[Bioperl-l] Bioperl 1.5.2 RC2

Nathan Haigh n.haigh at sheffield.ac.uk
Wed Oct 18 10:45:57 EDT 2006


Nathan Haigh wrote:
> I've just added test results for 1.5.2 RC2 to the wiki.
>
> There are lots of fails for packages other than bioperl-live. I'm not
> sure excatly how the test fails/skipps are/should be handled since my
> setups are as follows.
>
> Clean WinXP Pro:
> This is a clean install of WinXP Pro SP2 with no major software
> installed, other than ActivePerl 5.8.8.819 and a few tools for archive
> extracting, anti virus etc. Therefore, I'm unsure how tests in
> bioperl-network and bioperl-db should return. For example, I have made
> no effort to setup biosql-schema but I thought that maybe there would be
> a test that would detect this, and fail, then skip over other tests
> gracefully - like the bioperl-run tests when a piece of software is not
> installed???
>
> Debian Linux:
> This is a Bio-Linux machine with quite a lot of bioinformatics software
> installed in the Path. So most of the tests in bioperl-run should
> probably have passed. The same goes for bioperl-network and bioperl-db
> as with my Windows setup.
>
> If my thoughts are totally wrong - let me know!
> Nath
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   
Just looking into the failed Linux tests.

Several of the tests result in errors like:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unallowed parameter: ARGUMENTS !
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
STACK: Bio::Tools::Run::Alignment::Exonerate::AUTOLOAD
/home/bo1nsh/cvswc/bioperl-run-live/blib/lib/Bio/Tools/Run/Alignment/Exonerate.pm:126
STACK: Bio::Tools::Run::Alignment::Exonerate::new
/home/bo1nsh/cvswc/bioperl-run-live/blib/lib/Bio/Tools/Run/Alignment/Exonerate.pm:154
STACK: t/Exonerate.t:32
-----------------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unallowed parameter: 'arguments' !
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
STACK: Bio::Tools::Run::Hmmer::AUTOLOAD Bio/Tools/Run/Hmmer.pm:172
STACK: Bio::Tools::Run::Hmmer::_run Bio/Tools/Run/Hmmer.pm:253
STACK: Bio::Tools::Run::Hmmer::run Bio/Tools/Run/Hmmer.pm:228
STACK: t/Hmmer.t:54
-----------------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unallowed parameter: ARGUMENTS !
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
STACK: Bio::Tools::Run::Phrap::AUTOLOAD Bio/Tools/Run/Phrap.pm:137
STACK: Bio::Tools::Run::Phrap::new Bio/Tools/Run/Phrap.pm:165
STACK: t/Phrap.t:34
-----------------------------------------------------------

Any ideas??

Nath




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