I do have a problem with pybel while importing. Here are listings. I
suspect that I have messed up with PATH's, but I can't figure out what's
wrong.
# make test
(...)
Start 59: pybindtest__pybel
59/60 Test #59: pybindtest__pybel ................***Failed Error regular
expression found in output. Regex=[FAIL] 0.81 sec
(...)
98% tests passed, 1 tests failed out of 60
Total Test time (real) = 102.74 sec
The following tests FAILED:
59 - pybindtest__pybel (Failed)
Errors while running CTest
make: *** [test] Błąd 8
# python
Python 2.7.4 (default, Sep 26 2013, 03:20:56)
[GCC 4.7.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/pybel.py", line 69, in <module>
informats = _formatstodict(_obconv.GetSupportedInputFormat())
File "/usr/local/lib/pybel.py", line 65, in _formatstodict
broken = [(x,y.strip()) for x,y in broken]
ValueError: need more than 1 value to unpack
>>> import sys
>>> print sys.path
['',
'/usr/local/lib/python2.7/dist-packages/biopython-1.61-py2.7-linux-i686.egg',
'/usr/local/src/openbabel-2.3.2/build', '/usr/local/lib',
'/usr/local/lib/python', '/usr/lib/python2.7',
'/usr/lib/python2.7/plat-i386-linux-gnu', '/usr/lib/python2.7/lib-tk',
'/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload',
'/usr/local/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages/PILcompat',
'/usr/lib/python2.7/dist-packages/gtk-2.0',
'/usr/lib/python2.7/dist-packages/ubuntu-sso-client']
# whereis pybel
pybel: /usr/local/lib/pybel.py /usr/local/lib/pybel.pyc
# whereis openbabel
openbabel: /usr/local/lib/openbabel.pyc /usr/local/lib/openbabel.py
/usr/local/lib/openbabel /usr/local/openbabel
# cat /etc/profile
(...)
export PYTHONPATH=.:/usr/local/lib:/usr/local/lib/python
export PATH="$PATH:/usr/local"
export BABEL_DATADIR="/usr/local/openbabel/share/openbabel/2.3.1"
export BABEL_LIBDIR="/usr/local/openbabel/lib/openbabel/2.3.1"
export BABEL_INCLUDEDIR="/usr/local/openbabel/include/openbabel-2.0"
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:/usr/local/openbabel/lib"
--
Michael
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