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 _____________________________________________________ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
