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

Uri Laserson laserson@mit....
Tue Dec 14 09:23:58 CST 2010


Will do.  Thanks again for all the help!

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 10:20, Ralf Gommers <ralf.gommers@googlemail.com>wrote:

>
>
> On Tue, Dec 14, 2010 at 11:00 PM, Uri Laserson <laserson@mit.edu> wrote:
>
>> 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?
>>
>
> If it all works for you probably not, but there was an issue with those
> errors a few months ago. They are related to 32/64-bit architecture errors
> as well. If you have any problem with that again, please send me your full
> build and test logs.
>
> Cheers,
> Ralf
>
>
>
>> 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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