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.
> >>>> > 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
> >>>> >
> >>>
> >>>
> >>
> >
>
------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
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will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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