[Numpy-discussion] FWIW: "regressions" of dependees of numpy 1.7.0b1
Yaroslav Halchenko
lists at onerussian.com
Wed Sep 5 17:14:32 EDT 2012
and another, quite weird one -- initially it was crashing with the same
error on
np.dot(Vh.T, U.T)
but while adding print statements to troubleshoot it, started to fail on
print:
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/mappers/procrustean.py", line 164, in _train
print "Vh:", Vh
File "/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/numeric.py", line 1471, in array_str
return array2string(a, max_line_width, precision, suppress_small, ' ', "", str)
File "/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py", line 440, in array2string
elif reduce(product, a.shape) == 0:
TypeError: object of type 'float' has no len()
here is part of pdb session:
Vh: > /home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py(440)array2string()
-> elif reduce(product, a.shape) == 0:
(Pdb) up
> /home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/numeric.py(1471)array_str()
-> return array2string(a, max_line_width, precision, suppress_small, ' ', "", str)
(Pdb) print a
[[-0.99818262 0.06026149]
[ 0.06026149 0.99818262]]
*(Pdb) print a.__class__
<type 'numpy.ndarray'>
(Pdb) down
> /home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py(440)array2string()
-> elif reduce(product, a.shape) == 0:
(Pdb) print reduce(product, a.shape)
4
(Pdb) c
ERROR
it might be that this valgrind msg would be relevant ;) :
==10281== Invalid read of size 4
==10281== at 0x88C6973: _descriptor_from_pep3118_format (buffer.c:791)
==10281== by 0x88C6B0E: _array_from_buffer_3118 (ctors.c:1193)
==10281== by 0x88E7ABB: PyArray_GetArrayParamsFromObject (ctors.c:1378)
==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580)
==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758)
==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644)
==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EB221: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== Address 0x75c3a04 is 4 bytes inside a block of size 6 alloc'd
==10281== at 0x4C28BED: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==10281== by 0x88C6911: _descriptor_from_pep3118_format (buffer.c:776)
==10281== by 0x88C6B0E: _array_from_buffer_3118 (ctors.c:1193)
==10281== by 0x88E7ABB: PyArray_GetArrayParamsFromObject (ctors.c:1378)
==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580)
==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758)
==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644)
==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281==
==10281== Invalid read of size 4
==10281== at 0x88C6973: _descriptor_from_pep3118_format (buffer.c:791)
==10281== by 0x88E0BAB: PyArray_DTypeFromObjectHelper (common.c:287)
==10281== by 0x88E1012: PyArray_DTypeFromObject.constprop.277 (common.c:111)
==10281== by 0x88E7C74: PyArray_GetArrayParamsFromObject (ctors.c:1453)
==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580)
==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758)
==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644)
==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== Address 0x7852e94 is 4 bytes inside a block of size 6 alloc'd
==10281== at 0x4C28BED: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==10281== by 0x88C6911: _descriptor_from_pep3118_format (buffer.c:776)
==10281== by 0x88E0BAB: PyArray_DTypeFromObjectHelper (common.c:287)
