[SciPy-User] Problems installing scipy on OS X 10.6 (Snow Leopard): libarpack

Ralf Gommers ralf.gommers@googlemail....
Tue Dec 14 05:08:02 CST 2010


On Tue, Dec 14, 2010 at 12:38 AM, Uri Laserson <laserson@mit.edu> wrote:

> Hi Ralf,
>
> Sor for my delayed response, I missed this message in my inbox.
>

No problem at all.


> I have since moved forward with this problem, but I now have a runtime
> problem.
>
> I am using python2.7 I built myself through the homebrew package manager.
>
> Output from my compilers is as follows:
> laserson@hobbes:~$ gcc -v
> Using built-in specs.
> Target: i686-apple-darwin10
> Configured with: /var/tmp/gcc/gcc-5664~89/src/configure --disable-checking
> --enable-werror --prefix=/usr --mandir=/share/man
> --enable-languages=c,objc,c++,obj-c++
> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
> --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10-
> --host=x86_64-apple-darwin10 --target=i686-apple-darwin10
> --with-gxx-include-dir=/include/c++/4.2.1
> Thread model: posix
> gcc version 4.2.1 (Apple Inc. build 5664)
>
> laserson@hobbes:~$ g++ -v
> Using built-in specs.
> Target: i686-apple-darwin10
> Configured with: /var/tmp/gcc/gcc-5664~89/src/configure --disable-checking
> --enable-werror --prefix=/usr --mandir=/share/man
> --enable-languages=c,objc,c++,obj-c++
> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
> --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10-
> --host=x86_64-apple-darwin10 --target=i686-apple-darwin10
> --with-gxx-include-dir=/include/c++/4.2.1
> Thread model: posix
> gcc version 4.2.1 (Apple Inc. build 5664)
>
> laserson@hobbes:~$ gfortran -v
> Using built-in specs.
> Target: i686-apple-darwin8
> Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/local
> --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
> --build=i686-apple-darwin8 --host=i686-apple-darwin8
> --target=i686-apple-darwin8 --enable-languages=fortran
> Thread model: posix
> gcc version 4.2.3
>
> I installed numpy and scipy loosely based on the directions here:
> http://mail.scipy.org/pipermail/numpy-discussion/2010-August/052227.html
>
> I see that unfortunately that mail did not receive any response, I don't
remember seeing it. The info in it is not entirely correct.


> More specifically, after installing gfortran, I downloaded the following
> versions of numpy and scipy:
> numpy 1.5.1
> scipy 0.8.0
>

scipy 0.8.0 has one issue with python 2.7. You should either use the 0.8.x
svn branch or 0.9.0b1 from svn or Sourceforge.

>
> I then set the following environment variables:
> export MACOSX_DEPLOYMENT_TARGET=10.6
>
This is OK.


> export CFLAGS="-arch i386 -arch x86_64"
> export FFLAGS="-m32 -m64"
> export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386 -arch
> x86_64 -framework Accelerate"
>

This is incorrect. When you build with distutils, CFLAGS/FFLAGS will
overwrite all flags, not append them. You should just leave this out,
default flags work fine with numpy 1.5.1 + scipy as specified above.


>
> Then I built and installed numpy as follows (note: sudo is not needed, as I
> took ownership of /usr/local):
> python setup.py build --fcompiler=gnu95
> python setup.py install
>
> The results of numpy.test() are:
> >>> numpy.test()
>

Looks OK. As a sanity check, run numpy.test('full'). There are some extra
distutils tests that get run like that.


> Running unit tests for numpy
> NumPy version 1.5.1
> NumPy is installed in
> /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/numpy
> Python version 2.7.1 (r271:86832, Dec  7 2010, 12:37:47) [GCC 4.2.1 (Apple
> Inc. build 5664)]
> nose version 0.11.4
> ....
> Ran 3006 tests in 18.312s
>
> OK (KNOWNFAIL=4, SKIP=1)
> <nose.result.TextTestResult run=3006 errors=0 failures=0>
>
> Then I installed scipy as follows:
> python setup.py build --fcompiler=gnu95
> python setup.py install
>
> and ran the tests, giving output:
> >>> scipy.test()
> Running unit tests for scipy
> NumPy version 1.5.1
> NumPy is installed in
> /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/numpy
> SciPy version 0.8.0
> SciPy is installed in
> /usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/scipy
> Python version 2.7.1 (r271:86832, Dec  7 2010, 12:37:47) [GCC 4.2.1 (Apple
> Inc. build 5664)]
> nose version 0.11.4
> RuntimeError: module compiled against ABI version 2000000 but this version
> of numpy is 1000009
> ....
> Ran 4405 tests in 87.505s
>
> OK (KNOWNFAIL=19, SKIP=28)
> <nose.result.TextTestResult run=4405 errors=0 failures=0>
>
> Note the RuntimeError listed above:
> RuntimeError: module compiled against ABI version 2000000 but this version
> of numpy is 1000009
>

