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
