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

Paul Boutros paul.boutros at utoronto.ca
Wed Jun 7 18:35:46 EDT 2006


> 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?
Yup yup, you're right. I should have mentioned in my original message that I didn't run 
any remote-server tests, and unfortunately can't do so on this box.
Paul

Quoting David Messina <dmessina at wustl.edu>:

> 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
> 
> 




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