failures during testing with elderly numpy 1:1.5.1-1ubuntu2: AttributeError: 'memmap' object has no attribute 'filename' #259

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yarikoptic opened this Issue Feb 4, 2013 · 8 comments

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@yarikoptic
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on ubuntu 11.04

======================================================================
ERROR: nipy.modalities.fmri.tests.test_glm.test_high_level_glm_with_paths
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Traceback (most recent call last):
  File "/usr/lib/pymodules/python2.7/nose/case.py", line 186, in runTest
    self.test(*self.arg)
  File "/tmp/buildd/nipy-0.3.0/debian/tmp/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/tests/test_glm.py", line 58, in test_high_level_glm_with_paths
    assert_true(z_image.get_data().std() < 3.)
  File "/usr/lib/pymodules/python2.7/numpy/core/memmap.py", line 257, in __array_finalize__
    self.filename = obj.filename
AttributeError: 'memmap' object has no attribute 'filename'

======================================================================
ERROR: nipy.modalities.fmri.tests.test_glm.test_high_level_glm_with_data
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/pymodules/python2.7/nose/case.py", line 186, in runTest
    self.test(*self.arg)
  File "/tmp/buildd/nipy-0.3.0/debian/tmp/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/tests/test_glm.py", line 93, in test_high_level_glm_with_data
    assert_true(z_image.get_data().std() < 3. )
  File "/usr/lib/pymodules/python2.7/numpy/core/memmap.py", line 257, in __array_finalize__
    self.filename = obj.filename
AttributeError: 'memmap' object has no attribute 'filename'

----------------------------------------------------------------------

@matthew-brett
Member

Oh - dear - this looks like a numpy bug. The nibabel load / get_data is making a memmapped array z_image.get_data(), then I believe the error arises from deleting the temporary array in that expression. What should we do?

@yarikoptic
Member

ah -- what about just ignoring one way or another:

way A -- do not even upload for those ubuntus with buggy numpy
way B -- skip the test leading to the bug on those buggy numpy's?

On Mon, 04 Feb 2013, Matthew Brett wrote:

Oh - dear - this looks like a numpy bug. The nibabel load / get_data is
making a memmapped array z_image.get_data(), then I believe the error
arises from deleting the temporary array in that expression. What should
we do?


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  1. #259 (comment)

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

@yarikoptic
Member

btw -- this affects only ubuntu 11.04 and 11.10 . 12.04 seems to be
healthy again... no Debian is impaired

On Mon, 04 Feb 2013, Matthew Brett wrote:

Oh - dear - this looks like a numpy bug. The nibabel load / get_data is
making a memmapped array z_image.get_data(), then I believe the error
arises from deleting the temporary array in that expression. What should
we do?

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

@matthew-brett
Member

Yes, I would prefer to ignore this. Yarick - OK with you?

@yarikoptic
Member

I am ok with ignoring ;) thanks for asking

@yarikoptic
Member

just tomake clear -- by "ignoring" I meant skipping that test on the impaired systems

@matthew-brett
Member

OK - you want skips in nipy trunk for this? I don't have an ubuntu 11.04 to test on - do you?

@yarikoptic
Member

screw 11.04: "Support for Ubuntu 11.04 officially ended on 28 October 2012." ;)
otherwise

sudo debootstrap --include python-nipy --variant=buildd natty /tmp/natty http://archive.ubuntu.com/ubuntu/

should give you 11.04 in /tmp/natty, Then use schroot to get into it.

Here is my schroot config for another ubuntu chroot (no 11.04 handy atm)

$> sudo cat /etc/schroot/chroot.d/precise-amd64 
[precise-amd64]
description=Ubuntu precise (12.04) [amd64]
type=directory
directory=/var/cache/chroots/precise-amd64
users=yoh
aliases=ubuntu,precise
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