Re: [Open Babel] Perl bindings in current SVN
Fixed in r4872 by including the list of Perl link libraries when linking against Perl. On 31 May 2012 19:52, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Tried newest cmake, no success either. Actually it is not even looking for ptherad.h. I also found out in CMake file in tools/ directory that the check is made while you build OB staticly, Have you tried build_shared=off and on? Which variable exactly should contain -lpthreads? My perllibs='-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc'; Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com Yes - I doublechecked. The latest SWIG still fails. What I can do is add in the output of perl -V:perllibs. This solves the problem at the moment. I still don't understand the underlying problem though. - Noel On 31 May 2012 13:43, Maciek Wójcikowski mac...@wojcikowski.pl wrote: I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl
Re: [Open Babel] Perl bindings in current SVN
We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
For the record, on the Linux Mint 12 (64-bit) system I have tested, the compile works fine. But the command line contains -pthread (if this is removed, I get the same error message as reported). I don't quite understand where this comes from or why it's set on this OS but not on CentOS. On 31 May 2012 12:27, Maciek Wójcikowski mac...@wojcikowski.pl wrote: It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net
Re: [Open Babel] Perl bindings in current SVN
Yes - I doublechecked. The latest SWIG still fails. What I can do is add in the output of perl -V:perllibs. This solves the problem at the moment. I still don't understand the underlying problem though. - Noel On 31 May 2012 13:43, Maciek Wójcikowski mac...@wojcikowski.pl wrote: I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions
Re: [Open Babel] Perl bindings in current SVN
Tried newest cmake, no success either. Actually it is not even looking for ptherad.h. I also found out in CMake file in tools/ directory that the check is made while you build OB staticly, Have you tried build_shared=off and on? Which variable exactly should contain -lpthreads? My perllibs='-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc'; Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com Yes - I doublechecked. The latest SWIG still fails. What I can do is add in the output of perl -V:perllibs. This solves the problem at the moment. I still don't understand the underlying problem though. - Noel On 31 May 2012 13:43, Maciek Wójcikowski mac...@wojcikowski.pl wrote: I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com We changed to compiling the bindings directly rather than use Perl's build system. It seems to work fine on some Linux OSes but not on others. I haven't tracked down the problem but you could try VERBOSE=1 make to see the command that we are using to compile, and repeating it manually but adding -lpthread to see what happens. - Noel On 31 May 2012 09:56, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond.
