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. ------------------------------------------------------------------------------ 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
