[Numpy-discussion] FWIW: "regressions" of dependees of numpy 1.7.0b1

Aron Ahmadia aron@ahmadia....
Thu Sep 6 08:44:03 CDT 2012


Are you running the valgrind test with the Python suppression file:
http://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp ?

Cheers,
A

On Wed, Sep 5, 2012 at 10:14 PM, Yaroslav Halchenko <lists@onerussian.com>wrote:

> 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
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion@scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>
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