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
> >
> >
> ------------------------------------------------------------------------------
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> >
>
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