[Bioperl-l] bioperl 1.5.1 RC1 up

[Heikki Lehvaslaiho]

bioperl-live
============

This is perl, v5.8.4 built for i386-linux-thread-multi
All tests successful, 125 subtests skipped.


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:220
STACK 
Bio::Tools::Run::Alignment::Probcons::new /home/heikki/src/bioperl/run/blib/lib/Bio/Tools/Run/Alignment/Probcons.pm:209
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
>
>
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> Bioperl-l at portal.open-bio.org
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
___ _/_/_/_/_/________________________________________________________