py-scipy @0.16.1 +atlas build failure due to new atlas variants

[chanmhy@…]

The new revision of the atlas port released 7 weeks ago removes the +clang variant from the build. Instead, it defaults to that build if you don't specify any options.

As a result, it is now impossible to build py-scipy with the +atlas variant. Please see the attached log for more info.

[chanmhy@…]

build log

[seanfarley (Sean Farley)]

Thanks for the report. Looking into it today.

[seanfarley (Sean Farley)]

Sorry, it's taking forever to build atlas :-(

[chanmhy@…]

Hahaha story of my life. No worries. Thank for handling the ticket quickly.

[seanfarley (Sean Farley)]

I think I have a fix for this but need to test a few more things. Just need to rebuild atlas yet again.

[seanfarley (Sean Farley)]

Ok, I was finally able to build a bunch of versions of atlas and test the fix with scipy. Unfortunately, the test suite fails to run due to:

======================================================================
ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so, 2): Symbol not found: _cgegv_
  Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so
  Expected in: flat namespace
 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/__init__.py", line 94, in <module>
    from ._procrustes import procrustes
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/spatial/_procrustes.py", line 11, in <module>
    from scipy.linalg import orthogonal_procrustes
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 172, in <module>
    from .misc import *
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/misc.py", line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 356, in <module>
    from scipy.linalg import _flapack
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so, 2): Symbol not found: _cgegv_
  Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so
  Expected in: flat namespace
 in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/linalg/_flapack.so

======================================================================
ERROR: Failure: ImportError (cannot import name specfun)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/__init__.py", line 603, in <module>
    from .basic import *
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/basic.py", line 17, in <module>
    from . import specfun
ImportError: cannot import name specfun

This is due to scipy using the, now removed, function cgegv. The scipy 0.17-rc2 fixes this and I just tested it. When it is released everything should run smoothly again. I'll push my local change up soon.

[seanfarley (Sean Farley)]

Fixed in r144622.