Bug 446799

Summary:	import of scipy failed
Product:	[Fedora] Fedora	Reporter:	Kazuyoshi Furutaka <furutaka>
Component:	scipy	Assignee:	Jef Spaleta <jspaleta>
Status:	CLOSED WORKSFORME	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	medium	Docs Contact:
Priority:	low
Version:	9
Target Milestone:	---
Target Release:	---
Hardware:	i686
OS:	Linux
Whiteboard:
Fixed In Version:		Doc Type:	Bug Fix
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2008-05-16 15:34:15 UTC	Type:	---
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:

Description Kazuyoshi Furutaka 2008-05-16 06:10:06 UTC

From Bugzilla Helper:
User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9b5) Gecko/2008043010 Fedora/3.0-0.60.beta5.fc9 Firefox/3.0b5

Description of problem:
import of scipy failed as the following:

>>> import scipy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/scipy/__init__.py", line 25, in <module>
    from numpy import show_config as show_numpy_config
  File "/usr/lib/python2.5/site-packages/numpy/__init__.py", line 43, in <module>
    import linalg
  File "/usr/lib/python2.5/site-packages/numpy/linalg/__init__.py", line 4, in <module>
    from linalg import *
  File "/usr/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 25, in <module>
    from numpy.linalg import lapack_lite
ImportError: libgfortran.so.1: cannot open shared object file: No such file or directory
>>> 


Version-Release number of selected component (if applicable):
python-2.5.1-25.fc9.i386, scipy-0.6.0-5.fc9.i386

How reproducible:
Always


Steps to Reproduce:
1. invoke python
2. >>> import scipy
3. ImportError: libgfortran.so.1: cannot open shared object file: No such file or directory

Actual Results:
scipy not available/usable.

Expected Results:
no error message, scipy usable.

Additional info:
libgfortran-4.3.0-8.i386 is installed in the system.  Looking into a machine running Fedora 8, it seems that libgfortran-so.1 is contained in older packages such as libgfortran-4.1.2-33.

Comment 1 Jef Spaleta 2008-05-16 15:34:15 UTC

you'll notice that the error is actually associated with numpy and scipy is just
triggering it by internally importing numpy components.

rpm -q numpy
rpm -q atlas
rpm -q --requires atlas |grep fortran
rpm -q --whatprovides libfortran.so.1

On my F9 preview system... compat-libgfortran-41 was pulled in to fill the
libgfortran.so.1 that atlas needs... and numpy needs atlas.

Now somehow for F9 gold  the atlas from F8 is still shipped. A new atlas is in
updates-testing now that doesn't require the compat-libgfortran-41 package.

However, assuming you have the atlas from F9 gold installed, i do not understand
why compat-libgfortran-41 was not installed on your system to fill the necessary
libgfortran.so.1 requirement that atlas needs. 


Installing compat-libgfortran-41 should fix the problem.  

In any event the problem isn't scipy specific.  At worst its a numpy problem,
though its most likely atlas on your system, but you would need to confirm that
on your system by diagnosing whether the deps of the atlas package are filled
correctly using the instructions I've given above.  

And I have confirmation that the new atlas in updates-testing is built against
the newer libgfortran package and that scipy imports as expected using it.

I'm going to close this bug, if after updating your atlas you still have a
problem feel free to re-open it and I'll help you direct the report to the right
person.

-jef

Comment 2 Kazuyoshi Furutaka 2008-05-16 22:50:12 UTC

> you'll notice that the error is actually associated with numpy and scipy is just
> triggering it by internally importing numpy components.

You're right.

> rpm -q numpy

numpy-1.0.3.1-2.fc9.i386

> rpm -q atlas

atlas-3.6.0-12.fc8.i386

> rpm -q --requires atlas |grep gfortran

libgfortran.so.1  

> rpm -q --whatprovides libfortran.so.1

no package provides libgfortran.so.1


> However, assuming you have the atlas from F9 gold installed, i do not understand
> why compat-libgfortran-41 was not installed on your system to fill the necessary
> libgfortran.so.1 requirement that atlas needs. 

Neither do I.


> Installing compat-libgfortran-41 should fix the problem.  

Yes, after installing it scipy/numpy can be imported.

Just an additional report.