[Biopython-dev] Re: [BioPython] tests failing

[Iddo Friedberg]

Hi,

OK, I'm on to the test_SubsMat problem. I'll see what I can do to
accomodate this. Seems like a format-string handling problem, which may
arise from different OS versions. Doesn't seem to be from different python
versions, as I'm also using the 2.1, and the test was good in both 2.1 and
2.0. Brad is using a 2.1 on a FreeBSD machine, and is getting different
output than me.


On another matter: got a problem with test_unigene:

idoerg at arrakis:biopython/Tests> python run_tests.py  test_unigene.py
test_unigene ... FAIL

======================================================================
FAIL: test_unigene
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 153, in runTest
    expected_handle)
  File "run_tests.py", line 247, in compare_output
    assert expected_line == output_line, \
AssertionError:
Output  : '        key is AI616857\n'
Expected: '        key is AA495266\n'
----------------------------------------------------------------------
Ran 1 tests in 0.732s

FAILED (failures=1)

My machine:

idoerg at arrakis:biopython/Tests> uname -a
Linux arrakis.md.huji.ac.il 2.2.16-22enterprise #1 SMP Tue Aug 22 16:29:32
EDT 2000 i686 unknown

My Python:

idoerg at arrakis:biopython/Tests> python
Python 2.1 (#1, Jul 11 2001, 11:27:29)
[GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-85)] on linux2


Platform-independence-means-that-some-platforms-are-more-independent-than-others'ly

yours,

Iddo



 On Wed, 1 Aug 2001, Brad Chapman wrote:

: Jeff:
: > Thanks for letting us know about these.I'm moving this thread onto
: > the "biopython-dev" list, as it's probably more appropriate there.
:
: I'd like to second the thanks -- it's all around nice to have people
: using biopython regularly on non-UNIX platforms.
:
: > >Failure: test_SubsMat
: > >
: > >AssertionError:
: > >output: 'M0.00 0.40 0.70 0.80 1.00\n'
: > >Expected: 'M -0.00 0.40 0.70 0.80 1.00\n'
: >
: > It looks like this is from a difference in how windows and Iddo's OS
: > handles 0's.It's probably not serious, but should be fixed.Iddo,
: > can you write some code that will check for this?
:
: I think this actually might be a python version difference and not an
: OS difference. I'm also seeing it right now on my machine:
:
: $ uname -a
: NetBSD taxus.athen1.ga.home.com 1.5.1 NetBSD 1.5.1 (TAXUS) #1: Tue Jun 12 09:13:48 EDT 2001   chapmanb at taxus:/usr/src/sys/arch/macppc/compile/TAXUS macppc
:
: $ python
: Python 2.1 (#6, Jul8 2001, 17:18:01)
: [GCC egcs-2.91.66 19990314 (egcs-1.1.2 release)] on netbsd1
:
: FAIL: test_SubsMat
: ----------------------------------------------------------------------
: Traceback (most recent call last):
: File "run_tests.py", line 153, in runTest
:   expected_handle)
: File "run_tests.py", line 247, in compare_output
:   assert expected_line == output_line, \
: AssertionError:
: Output: 'M 0.00 0.40 0.70 0.80 1.00\n'
: Expected: 'M -0.00 0.40 0.70 0.80 1.00\n'
:
: This is just one I've thrown my hands up in the air about. It's not
: really a bug in SubsMat (hey, 0.00 and -0.00 are still the same, right
: :-), but I'm not sure how to make the regression checker recognize this.
:
: > >Failure: test_prodoc
: > >
: > >AssertionError:
: > >Output: 'J. \n'
: > >Expected: 'J. \n'
: >
: > Brad, this looks pretty odd.Is it a newline problem?
:
: This is another one I've seen on Windows and also on Yair's Mac stuff,
: but have to throw my hands up in the air about. What Mark reported
: here is different from what I've seen -- my error looks like:
:
: Output: 'J. \n'
: Expected: 'J.\n'
:
: So, there is, for some unknown reason, as extra space generated at the
: end of the line, that we don't see on UNIX platforms. I'm not sure
: what is going on here, or how we can make the regression tester stop
: choking on it (other than reintroducing my "end of the line whitespace
: isn't important stuff" :-).
:
: Any ideas for anyone? I'd definately like to clear up these two
: problems if we could.
:
: Brad
:
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: Biopython-dev at biopython.org
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:

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/