[SciPy-User] ANN: SciPy 0.10.1 release candidate 1

Ralf Gommers ralf.gommers@googlemail....
Mon Feb 13 00:02:20 CST 2012


On Sun, Feb 12, 2012 at 10:02 PM, Scott Lasley <slasley@space.umd.edu>wrote:

> I downloaded scipy-0.10.1rc1.tar.gz from sourceforge and installed it on a
> MacPro running OS X 10.7.3, XCode 4.2.1, gfortran from the R Project, numpy
> 1.6.1 from sourceforge, and python 2.7.2 from python.org with these
> commands
>
> export MACOSX_DEPLOYMENT_TARGET=10.7
> export CC=/usr/bin/gcc
> python setupegg.py build --fcompiler=gfortran
> python setupegg.py bdist_egg
> unset MACOSX_DEPLOYMENT_TARGET
> unset CC
> easy_install -U dist/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg
>
> scipy crashes python and python-32 in TestDoubleIFFT.  I get similar
> crashes with scipy 2.0.0.dev-8d1b91e and numpy 0.11.0.dev-912768f from
> github.
>

This looks like http://projects.scipy.org/scipy/ticket/1496, using 0.10.0
with the above build recipe should crash in the same way. Can you comment
on that ticket, double check that you're using non-LLVM gcc (looks
unrelated, but you forgot to export CXX) and the correct fortran compiler
(there are two from R-project, the one linked on the front page is the
wrong one last time I checked), and try the recipe linked to there?

OS X Lion build is still very painful, if someone wants to have a go at
making numpy/scipy work with llvm-gcc that would be very helpful.

Thanks,
Ralf


> $ python
> Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.test(verbose=10)
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
> SciPy version 0.10.1rc1
> SciPy is installed in
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy
> Python version 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) [GCC
> 4.2.1 (Apple Inc. build 5666) (dot 3)]
> nose version 1.1.2
> nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
> nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext',
> 'gen_ext', 'pyrex_ext', 'swig_ext']
> Tests cophenet(Z) on tdist data set. ... ok
> ...
> Check that updating stored values with exact ones worked. ... ok
> test_constants.test_fahrenheit_to_celcius ... ok
> test_constants.test_celcius_to_kelvin ... ok
> test_constants.test_kelvin_to_celcius ... ok
> test_constants.test_fahrenheit_to_kelvin ... ok
> test_constants.test_kelvin_to_fahrenheit ... ok
> test_constants.test_celcius_to_fahrenheit ... ok
> test_constants.test_lambda_to_nu ... ok
> test_constants.test_nu_to_lambda ... ok
> test_definition (test_basic.TestDoubleFFT) ... ok
> test_djbfft (test_basic.TestDoubleFFT) ... ok
> test_n_argument_real (test_basic.TestDoubleFFT) ... ok
> test_definition (test_basic.TestDoubleIFFT) ... FAIL
> test_definition_real (test_basic.TestDoubleIFFT) ... ok
> test_djbfft (test_basic.TestDoubleIFFT) ... FAIL
> test_random_complex (test_basic.TestDoubleIFFT) ... FAIL
> Python(68720) malloc: *** error for object 0x105312530: pointer being
> freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap: 6
> $
>
> $ python-32
> Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.test(verbose=10)
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
> SciPy version 0.10.1rc1
> SciPy is installed in
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy
> Python version 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) [GCC
> 4.2.1 (Apple Inc. build 5666) (dot 3)]
> nose version 1.1.2
> nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
> nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext',
> 'gen_ext', 'pyrex_ext', 'swig_ext']
> ...
> test_definition (test_basic.TestDoubleFFT) ... ok
> test_djbfft (test_basic.TestDoubleFFT) ... ok
> test_n_argument_real (test_basic.TestDoubleFFT) ... ok
> test_definition (test_basic.TestDoubleIFFT) ... Python(68743) malloc: ***
> error for object 0x3a33604: incorrect checksum for freed object - object
> was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> FAIL
> test_definition_real (test_basic.TestDoubleIFFT) ... ok
> test_djbfft (test_basic.TestDoubleIFFT) ... Python(68743) malloc: ***
> error for object 0x3a2e2c4: incorrect checksum for freed object - object
> was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> FAIL
> test_random_complex (test_basic.TestDoubleIFFT) ... FAIL
> test_random_real (test_basic.TestDoubleIFFT) ... Python(68743) malloc: ***
> error for object 0x354c604: incorrect checksum for freed object - object
> was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> FAIL
> test_size_accuracy (test_basic.TestDoubleIFFT) ... Bus error: 10
> $
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