc-linux-gnu/bits/gthr-default.h:35, from /usr/include/c++/12.1.1/x86_64-pc-linux-gnu/bits/gthr.h:148, from /usr/include/c++/12.1.1/ext/atomicity.h:35, from /usr/include/c++/12.1.1/bits/ios_base.h:39, from /usr/include/c++/12.1.1/ios:42, from /usr/include/c++/12.1.1/ostream:38, from /usr/include/openbabel3/openbabel/math/vector3.h:24, from ChemmineOB.cpp:1570: /usr/include/bits/time.h:34: note: it was later defined here 34 | #define CLOCKS_PER_SEC ((__clock_t) 1000000) | 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++/12.1.1/string:48, from /usr/include/openbabel3/openbabel/op.h:23: /usr/include/c++/12.1.1/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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: At global scope: /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++/12.1.1/string:48, from /usr/include/c++/12.1.1/stdexcept:39, from ChemmineOB.cpp:1559: /usr/include/c++/12.1.1/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++/12.1.1/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++/12.1.1/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++/12.1.1/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++/12.1.1/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++/12.1.1/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++/12.1.1/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++/12.1.1/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make: *** [/usr/lib64/R/etc/Makeconf:177: ChemmineOB.o] Error 1 ERROR: compilation failed for package ‘ChemmineOB’ * removing ‘/build/r-chemmineob/src/ChemmineOB’ * restoring previous ‘/build/r-chemmineob/src/ChemmineOB’ ==> ERROR:(B A failure occurred in build().(B  Aborting...(B