umath import error for Numpy builds on OSX 10.6
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From: hardcoreUFO on 10 Dec 2009 18:09 For the past several weeks, I have been unable to build numpy from source, at least nothing that works. The issue is that symbols appear to be missing from umath. When numpy is imported, I get the following: In [1]: import numpy ------------------------------------------------------------ Traceback (most recent call last): File "<ipython console>", line 1, in <module> File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- py2.6-macosx-10.6-universal.egg/numpy/__init__.py", line 132, in <module> import add_newdocs File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- py2.6-macosx-10.6-universal.egg/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- py2.6-macosx-10.6-universal.egg/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- py2.6-macosx-10.6-universal.egg/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- py2.6-macosx-10.6-universal.egg/numpy/core/__init__.py", line 6, in <module> import umath ImportError: dlopen(/Library/Python/2.6/site-packages/ numpy-1.5.0.dev_20091211-py2.6-macosx-10.6-universal.egg/numpy/core/ umath.so, 2): Symbol not found: _npy_cexp Referenced from: /Library/Python/2.6/site-packages/ numpy-1.5.0.dev_20091211-py2.6-macosx-10.6-universal.egg/numpy/core/ umath.so Expected in: flat namespace in /Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211-py2.6- macosx-10.6-universal.egg/numpy/core/umath.so I think my build script is good, but here it is just incase: #!/bin/sh export MACOSX_DEPLOYMENT_TARGET=10.6 export CFLAGS="-arch x86_64" #export FFLAGS="-arch i386 -arch x86_64" export FFLAGS="-arch x86_64" export LDFLAGS="-Wall -lgfortran -undefined dynamic_lookup -bundle - arch x86_64" rm -rf build python setup.py config -L/Users/fonnesbeck/Code/freetype -L/Users/ fonnesbeck/Code/libpng build python setupegg.py egg_info --tag-date bdist_egg I'm at my wits end with this one, so any help at all is most appreciated.
From: Robert Kern on 10 Dec 2009 18:29 On 2009-12-10 17:09 PM, hardcoreUFO wrote: > For the past several weeks, I have been unable to build numpy from > source, at least nothing that works. The issue is that symbols appear > to be missing from umath. When numpy is imported, I get the following: You will want to ask numpy questions on the numpy mailing list: http://www.scipy.org/Mailing_Lists > In [1]: import numpy > ------------------------------------------------------------ > Traceback (most recent call last): > File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- > py2.6-macosx-10.6-universal.egg/numpy/core/__init__.py", line 6, in > <module> > import umath > ImportError: dlopen(/Library/Python/2.6/site-packages/ > numpy-1.5.0.dev_20091211-py2.6-macosx-10.6-universal.egg/numpy/core/ > umath.so, 2): Symbol not found: _npy_cexp > Referenced from: /Library/Python/2.6/site-packages/ > numpy-1.5.0.dev_20091211-py2.6-macosx-10.6-universal.egg/numpy/core/ > umath.so > Expected in: flat namespace > in /Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211-py2.6- > macosx-10.6-universal.egg/numpy/core/umath.so > I think my build script is good, but here it is just incase: > > #!/bin/sh > export MACOSX_DEPLOYMENT_TARGET=10.6 > export CFLAGS="-arch x86_64" > #export FFLAGS="-arch i386 -arch x86_64" > export FFLAGS="-arch x86_64" > export LDFLAGS="-Wall -lgfortran -undefined dynamic_lookup -bundle - > arch x86_64" > rm -rf build > python setup.py config -L/Users/fonnesbeck/Code/freetype -L/Users/ > fonnesbeck/Code/libpng build > python setupegg.py egg_info --tag-date bdist_egg > > I'm at my wits end with this one, so any help at all is most > appreciated. Don't specify LDFLAGS if you don't have to. It is obliterating the -l flag for the npy_math library that numpy builds internally and tries to link with. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
From: hardcoreUFO on 10 Dec 2009 18:33 On Dec 11, 12:29 pm, Robert Kern <robert.k...(a)gmail.com> wrote: > On 2009-12-10 17:09 PM, hardcoreUFO wrote: > > > For the past several weeks, I have been unable to build numpy from > > source, at least nothing that works. The issue is that symbols appear > > to be missing from umath. When numpy is imported, I get the following: > > You will want to ask numpy questions on the numpy mailing list: > > http://www.scipy.org/Mailing_Lists > > > > > > > In [1]: import numpy > > ------------------------------------------------------------ > > Traceback (most recent call last): > > File "/Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211- > > py2.6-macosx-10.6-universal.egg/numpy/core/__init__.py", line 6, in > > <module> > > import umath > > ImportError: dlopen(/Library/Python/2.6/site-packages/ > > numpy-1.5.0.dev_20091211-py2.6-macosx-10.6-universal.egg/numpy/core/ > > umath.so, 2): Symbol not found: _npy_cexp > > Referenced from: /Library/Python/2.6/site-packages/ > > numpy-1.5.0.dev_20091211-py2.6-macosx-10.6-universal.egg/numpy/core/ > > umath.so > > Expected in: flat namespace > > in /Library/Python/2.6/site-packages/numpy-1.5.0.dev_20091211-py2.6- > > macosx-10.6-universal.egg/numpy/core/umath.so > > I think my build script is good, but here it is just incase: > > > #!/bin/sh > > export MACOSX_DEPLOYMENT_TARGET=10.6 > > export CFLAGS="-arch x86_64" > > #export FFLAGS="-arch i386 -arch x86_64" > > export FFLAGS="-arch x86_64" > > export LDFLAGS="-Wall -lgfortran -undefined dynamic_lookup -bundle - > > arch x86_64" > > rm -rf build > > python setup.py config -L/Users/fonnesbeck/Code/freetype -L/Users/ > > fonnesbeck/Code/libpng build > > python setupegg.py egg_info --tag-date bdist_egg > > > I'm at my wits end with this one, so any help at all is most > > appreciated. > > Don't specify LDFLAGS if you don't have to. It is obliterating the -l flag for > the npy_math library that numpy builds internally and tries to link with. > Thanks Robert. I was not able to solve the problem on the Numpy list, so I had to broaden the search.Will try what you suggest, though.
From: hardcoreUFO on 10 Dec 2009 18:41 On Dec 11, 12:29 pm, Robert Kern <robert.k...(a)gmail.com> wrote: > Don't specify LDFLAGS if you don't have to. It is obliterating the -l flag for > the npy_math library that numpy builds internally and tries to link with. Unfortunately, that did not eliminate the error. I thought it was something that was changed in Numpy, because my first go at building was successful on Snow Leopard; it suddenly stopped working a few weeks ago.
From: Robert Kern on 10 Dec 2009 23:44
On 2009-12-10 17:33 PM, hardcoreUFO wrote: > Thanks Robert. I was not able to solve the problem on the Numpy list, > so I had to broaden the search.Will try what you suggest, though. There's no one here who can help you with this who isn't on the numpy list. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco |