Bug 365877 – Stabilize sci-biology/biopython-1.57

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Arfrever Frehtes Taifersar Arahesis (RETIRED) 2011-05-03 21:32:33 UTC]

Stabilize sci-biology/biopython-1.57.

[Comment 1 Ian Delaney (RETIRED) 2011-05-04 15:45:00 UTC]

amd64

emerged straight in with use mysql
ran 

gentoo64 / # ebuild $PORTDIR/sci-biology/biopython/biopython-1.57.ebuild prepare compile test

For a FULL test, requires Install MAFFT, Install MUSCLE, Install the NCBI BLAST+ command line tools which is sci-biology/rmblast

completed with 

Bio.Statistics.lowess docstring test ... ok
Bio.PDB.Polypeptide docstring test ... ok
======================================================================
ERROR: test_doctests (test_Tutorial.TutorialTestCase)
Run tutorial doctests.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/sci-biology/biopython-1.57/work/biopython-1.57-2.7/Tests/test_Tutorial.py", line 115, in test_doctests
    (len(failures), ", ".join(failures)))
ValueError: 6 Tutorial doctests failed: test_from_line_02697, test_from_line_02816, test_from_line_02849, test_from_line_03390, test_from_line_03413, test_from_line_03920

----------------------------------------------------------------------
Ran 149 tests in 113.851 seconds

FAILED (failures = 1)
Python version: 2.7.1 (r271:86832, Apr  7 2011, 09:45:23) 
[GCC 4.4.5]
Operating system: posix linux2
 * Testing failed with CPython 2.7 in testing() function

Can only guess as to a cause.  Leave that one

[Comment 2 Ian Delaney (RETIRED) 2011-05-04 15:45:28 UTC]

Created attachment 272095 [details]
my emerge --info

[Comment 3 Arfrever Frehtes Taifersar Arahesis (RETIRED) 2011-05-04 15:47:47 UTC]

Some tests are known to fail and it's not a regression.

[Comment 4 Agostino Sarubbo 2011-05-04 16:52:24 UTC]

amd64 ok

[Comment 5 Markos Chandras (RETIRED) 2011-05-05 19:21:44 UTC]

amd64 done. Thanks Agostino and Ian

[Comment 6 David Abbott (RETIRED) 2011-05-20 23:03:01 UTC]

Arch tested on x86, all good here ...

[Comment 7 Markus Meier 2011-05-24 21:04:35 UTC]

x86 stable, thanks David

[Comment 8 Brent Baude (RETIRED) 2011-05-28 13:52:53 UTC]

ppc done; closing as last arch