[Bioperl-l] Re: SeqFactory diff

[Hilmar Lapp]

Could you post your code too? Otherwise it will be very tedious to try
to reproduce the error. Ideally, if you can provide a self-contained
script or collection of files/scripts that demonstrate the error, that'd
be very helpful.

Otherwise the chances of somebody sitting down and trying to debug this
are not sky high ...

	-hilmar

> -----Original Message-----
> From: Michal Kurowski [mailto:mkur at poczta.gazeta.pl] 
> Sent: Friday, September 05, 2003 9:10 AM
> To: Hilmar Lapp
> Cc: Bioperl
> Subject: [Bioperl-l] Re: SeqFactory diff
> 
> 
> Hilmar Lapp [hlapp at gmx.net] wrote:
> 
> > could you post a test case please along with the error that it 
> > produces.
> 
> MSG: Can't locate MySeq.pm in @INC (@INC contains: CODE(0x84d79b8) 
> /usr/lib/perl5/i386-linux /usr/lib/perl5 
> /usr/lib/perl5/site_perl/i386-linux 
> /usr/lib/perl5/site_perl /usr/lib/perl5/site_perl .) at (eval 
> 8) line 3.
> : Unrecognized Sequence type for SeqFactory 'MySeq'
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/lib/perl5/site_perl/Bio/Root/Root.pm:342
> STACK: Bio::Seq::SeqFactory::type 
> /usr/lib/perl5/site_perl/Bio/Seq/SeqFactory.pm:144
> STACK: Bio::Seq::SeqFactory::new 
> /usr/lib/perl5/site_perl/Bio/Seq/SeqFactory.pm:103
> STACK: /home/michal/bin/uploader2.pl:49
> 
> > The lines you're commenting out are there for a conscious 
> reason, and
> > just removing them is unlikely to be accepted into the code 
> base without 
> > further grounds that that would be the sole way to let you 
> do what you 
> > wanted to do.
> 
> You're right. The change breaks a lot of code and I reverted 
> it. Sorry, a long working hours case ;-).
> 
> The problem remains though. require/use will not do if you have 
> a PrimarySeq derived class and a client  code in the same file.
> 
> 
> -- 
> Michal Kurowski
> <mkur at poczta.gazeta.pl> 
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