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Tasklist

FS#47049 - [atlas-lapack-base] __odrpack.so: undefined symbol: dswap_ in scipy

Attached to Project: Community Packages
Opened by M. Greyson Christoforo (greyltc) - Thursday, 12 November 2015, 18:30 GMT
Last edited by Antonio Rojas (arojas) - Saturday, 14 November 2015, 08:14 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Antonio Rojas (arojas)
Architecture All
Severity Medium
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Description:
The ODR module is broken.

Additional info:
* package version(s): 0.16.1-1

Steps to reproduce:
pacman -S python2-scipy
python2 /usr/lib/python2.7/site-packages/scipy/odr/tests/test_odr.py

This test fails with the following output:
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/scipy/odr/tests/test_odr.py", line 8, in <module>
from scipy.odr import Data, Model, ODR, RealData, odr_stop
File "/usr/lib/python2.7/site-packages/scipy/odr/__init__.py", line 114, in <module>
from .odrpack import *
File "/usr/lib/python2.7/site-packages/scipy/odr/odrpack.py", line 42, in <module>
from scipy.odr import __odrpack
ImportError: /usr/lib/python2.7/site-packages/scipy/odr/__odrpack.so: undefined symbol: dswap_
This task depends upon

Closed by  Antonio Rojas (arojas)
Saturday, 14 November 2015, 08:14 GMT
Reason for closing:  Fixed
Additional comments about closing:  atlas-lapack-base 3.10.2-3
Comment by Antonio Rojas (arojas) - Thursday, 12 November 2015, 23:17 GMT
Which blas/lapack package are you using?
Comment by Doug Newgard (Scimmia) - Friday, 13 November 2015, 03:33 GMT
Cannot reproduce. I'm with arojas, this does sound like a partial update issue.
Comment by M. Greyson Christoforo (greyltc) - Friday, 13 November 2015, 09:43 GMT
I have atlas-lapack-base (3.10.2-2) providing blas and lapack.
I've reinstalled both packages, and still I get this error.
Comment by M. Greyson Christoforo (greyltc) - Friday, 13 November 2015, 14:55 GMT
I've just built and installed atlas-lapack from the AUR and still I get the same error.
Comment by M. Greyson Christoforo (greyltc) - Friday, 13 November 2015, 15:02 GMT
By the way, python-scipy odr also seems to be malfunctioning in a similar way (tested with atlas-lapack compiled from the AUR again):

$ python /usr/lib/python3.5/site-packages/scipy/odr/tests/test_odr.py
Traceback (most recent call last):
File "/usr/lib/python3.5/site-packages/scipy/odr/tests/test_odr.py", line 8, in <module>
from scipy.odr import Data, Model, ODR, RealData, odr_stop
File "/usr/lib/python3.5/site-packages/scipy/odr/__init__.py", line 114, in <module>
from .odrpack import *
File "/usr/lib/python3.5/site-packages/scipy/odr/odrpack.py", line 42, in <module>
from scipy.odr import __odrpack
ImportError: /usr/lib/python3.5/site-packages/scipy/odr/__odrpack.cpython-35m-x86_64-linux-gnu.so: undefined symbol: dswap_
Comment by M. Greyson Christoforo (greyltc) - Friday, 13 November 2015, 15:33 GMT
I've just rebuilt python-scipy and python2-scipy locally from their PKGBUILD: https://projects.archlinux.org/svntogit/community.git/tree/trunk/PKGBUILD?h=packages/python-scipy

and replaced my downloaded packages with these locally built copies and I'm getting the same thing.

I'm at a loss. I don't see any upstream reports about this.

Build and check logs attached.
   python-scipy-0.16.1-1-x86_64-... (1.15 MiB)
   python-scipy-0.16.1-1-x86_64-... (415.6 KiB)
Comment by Antonio Rojas (arojas) - Friday, 13 November 2015, 19:21 GMT
A simple rebuild is not going to fix this. This is an underlinking issue in atlas-lapack-base, libcblas.so should link to libblas.so. A fix is coming up but it takes a few hours to build. Please also report this to the atlas-lapack AUR page so it's fixed there too.

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