[Bioperl-l] Disabling web tests [some tests fail on Mac OS X]

[Heikki Lehvaslaiho]

Koen,

I really like you being picky. ;-) All the help in debbugging bioperl is 
welcome!

That error must be caused by me deleting outdated psiblast from distribution. 
I'll fix that later today.

Jason,

There are still two psiblast scripts left in core:
	examples/searchio/psiblast_features.pl
	examples/searchio/psiblast_iterations.pl
Do you have any interest in migrating them into new code base (like Steve 
suggested) or shall I remove them?

	-Heikki


On Friday 19 Dec 2003 2:43 am, Koen van der Drift wrote:
> Hi,
>
> Thanks for fixing all those tests which fail when offline. I want to
> include the tests in the fink-package for the upcoming, which is why I
> am so picky ;-)
>
> I found one more oddity, though. When an older bioperl is present, the
> Search.t test passes, however, if no bioperl is installed, it fails as
> follows:
>
> ...
> ...
> ok 930
> Bio::SearchIO: psiblast cannot be found
> Exception
> ------------- EXCEPTION  -------------
> MSG: Failed to load module Bio::SearchIO::psiblast. Can't locate
> Bio/Search/Result/PsiBlastResult.pm in @INC (@INC contains: t .
> /sw/lib/perl5/5.8.1/darwin-thread-multi-2level /sw/lib/perl5/5.8.1
> /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5
> /sw/lib/perl5/darwin /sw/lib/perl5//5.8.1/darwin-thread-multi-2level
> /sw/lib/perl5//5.8.1 /sw/lib/perl5//darwin-thread-multi-2level
> /sw/lib/perl5/ /System/Library/Perl/5.8.1/darwin-thread-multi-2level
> /System/Library/Perl/5.8.1
> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1
> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level
> /Network/Library/Perl/5.8.1 /Network/Library/Perl) at
> Bio/SearchIO/psiblast.pm line 152, <GEN55> line 245.
> BEGIN failed--compilation aborted at Bio/SearchIO/psiblast.pm line 152,
> <GEN55> line 245.
> Compilation failed in require at Bio/Root/Root.pm line 394, <GEN55>
> line 245.
>
> STACK Bio::Root::Root::_load_module Bio/Root/Root.pm:396
> STACK (eval) Bio/SearchIO.pm:387
> STACK Bio::SearchIO::_load_format_module Bio/SearchIO.pm:386
> STACK Bio::SearchIO::new Bio/SearchIO.pm:166
> STACK toplevel t/SearchIO.t:1303
>
> --------------------------------------
>
> For more information about the SearchIO system please see the SearchIO
> docs.
> This includes ways of checking for formats at compile time, not run time
> Can't call method "next_result" on an undefined value at t/SearchIO.t
> line 1307.
> [ModusOperandi:~/Desktop/bioperl-live] koen%
>
>
>
> - Koen.
>
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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
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________