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Bug 664248 - dev-python/numpy-1.14.5[lapack] gcc-8.2.0 incompatibility
Summary: dev-python/numpy-1.14.5[lapack] gcc-8.2.0 incompatibility
Status: RESOLVED INVALID
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal minor (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-08-22 12:25 UTC by ecat
Modified: 2018-09-04 07:18 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge info (info.txt,6.23 KB, text/plain)
2018-08-22 12:25 UTC, ecat
Details

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Description ecat 2018-08-22 12:25:12 UTC
Created attachment 544452 [details]
emerge info

GCC 8.2.0 bumps libgfortran.so version to 5, but numpy-1.14.5[lapack] requires libgfortran.so.4.

>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python3.5/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/usr/lib64/python3.5/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python3.5/site-packages/numpy/lib/__init__.py", line 19, in <module>
    from .polynomial import *
  File "/usr/lib64/python3.5/site-packages/numpy/lib/polynomial.py", line 20, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/usr/lib64/python3.5/site-packages/numpy/linalg/__init__.py", line 51, in <module>
    from .linalg import *
  File "/usr/lib64/python3.5/site-packages/numpy/linalg/linalg.py", line 31, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory
Comment 1 ecat 2018-08-22 13:29:07 UTC
To reproduce:
install sys-devel/gcc-8.2.0[fortran] dev-python/numpy-1.14.5[lapack], open python shell and import numpy

Expected result: numpy-1.14.5[lapack] should depend on <gcc-8.2.0, 7.3.0 works.
Comment 2 Chris Mayo 2018-09-03 18:55:57 UTC
For me it turned out not to be a numpy problem. Rebuilt:

sci-libs/lapack-reference
sci-libs/blas-reference

and import numpy works again.

I guess the point is as the wiki suggests:
https://wiki.gentoo.org/wiki/Upgrading_GCC

to run revdep-rebuild *after* uninstalling the old gcc.
Comment 3 ecat 2018-09-04 07:18:44 UTC
(In reply to Chris Mayo from comment #2)
> For me it turned out not to be a numpy problem. Rebuilt:
> 
> sci-libs/lapack-reference
> sci-libs/blas-reference
> 
> and import numpy works again.
> 
> I guess the point is as the wiki suggests:
> https://wiki.gentoo.org/wiki/Upgrading_GCC
> 
> to run revdep-rebuild *after* uninstalling the old gcc.

rebuilding after uninstalling the old gcc solved the problem. Thank you.