[Bioperl-l] bioperl 1.5.1 RC1 up

[Heikki Lehvaslaiho]

After Jason and Albert's fixes on tests and run modules today, all tests pass.

I'd say that bioperl-run 1.5.1 RC1 is ready for release.

  -Heikki 

On Thursday 22 September 2005 10:05, Heikki Lehvaslaiho wrote:
> bioperl-run
> ===========
>
> We've usually released bioperl run at the same time as the live without
> separate testing cycle. It would be great to have some one to do that but
> as it is now, we could fix obvious errors and release it.
>
> Not having almost any binaries on my path I detected only two errors when
> running 'make test':
>
> Failed Test   Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------------
>---- t/Exonerate.t    2   512     5   10 200.00%  1-5
> t/Probcons.t   255 65280     7    0   0.00%  ??
> 372 subtests skipped.
> Failed 2/45 test scripts, 95.56% okay. 5/466 subtests failed, 98.93% okay.
>
>
> The Exonerate error seems to be caused by script looking for
> Bio::SearchIO::Exonerate when it is in Bio::Tool::Run::Alignment::Exonerate
>
>
>
>
> Probcons:
> ------------- EXCEPTION  -------------
> MSG: Unallowed parameter: QUIET !
> STACK
> Bio::Tools::Run::Alignment::Probcons::AUTOLOAD
> /home/heikki/src/bioperl/run/blib/lib/Bio/Tools/Run/Alignment/Probcons.pm:2
>20 STACK
> Bio::Tools::Run::Alignment::Probcons::new
> /home/heikki/src/bioperl/run/blib/lib/Bio/Tools/Run/Alignment/Probcons.pm:2
>09 STACK toplevel t/Probcons.t:33
>
>
>  -Heikki
>
> On Thursday 22 September 2005 04:44, Jason Stajich wrote:
> > Release candidates for Bioperl 1.5.1 is up -I've not tagged anything
> > in CVS so commits should continue to be made to the repository HEAD:
> >
> > http://bioperl.org/DIST/bioperl-1.5.1-rc1.tar.gz
> > http://bioperl.org/DIST/bioperl-1.5.1-rc1.zip
> >
> > Tests pass for me on OSX with some, but not all dependancies installed.
> >
> > I do see this for t/OntologyStore.t and a failed test --
> > MSG: [5/5] tried to fetch http://cvs.sourceforge.net/viewcvs.py/
> > *checkout*/song/ontology/so.definition?rev=HEAD, but server threw
> > 500.  re
> >
> > ------------------------------------------------------------------------
> > -------
> > t/OntologyStore.t                6    4  66.67%  3-6
> > 125 subtests skipped.
> > Failed 1/220 test scripts, 99.55% okay. 4/9916 subtests failed,
> > 99.96% okay.
> >
> > I believe aspects of this test should be disabled without
> > BIOPERLDEBUG=1.
> >
> > I think the Changes file and README will need to be checked over and
> > corrected for this release.
> >
> > Can folks check over for any test failures.  I believe RestrictionIO
> > is going to fail on perl 5.6.x but I don't know exactly what the
> > workaround is - other than detect perl version and skip tests where
> > appropriate.
> >
> > Can anyone speak up for bioperl-run and bioperl-ext as to whether or
> > not we can tag and put these out as developer release as well?  I
> > need someone to help out with testing these packages and getting them
> > ship-shape for a release too.
> >
> > -jason
> > --
> > Jason Stajich
> > Duke University
> > http://www.duke.edu/~jes12
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________