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Re: [igraph] Python3 igraph import error on Cygwin
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From: |
Stephen J. Gaffigan |
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Subject: |
Re: [igraph] Python3 igraph import error on Cygwin |
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Date: |
Thu, 25 Apr 2013 00:35:36 -0400 |
Hi Tamas,
Thanks a lot for your detailed suggestions. I tried again with /usr/local/igraph/lib (which contains the .dll) in the LD_LIBRARY_PATH, but still get the same error. Some more output is below. It doesn't look like LD_DEBUG is working for me under Cygwin, though it could be that I'm missing something in my Cygwin environment that would enable support for this. I have a very minimal set of packages installed. It was _igraph.py that I was looking at, though there's also an _igraph.cpython-32m.dll, which is loaded through _igraph.py (see below).
$ ls /usr/local/igraph/lib
cygigraph-0.dll libigraph.a libigraph.dll.a libigraph.la pkgconfig
$ set | grep LD_LIBRARY_PATH
LD_LIBRARY_PATH=/usr/local/igraph/lib
$ LD_DEBUG=all python3 -c "import igraph"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/lib/python3.2/site-packages/python_igraph-0.6.5-py3.2-cygwin-1.7.18-i686.egg/igraph/__init__.py", line 34, in <module>
from igraph._igraph import *
ImportError: No such file or directory
$ ls /usr/local/lib/python3.2/site-packages/python_igraph-0.6.5-py3.2-cygwin-1.7.18-i686.egg/igraph/
__init__.py clustering.py drawing remote vendor
__pycache__ compat.py formula.py statistics.py
_igraph.cpython-32m.dll configuration.py layout.py summary.py
_igraph.py cut.py matching.py test
app datatypes.py nexus.py utils.py
$ cat /usr/local/lib/python3.2/site-packages/python_igraph-0.6.5-py3.2-cygwin-1.7.18-i686.egg/igraph/_igraph.py
def __bootstrap__():
global __bootstrap__, __loader__, __file__
import sys, pkg_resources, imp
__file__ = pkg_resources.resource_filename(__name__,'_igraph.cpython-32m.dll')
__loader__ = None; del __bootstrap__, __loader__
imp.load_dynamic(__name__,__file__)
__bootstrap__()
At this point I don't really need to figure this out. I was able to run my script by installing the pre-compiled Python, igraph, etc. Windows binaries and calling python3.exe through Cygwin. I just needed to provide instructions how to run my script, which uses igraph, through Cygwin.
Thanks again for your help. Let me know if there's anything else you want me to try or look at on this.
Steve
On Wed, Apr 24, 2013 at 2:45 PM, Tamás Nepusz
<address@hidden> wrote:
Hi,
> No such luck. The usual import error I get with a fresh install of igraph from source is because the shared library isn't found because I forget to add a /etc/ld.so.conf.d/igraph.conf file or update LD_LIBRARY_PATH. This is different (though I admit I did still try LD_LIBRARY_PATH with /usr/local/igraph/lib and even the egg/igraph directory, which contains a .dll).
Okay, so the story is as follows. You should have a file named libigraph.so (or .dll, not sure what extension Cygwin uses) somewhere in your file system. This is the C core of igraph, and the folder that contains this file should be on your library path. If this folder is not /lib, /usr/lib or /usr/local/lib, chances are that you need to add this permanently to your LD_LIBRARY_PATH.
On top of libigraph.so, we have a glue layer that sits between the Python interface of igraph and the C core of igraph. This glue layer is the magic igraph._igraph module that Python is looking for, and it should be in the very same folder where the root __init__.py file of the Python interface is. (Should be right within the .egg directory). The glue layer is usually named _igraph.so, _igraph.dll, _igraph.pyd, _igraph.dylib or something like that, depending on your platform. (Again, I'm not sure which one Cygwin uses). The folder containing this file does not have to be added to LD_LIBRARY_PATH because Python will do that automatically when the igraph module is loaded, but the file should be there in the right place.
Please check that you have both of these files at the right places. The .egg-info file is not necessary as far as I know, it only contains metadata that makes it easier for distutils and/or pip to uninstall or upgrade the package.
> I tried adding the egg directory to PYTHONPATH with no success. But the original error suggests that it was already finding the module in the egg. It's inside igraph/__init__.py when the import error occurs. But igraph/_igraph.py is there too, which is why I'm lost why it's not finding it.
Is it really called _igraph.py and not _igraph.dll, _igraph.pyd or something like that? Also, another option is to try debugging what the dynamic library loader is actually doing when you try to import igraph. Try this:
LD_DEBUG=libs python3 -c "import igraph"
This will give you lots of information about what ld is doing (and you can get even more info with LD_DEBUG=all); the relevant section looks like this for me:
25408: calling init: /home/tamas/lib/libigraph.so.0
25408:
25408:
25408: calling init: /home/tamas/virtualenvs/default/local/lib/python2.7/site-packages/python_igraph-0.7-py2.7-linux-x86_64.egg/igraph/_igraph.so
25408: