[Bioperl-l] [Fwd: Enquiry about Remoteblast.pm]

Chris Fields cjfields at illinois.edu
Thu Mar 4 11:49:01 EST 2010


Okay, I'm able to replicate this (and the tests now correctly attempt to
catch it).  It appears that this may be a general RemoteBlast issue, as
regular RemoteBlast tests are also taking forever.  

This shouldn't be related to the email issue (this isn't in
RemoteBlast.pm yet).  At least, I would hope NCBI would pass back
another status besides 'WAITING' in cases where the email isn't
provided.

chris

On Thu, 2010-03-04 at 09:30 -0600, Chris Fields wrote:
> Palani,
> 
> We have a few regression tests that should have caught this but aren't
> quite set up correctly (they silently pass if no report is returned).
> This may be smoething on NCBI's end though; any remote database or
> analyses are notoriously brittle, hence the need to skip these by
> default when installing tests.
> 
> Final note, but hopefully you aren't using bioperl 1.4 (as indicated by
> the docs).  We're now on the 1.6 release series and are now on v. 1.6.1;
> 1.4 isn't supported anymore.
> 
> chris
> 
> On Thu, 2010-03-04 at 14:40 +0000, Jason Stajich wrote:
> > Palani -
> > This should be directed to the mailing list.
> > 
> > -------- Original Message --------
> > From: 	PalaniKannan K <kpalanikannan at gmail.com>
> > Subject: 	Enquiry about Remoteblast.pm
> > Date: 	Thu, 4 Mar 2010 10:23:45 +0530
> > 
> > 	
> > 
> > 
> > 
> > I am using nr, CDD/CDSearch KOG, CDD/CDSearch PFAM. I am accessing through
> > Remoteblast.pm script available through CPAN. When i am submitting my
> > query... it shows waiting for much time. Ex. (waiting .....................)
> > 
> > http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/RemoteBlast.html
> > 
> > This is the reference script i am using through Remoteblast perl module.
> > 
> > It worked upto last 02/03/2010. Now it is not working
> > 
> > We had developed 3 applications using this module. The same error comes in 3
> > applications we developed. So, i confim that our script dont have problem.
> > Kindly help me in this regard.
> > 
> > --
> > With Regards,
> > palani kannan. k
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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