[MacPorts] #50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants -----------------------+-------------------------------- Reporter: chanmhy@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: py-scipy -----------------------+-------------------------------- 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. -- Ticket URL: <https://trac.macports.org/ticket/50283> MacPorts <https://www.macports.org/> Ports system for OS X
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants ------------------------+---------------------- Reporter: chanmhy@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-scipy | ------------------------+---------------------- Changes (by sean@…): * status: new => assigned * owner: macports-tickets@… => sean@… Comment: Thanks for the report. Looking into it today. -- Ticket URL: <https://trac.macports.org/ticket/50283#comment:1> MacPorts <https://www.macports.org/> Ports system for OS X
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants ------------------------+---------------------- Reporter: chanmhy@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-scipy | ------------------------+---------------------- Comment (by sean@…): Sorry, it's taking forever to build atlas :-( -- Ticket URL: <https://trac.macports.org/ticket/50283#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants ------------------------+---------------------- Reporter: chanmhy@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-scipy | ------------------------+---------------------- Comment (by chanmhy@…): Hahaha story of my life. No worries. Thank for handling the ticket quickly. -- Ticket URL: <https://trac.macports.org/ticket/50283#comment:3> MacPorts <https://www.macports.org/> Ports system for OS X
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants ------------------------+---------------------- Reporter: chanmhy@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-scipy | ------------------------+---------------------- Comment (by sean@…): I think I have a fix for this but need to test a few more things. Just need to rebuild atlas yet again. -- Ticket URL: <https://trac.macports.org/ticket/50283#comment:4> MacPorts <https://www.macports.org/> Ports system for OS X
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants ------------------------+---------------------- Reporter: chanmhy@… | Owner: sean@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: py-scipy | ------------------------+---------------------- Comment (by sean@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/50283#comment:5> MacPorts <https://www.macports.org/> Ports system for OS X
#50283: py-scipy @0.16.1 +atlas build failure due to new atlas variants ------------------------+-------------------- Reporter: chanmhy@… | Owner: sean@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: fixed | Keywords: Port: py-scipy | ------------------------+-------------------- Changes (by sean@…): * status: assigned => closed * resolution: => fixed Comment: Fixed in r144622. -- Ticket URL: <https://trac.macports.org/ticket/50283#comment:6> MacPorts <https://www.macports.org/> Ports system for OS X
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