[Bioperl-l] For CVS developers-potentialpitfall with "return undef"

Chris Fields cjfields at uiuc.edu
Wed Jun 7 19:38:10 EDT 2006


I saw a ton of activity from Jason on bioperl-guts for test files and  
modules; you may want to check your tests vs. his changes in case  
they were fixed.  I'll be running similar tests on WinXP ad Mac OS X;  
would be nice to see how my results compare to Dave's

Chris

On Jun 7, 2006, at 5:26 PM, David Messina wrote:

> To look for problems related to Heikki's "return undef" sweep, I ran
> 'make test' on both today's version of bioperl-live and on an older
> version I had checked out on May 12. This was done on OS X 10.4.6 and
> perl 5.8.6.
>
>
> Here are the results:
>
> Failures in today's version of bioperl-live but NOT in 5/12 version
> ===================================================================
> - psm.t -
> The psm.t error appears to be new, so the changes made to Bio/Matrix/
> PSM/SiteMatrix.pm, particularly the one in _uncompress_string, may
> need to be examined.
>
> Here's the error message:
> Illegal division by zero at t/psm.t line 147, <GEN1> line 36.
> t/psm........................dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 29, 32-48
>          Failed 18/48 tests, 62.50% okay
>
>
> Failures in 5/12 version of bioperl-live but NOT in today's version
> ===================================================================
> - OntologyStore.t -
> Neither OntologyStore.t or Bio/Ontology/OntologyStore.pm have been
> touched between 5/12 and today.
>
> The error looks like a transient network problem to me, but I'm not
> sure:
> -------------------- WARNING ---------------------
> MSG: [1/5] tried to fetch http://cvs.sourceforge.net/viewcvs.py/
> *checkout*/song/ontology/so.definition?rev=HEAD, but server threw
> 500.  retrying...
> ---------------------------------------------------
> [REPEATED 5 times -Dave]
>
> t/OntologyStore..............FAILED tests 3-6
>          Failed 4/6 tests, 33.33% okay
>
>
> - RepeatMasker.t -
> Jason made commits to RepeatMasker.t and Bio/Tools/RepeatMasker.pm
> between 5/12 and today, so this appears to be not 'return undef'-
> related.
>
> - SeqVersion.t -
> The SeqVersion error was due to a failure to find and load
> Bio::DB::SeqVersion::gi, which Brian O. noticed and corrected between
> 5/12 and today, so this is not 'return undef'-related.
>
>
>
> All the other test failures appear in both versions of bioperl-live,
> so presumably they are not affected by the 'return undef' changes.
>
> Comparing with Paul Boutros's earlier report, I saw errors in DBCUTG
> that he didn't. Those only pop up when I run the optional remote-
> server tests, however. Perhaps Paul didn't run those and that
> accounts for the discrepancy?
>
> Also, he saw errors in Biblio.t, Repeatmasker.t, and
> StandAloneBlast.t that I did not.
>
> Dave
>
>
> Today's bioperl-live test results:
>
> Failed Test        Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------- 
> --
> -------
> t/Annotation.t                   89    2   2.25%  79 88
> t/DBCUTG.t                       29    5  17.24%  26 30-32
> t/LocusLink.t                    23    1   4.35%  23
> t/PhysicalMap.t                  14    2  14.29%  11-12
> t/TaxonTree.t                    17   30 176.47%  11 18-42
> t/alignUtilities.t                9    1  11.11%  9
> t/psm.t             255 65280    48   35  72.92%  29 32-48
> t/tutorial.t                     21   15  71.43%  7-21
> 114 subtests skipped.
> Failed 8/232 test scripts, 96.55% okay. 18/11057 subtests failed,
> 99.84% okay.
>
> Note that this is including tests requiring a remote server.
>
> And here's the output from a May 12 checkout of bioperl-live:
>
> Failed Test        Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------- 
> --
> -------
> t/Annotation.t                   89    2   2.25%  79 88
> t/DBCUTG.t                       29    5  17.24%  26 30-32
> t/LocusLink.t                    23    1   4.35%  23
> t/OntologyStore.t                 6    4  66.67%  3-6
> t/PhysicalMap.t                  14    2  14.29%  11-12
> t/RepeatMasker.t                  6    3  50.00%  1-2 6
> t/SeqVersion.t      255 65280     6   10 166.67%  2-6
> t/TaxonTree.t                    17   30 176.47%  11 18-42
> t/alignUtilities.t                9    1  11.11%  9
> t/tutorial.t                     21   15  71.43%  7-21
> 114 subtests skipped.
> Failed 10/232 test scripts, 95.69% okay. 12/11049 subtests failed,
> 99.89% okay.
>
>
>
>
> On Jun 7, 2006, at 12:03 PM, Paul Boutros wrote:
>
>> Hi,
>>
>> Just did a make test on bioperl-live on AIX 5.2.0.0 and perl 5.8.7
>> and I had a few
>> failures:
>>
>> Failed Test         Stat Wstat Total Fail  List of Failed
>> --------------------------------------------------------------------- 
>> -
>> ---------
>> t/Annotation.t                    89    2  79 88
>> t/Biblio.t                        24    1  2
>> t/LocusLink.t                     23    1  23
>> t/PhysicalMap.t                   14    2  11-12
>> t/RepeatMasker.t                   6    3  1-2 6
>> t/StandAloneBlast.t               18    4  19-22
>> t/TaxonTree.t                     17   30  11 18-42
>> t/alignUtilities.t                 9    1  9
>> t/psm.t              255 65280    48   35  29 32-48
>> t/tutorial.t                      21   15  7-21
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list