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

Uri Laserson laserson@mit....
Tue Dec 14 09:00:11 CST 2010


Thanks for the help.  I will probably retry with scipy 0.9.0.  Strangely
enough, I did something on my computer and it worked.  I think that what
ended up happening was building numpy 1.5.1 with all the normal defaults on
the computer.  Building MPL on top of that was then fine.  And finally, I
used the special compile flags only for scipy 0.8.0.  Both numpy as scipy
pass numpy.test() and scipy.test()

When I perform numpy.test('full') as you suggest, I get some fortran-related
errors, like:
ERROR: test_return_real.TestF90ReturnReal.test_all
ERROR: test_return_integer.TestF77ReturnInteger.test_all
etc. (12 in total)

Are these significant?

Uri

...................................................................................
Uri Laserson
Graduate Student, Biomedical Engineering
Harvard-MIT Division of Health Sciences and Technology
M +1 917 742 8019
laserson@mit.edu


On Tue, Dec 14, 2010 at 06:08, Ralf Gommers <ralf.gommers@googlemail.com>wrote:

>
>
> 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
>>> http://mail.scipy.org/mailman/listinfo/scipy-user
>>>
>>>
>>
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>
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