That looks like you have some other numpy install hanging around.


>
> I can still import scipy fine.  However, I then have a problem after
> building matplotlib (GitHub).  I can build it fine:
>
> ============================================================================
> BUILDING MATPLOTLIB
>             matplotlib: 1.0.0
>                 python: 2.7.1 (r271:86832, Dec  7 2010, 12:37:47)  [GCC
>                         4.2.1 (Apple Inc. build 5664)]
>               platform: darwin
>
> REQUIRED DEPENDENCIES
>                  numpy: 1.5.1
>              freetype2: 12.0.6
>
> OPTIONAL BACKEND DEPENDENCIES
>                 libpng: 1.2.44
>                Tkinter: Tkinter: 81008, Tk: 8.5, Tcl: 8.5
>                   Gtk+: no
>                         * Building for Gtk+ requires pygtk; you must be
> able
>                         * to "import gtk" in your build/install environment
>        Mac OS X native: yes
>                     Qt: no
>                    Qt4: no
>                  Cairo: no
>
> However, when I import matplotlib.pyplot, I get:
> >>> import matplotlib.pyplot
> RuntimeError: module compiled against ABI version 2000000 but this version
> of numpy is 1000009
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/pyplot.py",
> line 23, in <module>
>     from matplotlib.figure import Figure, figaspect
>   File
> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/figure.py",
> line 16, in <module>
>     import artist
>   File
> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/artist.py",
> line 6, in <module>
>     from transforms import Bbox, IdentityTransform, TransformedBbox,
> TransformedPath
>   File
> "/Users/laserson/matplotlib/lib/python2.7/site-packages/matplotlib/transforms.py",
> line 34, in <module>
>     from matplotlib._path import affine_transform
> ImportError: numpy.core.multiarray failed to import
>
>
> However, when I separately try to import numpy.core.multiarray, I have no
> problem.
>
> Same problem as with scipy I guess.

Cheers,
Ralf


Any ideas?
>
> Thanks!
> Uri
>
>
>
>
> On Wed, Dec 8, 2010 at 06:18, Ralf Gommers <ralf.gommers@googlemail.com>wrote:
>
>>
>>
>> On Wed, Dec 8, 2010 at 4:06 AM, Uri Laserson <laserson@mit.edu> wrote:
>>
>>> Hi all,
>>>
>>> I am on a MacMini with Intel processor.  I just installed OS X 10.6 and
>>> the latest Xcode that I could download, which included gcc 4.2.  I am using
>>> python 2.7 built from source using homebrew.  I installed the gfortran 4.2.3
>>> binaries from http://r.research.att.com/tools/.
>>>
>>> I am trying to install numpy and scipy.  numpy installs fine with or
>>> without switching to g++-4.0.  I have successfully installed it using pip
>>> and also directly from source from the git repository.
>>>
>>> Scipy is giving me errors on install (the same errors whether I use pip
>>> or try the svn repository).  I installed it successfully yesterday on a new
>>> Macbook Air using pip, after changing the symlinks to point to g++-4.0.
>>>  However, today on my MacMini, I am getting errors after following the same
>>> protocol.
>>>
>>> The errors I am getting are here:
>>> https://gist.github.com/732293
>>>
>>
>> The error indicates that 32 and 64 bit binaries are being mixed. Can you
>> tell us the following:
>> - what build command you used
>> - what Python you are using (from python.org, from Apple, self-compiled?)
>> - the output of "gcc -v", "g++ -v" and "gfortran -v"
>>
>> Ralf
>>
>>
>>
>> _______________________________________________
>> SciPy-User mailing list
>> SciPy-User@scipy.org
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>>
>>
>
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