[MacPorts] #34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module ------------------------------+--------------------------------------------- Reporter: ith140@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Keywords: | Port: py27-scipy ------------------------------+--------------------------------------------- py27-scipy +atlas builds correctly, but crashes upon importing interpolate as shown in the ipython session below. Python 2.7.3 (default, Apr 13 2012, 08:56:00) Type "copyright", "credits" or "license" for more information. IPython 0.12 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. In [1]: from scipy import interpolate --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /Users/ianhoffman/<ipython-input-1-e8ca003dcbfa> in <module>() ----> 1 from scipy import interpolate /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/interpolate/__init__.py in <module>() 150 from fitpack2 import * 151 --> 152 from rbf import Rbf 153 154 from polyint import * /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/interpolate/rbf.py in <module>() 47 from numpy import (sqrt, log, asarray, newaxis, all, dot, exp, eye, 48 float_) ---> 49 from scipy import linalg 50 51 __all__ = ['Rbf'] /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/__init__.py in <module>() 113 from linalg_version import linalg_version as __version__ 114 --> 115 from misc import * 116 from basic import * 117 from decomp import * /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/misc.py in <module>() 1 import numpy as np 2 from numpy.linalg import LinAlgError ----> 3 import fblas 4 5 __all__ = ['LinAlgError', 'norm'] ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so, 2): Symbol not found: __gfortran_transfer_character_write Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so Expected in: flat namespace in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so -- Ticket URL: <https://trac.macports.org/ticket/34657> MacPorts <http://www.macports.org/> Ports system for Mac OS
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module ------------------------------+--------------------------------------------- Reporter: ith140@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Keywords: | Port: py27-scipy ------------------------------+--------------------------------------------- Comment(by vince@…): I can’t reproduce this: {{{ -> python2.7 Python 2.7.3 (default, Apr 24 2012, 16:15:37) Type "help", "copyright", "credits" or "license" for more information.
from scipy import interpolate
}}}
-- Ticket URL: <https://trac.macports.org/ticket/34657#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module ------------------------------+--------------------------------------------- Reporter: ith140@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Keywords: | Port: py27-scipy ------------------------------+--------------------------------------------- Comment(by ith140@…): I'm using atlas 3.9.76 (gcc46),py27-scipy 0.10.1 +atlas (gcc45), py27-numpy 1.6.2 +atlas. -- Ticket URL: <https://trac.macports.org/ticket/34657#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module ------------------------------+--------------------------------------------- Reporter: ith140@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Keywords: | Port: py27-scipy ------------------------------+--------------------------------------------- Comment(by vince@…): The gcc versions you use must be consistent, I guess; otherwise you will mess up the various libraries (precisely what you get). Try rebuilding scipy with gcc46 instead. -- Ticket URL: <https://trac.macports.org/ticket/34657#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module ------------------------------+--------------------------------------------- Reporter: ith140@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Keywords: | Port: py27-scipy ------------------------------+--------------------------------------------- Comment(by ith140@…): Got it fixed. I couldn't build using gcc46, but I could rebuild all three forcing the use of gcc45 and get it working. Not sure how all these things got out of alignment (too bad there isn't a better mechanism to keep gcc consistent), but thanks so much for your help. -- Ticket URL: <https://trac.macports.org/ticket/34657#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module ------------------------------+--------------------------------------------- Reporter: ith140@… | Owner: ram@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Keywords: | Port: py27-scipy ------------------------------+--------------------------------------------- Changes (by ryandesign@…): * cc: ith140@… (removed) * owner: macports-tickets@… => ram@… Old description:
py27-scipy +atlas builds correctly, but crashes upon importing interpolate as shown in the ipython session below.
Python 2.7.3 (default, Apr 13 2012, 08:56:00) Type "copyright", "credits" or "license" for more information.
IPython 0.12 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details.
In [1]: from scipy import interpolate --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /Users/ianhoffman/<ipython-input-1-e8ca003dcbfa> in <module>() ----> 1 from scipy import interpolate
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/interpolate/__init__.py in <module>() 150 from fitpack2 import * 151 --> 152 from rbf import Rbf 153 154 from polyint import *
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/interpolate/rbf.py in <module>() 47 from numpy import (sqrt, log, asarray, newaxis, all, dot, exp, eye, 48 float_) ---> 49 from scipy import linalg 50 51 __all__ = ['Rbf']
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/__init__.py in <module>() 113 from linalg_version import linalg_version as __version__ 114 --> 115 from misc import * 116 from basic import * 117 from decomp import *
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/misc.py in <module>() 1 import numpy as np 2 from numpy.linalg import LinAlgError ----> 3 import fblas 4 5 __all__ = ['LinAlgError', 'norm']
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so, 2): Symbol not found: __gfortran_transfer_character_write Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so Expected in: flat namespace in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so
New description: py27-scipy +atlas builds correctly, but crashes upon importing interpolate as shown in the ipython session below. {{{ Python 2.7.3 (default, Apr 13 2012, 08:56:00) Type "copyright", "credits" or "license" for more information. IPython 0.12 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. In [1]: from scipy import interpolate --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /Users/ianhoffman/<ipython-input-1-e8ca003dcbfa> in <module>() ----> 1 from scipy import interpolate /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/interpolate/__init__.py in <module>() 150 from fitpack2 import * 151 --> 152 from rbf import Rbf 153 154 from polyint import * /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/interpolate/rbf.py in <module>() 47 from numpy import (sqrt, log, asarray, newaxis, all, dot, exp, eye, 48 float_) ---> 49 from scipy import linalg 50 51 __all__ = ['Rbf'] /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/__init__.py in <module>() 113 from linalg_version import linalg_version as __version__ 114 --> 115 from misc import * 116 from basic import * 117 from decomp import * /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/misc.py in <module>() 1 import numpy as np 2 from numpy.linalg import LinAlgError ----> 3 import fblas 4 5 __all__ = ['LinAlgError', 'norm'] ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so, 2): Symbol not found: __gfortran_transfer_character_write Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so Expected in: flat namespace in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/scipy/linalg/fblas.so }}} -- -- Ticket URL: <https://trac.macports.org/ticket/34657#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS
#34657: py27-scipy +atlas builds correctly but crashes on importing interpolate module -------------------------------+-------------------------------------------- Reporter: ith140@… | Owner: ram@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.1 Resolution: invalid | Keywords: Port: py27-scipy | -------------------------------+-------------------------------------------- Changes (by macsforever2000@…): * status: new => closed * resolution: => invalid Comment: Replying to [comment:4 ith140@…]:
Got it fixed. I couldn't build using gcc46, but I could rebuild all three forcing the use of gcc45 and get it working. Not sure how all these things got out of alignment (too bad there isn't a better mechanism to keep gcc consistent), but thanks so much for your help.
There is a way. In your /opt/local/etc/macports/variants.conf file add {{{+gcc45}}} or whatever desired gcc version you want. -- Ticket URL: <https://trac.macports.org/ticket/34657#comment:6> MacPorts <http://www.macports.org/> Ports system for Mac OS
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