[SciPy-user] Build problems with scipy-0.6.0 seg fault in tests, rpm build fails

Tue Oct 23 11:53:29 EDT 2007

Hi all:

I have built and installed numpy-1.0.3.1 using:

   python setup.py bdist_rpm

and run the test:

  python -c "import numpy; numpy.test(1,10)"

it passed with "Ran 586 tests in 1.074s" and exited OK.

When trying the same recipe for scipy, the bdist_rpm failed with:

  running sdist
  warning: sdist: manifest template 'MANIFEST.in' does not exist (using
  default file list)
  error: scipy/sandbox/multigrid/multigridtools/numpy.i: No such file or
  directory

and sure enough numpy.i was pointing to an invalid location.

   numpy.i -> ../../../sparse/sparsetools/numpy.i

../../../sparse/sparsetools had:

  complex_ops.h         sparsetools.py        
  sparsetools.h         sparsetools_wrap.cxx

but no numpy.i there, or in any other place in the source tree. I
removed the symbolic link and tried to get further with the rpm build.

My next build failure was at:

  umfpack_info:
  libraries umfpack not found in /usr/local/lib
  libraries umfpack not found in /usr/lib
  /usr/lib/python2.3/site-packages/numpy/distutils/system_info.py:403:
  UserWarning:
  UMFPACK sparse solver
  (http://www.cise.ufl.edu/research/sparse/umfpack/)
  not found. Directories to search for the libraries can be specified
  in the
  numpy/distutils/site.cfg file (section [umfpack]) or by setting
  the UMFPACK environment variable.
  warnings.warn(self.notfounderror.__doc__)
  NOT AVAILABLE

  non-existing path in 'Lib/maxentropy': 'doc'
  Traceback (most recent call last):
  File "setup.py", line 55, in ?
  setup_package()
  File "setup.py", line 47, in setup_package
  configuration=configuration )
  File "/usr/lib/python2.3/site-packages/numpy/distutils/core.py", line
  142, in setup
  config = configuration()
  File "setup.py", line 19, in configuration
  config.add_subpackage('Lib')
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 798, in add_subpackage
  caller_level = 2)
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 781, in get_subpackage
  caller_level = caller_level + 1)
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 728, in _get_configuration_from_setup_py
  config = setup_module.configuration(*args)
  File "Lib/setup.py", line 23, in configuration
  config.add_subpackage('stsci')
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 798, in add_subpackage
  caller_level = 2)
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 781, in get_subpackage
  caller_level = caller_level + 1)
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 728, in _get_configuration_from_setup_py
  config = setup_module.configuration(*args)
  File "Lib/stsci/setup.py", line 5, in configuration
  config.add_subpackage('convolve')
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 798, in add_subpackage
  caller_level = 2)
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 774, in get_subpackage
  caller_level = caller_level+1)
  File "/usr/lib/python2.3/site-packages/numpy/distutils/misc_util.py",
  line 574, in __init__
  raise ValueError("%r is not a directory" % (package_path,))
  ValueError: 'Lib/stsci/convolve' is not a directory
  error: Bad exit status from
  /home/rouilj/develop/rpm_build/tmp/rpm-tmp.37699 (%build)

however the tarball I unpacked does shows a directory
scipy/stsci/convolve, which I assume is used as the source for the
Lib/stsci/convolve directory.

Since I was having no luck with a bdist_rpm, I tried a normal bdist
build see if it would work. "python setup.py bdist" ran without
failure and created dist/scipy-0.6.0.linux-i686.tar.gz.  I manually
installed it and ran the tests using:

  python -c 'import numpy; import scipy; scipy.test(1,10)'

  generation of a binary structure 4 ... ok
  generic filter 1 ... ERROR
  generic 1d filter 1 ... ERROR
  generic gradient magnitude 1 ... ok
  generic laplace filter 1 ... ok
  geometric transform 1 ... ok
  geometric transform 2 ... ok
  geometric transform 3 ... ok
  geometric transform 4 ... ok
  geometric transform 5 ... ok
  geometric transform 6 ... ok
  geometric transform 7 ... ok
  geometric transform 8 ... ok
  geometric transform 10 ... ok
  geometric transform 13 ... ok
  geometric transform 14 ... ok
  geometric transform 15 ... ok
  geometric transform 16 ... ok
  geometric transform 17 ... ok
  geometric transform 18 ... ok
  geometric transform 19 ... ok
  geometric transform 20 ... ok
  geometric transform 21 ... ok
  geometric transform 22 ... ok
  geometric transform 23 ... ok
  geometric transform 24 ... ok
  grey closing 1 ... ok
  grey closing 2 ... ok
  grey dilation 1 ... ok
  grey dilation 2 ... ok
  grey dilation 3 ... ok
  grey erosion 1 ... ok
  grey erosion 2 ... ok
  grey erosion 3 ... ok
  grey opening 1 ... ok
  grey opening 2 ... ok
  histogram 1*** glibc detected *** free(): invalid next size (fast):
  0x098c0468 ***

using

   python -c 'import scipy; import numpy; scipy.test'
  or
   python -c 'import scipy; scipy.test'

produces:

  ...
  gaussian filter 1 ... ok
  gaussian filter 2 ... ok
  gaussian filter 3 ... ok
  gaussian filter 4 ... ok
  gaussian filter 5 ... ok
  gaussian filter 6 ... ok
  gaussian gradient magnitude filter 1 ... ok
  gaussian gradient magnitude filter 2 ... ok
  gaussian laplace filter 1 ... ok
  gaussian laplace filter 2 ... ok
  generation of a binary structure 1 ... ok
  generation of a binary structure 2 ... ok
  generation of a binary structure 3 ... ok
  generation of a binary structure 4 ... ok
  generic filter 1Segmentation fault

Running:

  python -c 'import numpy; import scipy; scipy.test(1)'

produced:

  ****************************************************************
  WARNING: clapack module is empty
  -----------
  See scipy/INSTALL.txt for troubleshooting.
  Notes:
  * If atlas library is not found by numpy/distutils/system_info.py,
    then scipy uses flapack instead of clapack.
  ****************************************************************

  ..E......................................................................................................../usr/lib/python2.3/site-packages/scipy/ndimage/interpolation.py:41:
  UserWarning: Mode "reflect" may yield incorrect results on
  boundaries. Please use "mirror" instead.
    warnings.warn('Mode "reflect" may yield incorrect results on '
  .............................................................................................EE.................................***
  glibc detected *** free(): invalid next size (fast): 0x09eaeb88 ***
  Aborted

System info is:
  OS: Fedora Core 3
  python -V: Python 2.3.4
  uname -a: Linux hostname 2.6.12-1.1381_FC3
            #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux

So how do I build a working bdist_rpm using 0.6.0 release of scipy?

Thanks for your help.

-- 
				-- rouilj

John Rouillard
System Administrator
Renesys Corporation
603-643-9300 x 111