==10281== by 0x88E1012: PyArray_DTypeFromObject.constprop.277 (common.c:111)
==10281== by 0x88E7C74: PyArray_GetArrayParamsFromObject (ctors.c:1453)
==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580)
==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758)
==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644)
==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python)
==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
On Wed, 05 Sep 2012, Yaroslav Halchenko wrote:
> Recently Sandro uploaded 1.7.0b1 into Debian experimental so I decided to see
> if this bleeding edge version doesn't break some of its dependees... Below is
> a copy of
> http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid.summary
> first FAILED/ok column is when building against sid numpy version 1.6.2-1 and
> the second one is against 1.7.0~b1. I think some 'ok -> FAILED' might be
> indicative of regressions (myself looking into two new funny failures in
> pymvpa2's master). Some FAILED->FAILED could be ignored (e.g. I forgotten to
> provide /dev/shm so multiprocessing was failing)... Enjoy
> Testing builds against python-numpy_1.7.0~b1-1.dsc
> aster_10.6.0-1-4.dsc FAILED FAILED aster_10.6.0-1-4_amd64.build
> avogadro_1.0.3-5.dsc FAILED ok
> babel_1.4.0.dfsg-8.dsc ok ok
> basemap_1.0.3+dfsg-2.dsc ok ok
> biosig4c++_1.3.0-2.dsc ok ok
> brian_1.3.1-1.dsc ok ok
> cfflib_2.0.5-1.dsc ok ok
> cmor_2.8.0-2.dsc ok ok
> connectomeviewer_2.1.0-1.dsc ok ok
> cython_0.15.1-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/cython_0.15.1-2_amd64.build
> dballe_5.18-1.dsc ok ok
> dipy_0.5.0-3.dsc ok ok
> dolfin_1.0.0-7.dsc FAILED ok
> flann_1.7.1-4.dsc ok ok
> fonttools_2.3-1.dsc ok ok
> gamera_3.3.3-2.dsc ok ok
> gdal_1.9.0-3.dsc ok ok
> getfem++_4.1.1-10.dsc FAILED ok
> gnudatalanguage_0.9.2-4.dsc ok ok
> gnuradio_3.6.1-1.dsc FAILED ok
> guiqwt_2.1.6-4.dsc FAILED ok
> h5py_2.0.1-2.dsc ok ok
> joblib_0.6.4-3.dsc ok ok
> lazyarray_0.1.0-1.dsc ok ok
> libfreenect_0.1.2+dfsg-6.dsc ok ok
> libgetdata_0.7.3-6.dsc ok ok
> libmpikmeans_1.5-1.dsc ok ok
> libvigraimpex_1.7.1+dfsg1-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/libvigraimpex_1.7.1+dfsg1-3_amd64.build
> lintian_2.5.10.1.dsc FAILED ok
> magics++_2.14.11-4.dsc ok ok
> mathgl_1.11.2-14.dsc FAILED ok
> matplotlib_1.1.1~rc2-1.dsc FAILED ok
> mayavi2_4.1.0-1.dsc FAILED ok
> mdp_3.2+git78-g7db3c50-3.dsc ok ok
> mgltools-bhtree_1.5.6~rc3~cvs.20120206-1.dsc ok ok
> mgltools-dejavu_1.5.6~rc3~cvs.20120206-1.dsc ok ok
> mgltools-geomutils_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-gle_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-molkit_1.5.6~rc3~cvs.20120206-1.dsc ok ok
> mgltools-opengltk_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-pyglf_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-sff_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-utpackages_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-vision_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mgltools-visionlibraries_1.5.6~rc3~cvs.20120601-1.dsc ok ok
> mlpy_2.2.0~dfsg1-2.dsc ok ok
> mmass_5.2.0-2.dsc ok ok
> model-builder_0.4.1-6.dsc ok ok
> mpi4py_1.3+hg20120611-1.dsc ok ok
> mypaint_1.0.0-1.dsc ok ok
> necpp_1.5.0+cvs20101003-2.1.dsc ok ok
> neo_0.2.0-1.dsc ok ok
> nexus_4.2.1-svn1614-1.dsc FAILED ok
> nibabel_1.2.2-1.dsc ok ok
> nipy_0.2.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/nipy_0.2.0-1_amd64.build
