Since I know little about the language python (I prefer the .NET bindings
and Perl), this may not work, but could instlling a python program that
uses the python OB bindings solve the problem?
Sorry if this is too ignorant a responce.
On Fri, Nov 14, 2014 at 5:05 AM, Douglas Houston <
dhous...@staffmail.ed.ac.uk> wrote:
> Hi all,
>
> I am trying to install a Pymol plugin and it requires my Open Babel to
> be re-installed, this time including the Python bindings:
>
> Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07)
> [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> import openbabel
> Traceback (most recent call last): File "<stdin>", line 1, in <module>
> ImportError: No module named openbabel
>
>
> I have tried recompiling Open Babel as root with the Python bindings using:
>
> tar -xvf openbabel-2.3.2.tar.gz
> cd openbabel-2.3.2
> mkdir build
> cd build/
> ~douglas/programs/cmake-2.8.7/bin/cmake ~/openbabel-2.3.2
> -DPYTHON_BINDINGS=ON
> make -j2
>
>
> but it fails with the following errors; can anyone help?:
>
>
> [100%] Building CXX object
> scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
> Linking CXX executable ../bin/test_unitcell
> [100%] Built target test_unitcell
> Linking CXX shared module ../lib/_openbabel.so
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `_pythread_pthread_set_stacksize':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined
> reference to `pthread_attr_setstacksize'
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `PyThread_release_lock':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined
> reference to `sem_post'
> /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined
> reference to `sem_destroy'
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `PyThread_allocate_lock':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined
> reference to `sem_init'
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `PyThread_acquire_lock':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined
> reference to `sem_trywait'
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined
> reference to `sem_wait'
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `PyThread_start_new_thread':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined
> reference to `pthread_attr_setstacksize'
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined
> reference to `pthread_create'
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined
> reference to `pthread_detach'
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `PyThread_release_lock':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined
> reference to `sem_post'
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined
> reference to `sem_post'
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined
> reference to `sem_post'
> /usr/local/lib/libpython2.7.a(thread.o): In function
> `PyThread_allocate_lock':
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined
> reference to `sem_init'
> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined
> reference to `sem_init'
> /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty':
> /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined
> reference to `forkpty'
> /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty':
> /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined
> reference to `openpty'
> collect2: ld returned 1 exit status
> make[2]: *** [lib/_openbabel.so] Error 1
> make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
> make: *** [all] Error 2
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>
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--Nathan Pimental,
--Peppertree Labs (http://ptp.x10.mx)
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