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
>> >
>> >
>> ------------------------------------------------------------------------------
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>> > will include endpoint security, mobile security and the latest in
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>> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> > _______________________________________________
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>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>>
>
>
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