> nitime_0.4-2.dsc ok ok
> nlopt_2.2.4+dfsg-2.dsc ok ok
> numexpr_2.0.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/numexpr_2.0.1-3_amd64.build
> numm_0.4-1.dsc FAILED ok
> opencv_2.3.1-11.dsc ok ok
> openmeeg_2.0.0.dfsg-5.dsc FAILED ok
> openopt_0.38+svn1589-1.dsc ok ok
> pandas_0.8.1-1.dsc ok ok
> pdb2pqr_1.8-1.dsc ok ok
> pebl_1.0.2-2.dsc ok ok
> plplot_5.9.9-5.dsc FAILED ok
> psignifit3_3.0~beta.20120611.1-1.dsc ok ok
> pycuda_2012.1-1.dsc ok ok
> pydicom_0.9.6-1.dsc ok ok
> pyentropy_0.4.1-1.dsc ok ok
> pyepr_0.6.1-2.dsc ok ok
> pyevolve_0.6~rc1+svn398+dfsg-2.dsc ok ok
> pyfai_0.3.5-1.dsc ok ok
> pyfits_3.0.8-2.dsc ok ok
> pyformex_0.8.6-4.dsc ok ok
> pygame_1.9.1release+dfsg-6.dsc FAILED ok
> pygrib_1.9.3-1.dsc ok ok
> pygtk_2.24.0-3.dsc ok ok
> pylibtiff_0.3.0~svn78-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/pylibtiff_0.3.0~svn78-3_amd64.build
> pymca_4.6.0-2.dsc ok ok
> pymol_1.5.0.1-2.dsc ok ok
> pymvpa_0.4.8-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/pymvpa_0.4.8-1_amd64.build
> pymvpa2_2.1.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/pymvpa2_2.1.0-1_amd64.build
> pynifti_0.20100607.1-4.dsc ok ok
> pynn_0.7.4-1.dsc ok ok
> pyopencl_2012.1-1.dsc ok ok
> pyqwt3d_0.1.7~cvs20090625-9.dsc FAILED ok
> pyqwt5_5.2.1~cvs20091107+dfsg-6.dsc FAILED ok
> pysparse_1.1-1.dsc ok ok
> pysurfer_0.3+git15-gae6cbb1-1.1.dsc ok ok
> pytables_2.3.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/pytables_2.3.1-3_amd64.build
> pytango_7.2.3-2.dsc ok ok
> python-ase_3.6.0.2515-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/python-ase_3.6.0.2515-1_amd64.build
> python-biggles_1.6.6-1.dsc ok ok
> python-biom-format_1.0.0-1.dsc ok ok
> python-biopython_1.59-1.dsc ok ok
> python-chaco_4.1.0-1.dsc ok ok
> python-cogent_1.5.1-2.dsc ok ok
> python-cpl_0.3.6-1.dsc ok ok
> python-csa_0.1.0-1.1.dsc ok ok
> python-enable_4.1.0-1.dsc ok ok
> python-fabio_0.0.8-1.dsc ok ok
> python-fftw_0.2.2-1.dsc ok ok
> python-gnuplot_1.8-1.1.dsc ok ok
> python-networkx_1.7~rc1-3.dsc ok ok
> python-neuroshare_0.8.5-1.dsc ok ok
> python-pywcs_1.11-1.dsc ok ok
> python-scientific_2.8-3.dsc ok ok
> python-scipy_0.10.1+dfsg1-4.dsc ok ok
> python-shapely_1.2.14-1.dsc ok ok
> python-visual_5.12-1.4.dsc ok ok
> pytools_2011.5-2.dsc ok ok
> pywavelets_0.2.0-5.dsc ok ok
> pyzmq_2.2.0-1.dsc ok ok
> qiime_1.5.0-2.dsc ok ok
> rdkit_201203-3.dsc ok ok
> rpy_1.0.3-22.dsc ok ok
> rpy2_2.2.6-1.dsc ok ok
> scikit-learn_0.11.0-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/scikit-learn_0.11.0-2_amd64.build
> shogun_1.1.0-6.dsc FAILED ok
> skimage_0.6.1-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/skimage_0.6.1-1_amd64.build
> spherepack_3.2-4.dsc ok ok
> statsmodels_0.4.2-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/statsmodels_0.4.2-1_amd64.build
> stimfit_0.10.18-1.1.dsc ok ok
> syfi_1.0.0.dfsg-1.dsc ok ok
> taurus_3.0.0-1.dsc FAILED ok
> tifffile_20120421-1.dsc ok ok
> uncertainties_1.8-1.dsc ok ok
> veusz_1.15-1.dsc FAILED ok
> vistrails_2.0.alpha~1-3.dsc ok ok
> wrapitk-python_3.20.1.5.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/wrapitk-python_3.20.1.5_amd64.build
> wsjt_5.9.7.r383-1.6.dsc ok ok
> yade_0.80.1-2.dsc FAILED ok
> yp-svipc_0.14-2.dsc ok ok
--
Yaroslav O. Halchenko
Postdoctoral Fellow, Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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