On 11/22/2011 04:38 PM, Mathieu Malaterre wrote:
[CC me please]
Hi all,
The issue with multiarray came back. I manage to get things working
for the tifffile package installing the tifffile.py into
/usr/bin/tiffile (removing the py extension). However another package
is now failing: CellProfiler. Symptoms are:
$ python /usr/lib/python2.7/dist-packages/CellProfiler.py
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/CellProfiler.py", line 17, in<module>
import numpy as np
File "/usr/share/pyshared/numpy/__init__.py", line 136, in<module>
import add_newdocs
File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in<module>
from numpy.lib import add_newdoc
File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in<module>
from type_check import *
File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in<module>
import numpy.core.numeric as _nx
File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in<module>
import multiarray
ImportError: No module named multiarray
Hi Mathieu,
I don't think that your problem can be solved in any simple way, apart
from physically moving the script or providing a second helper script.
This is a very unfortunate interaction between Python semantics (prepend
realpath of script to sys.path) and the Debian way of installing modules
(symlink farm between Python versions). Nevertheless, I think that
Python is wrong, and Debian is right. What Python does means that it is
not possible to run a Python script from /tmp or any other directory
writeable by other users securely. Even if this is by design, it is not
advertised well (or maybe even at all?) and is thus a big security hole.
Now if I do:
$ cp /usr/lib/python2.7/dist-packages/CellProfiler.py /tmp
$ python /tmp/CellProfiler.py
Traceback (most recent call last):
File "/tmp/CellProfiler.py", line 193, in<module>
os.chdir(os.path.join(root, script_path))
OSError: [Errno 2] No such file or directory: '/tmp/cellprofiler/cpmath'
Could someone please point me to some documentation get rid definitely
of this kind of issues.
You can wait for Python 3.2 and the PEP 3149 (ABI version tagged .so
files) which makes the Debian-style symlinks farms unnecessary (just
joking :).
Best,
Zbyszek
> I'd like to keep as much as the original
package as possible, therefore I would like to keep the
/usr/lib/python2.7/dist-packages/CellProfiler.py (or pyshared
equivalent). But how do I load this file ?
Thanks very much.
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