[Bioperl-l] For CVS developers-potentialpitfall with "returnundef"

Chris Fields cjfields at uiuc.edu
Thu Jun 8 15:28:18 EDT 2006


Here are tests run from WinXP, ActivePerl 5.8.817; almost everything passes.
Not sure what's going on with StandAloneBlast or the protgraph tests, so
I'll check into it.  The psm.t tests that failed are the same as the ones
mentioned previously on other systems.
As an aside, I hate that using '-w' flag with ActivePerl gives a thousand
useless 'subroutines redefined' warnings; only way I found to turn it off is
to not use the flag.  Anyway, I pulled out the relevant chunks of code here;
I'll submit the Mac results separately to not confuse the two.  

...
t/StandAloneBlast............FAILED tests 19-22
	Failed 4/18 tests, 77.78% okay
...
t/protgraph..........................FAILED tests 11, 13, 20-21, 26, 33,
36-37, 45, 48-56, 59-60, 65-66
	Failed 22/66 tests, 66.67% okay
...
t/psm........................Illegal division by zero at t/psm.t line 147,
<GEN1> line 36.
dubious
	Test returned status 9 (wstat 2304, 0x900)
DIED. FAILED tests 29, 32-48
Failed 18/48 tests, 62.50% okay
...
Failed Test         Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
---
t/StandAloneBlast.t               18    4  22.22%  19-22
t/protgraph.t                     66   22  33.33%  11 13 20-21 26 33 36-37
45
                                                   48-56 59-60 65-66
t/psm.t                9  2304    48   35  72.92%  29 32-48
39 subtests skipped.
Failed 3/233 test scripts, 98.71% okay. 36/11100 subtests failed, 99.68%
okay.
NMAKE :  U1077: 
Stop.


Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho
> Sent: Thursday, June 08, 2006 3:50 AM
> To: bioperl-l at lists.open-bio.org
> Cc: Paul.Boutros at utoronto.ca; BioPerl Mailing List; Chris Fields
> Subject: Re: [Bioperl-l] For CVS developers-potentialpitfall with
> "returnundef"
> 
> Looks like we survived the sweeping change - and fixed a number of
> existing
> bugs in the process. Thanks for everyone who helped!
> 
> 	-Heikki
> 
> On Thursday 08 June 2006 02:50, David Messina wrote:
> > Thanks for letting me know, Chris.
> >
> > Here's a new round of results on bioperl-live checked out moments ago:
> > [OS X 10.4.6, perl 5.8.6]
> >
> > Failed Test   Stat Wstat Total Fail  Failed  List of Failed
> > ------------------------------------------------------------------------
> > -------
> > t/DBCUTG.t                  29    5  17.24%  26 30-32
> > t/LocusLink.t               23    1   4.35%  23
> > t/PopGen.t                  89    1   1.12%  85
> > t/psm.t        255 65280    48   35  72.92%  29 32-48
> > t/tutorial.t                21   15  71.43%  7-21
> > 121 subtests skipped.
> > Failed 5/232 test scripts, 97.84% okay. 34/11099 subtests failed,
> > 99.69% okay.
> >
> > Fixed since earlier today
> > =========================
> > Annotation.t
> > PhysicalMap.t
> > TaxonTree.t
> > alignUtilities.t
> >
> > New since earlier today
> > =======================
> > PopGen.t
> >
> > t/PopGen.....................FAILED test 85
> >          Failed 1/89 tests, 98.88% okay (less 2 skipped tests: 86
> > okay, 96.63%)
> >
> > Unchanged
> > =========
> > DBCUTG.t
> > LocusLink.t
> > psm.t
> > tutorial.t
> >
> > Remote-server tests were run like before. I forgot to mention last
> > time that I skipped the local DB tests and I don't have bioperl-ext
> > installed, so several staden-related tests were also skipped.
> >
> > Dave
> >
> > My results from earlier today for reference:
> > > 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.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>   _/  _/  _/  University of Western Cape, South Africa
>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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