[Bioperl-l] remoteBlast problem

[Chris Fields]

1)  Before I get wound up in the obvious here, you need to upgrade to CVS;
RemoteBlast and SearchIO::blast were fixed post v.-1.5.1 (i.e. in CVS) to
account for changes in BLAST output at the NCBI

2)  The Bio::Tools::Run::StandAloneBlast.pm bit worried me a little, so I
did a little digging; that's a typo.  Now corrected in CVS, along with some
BPLite cruft left over.

3)  Speaking bluntly?  Come on.  The error is stated as plainly as possible.
No?  How about this (note the arrows):

-----------> **Warning**: Couldn't connect to NCBI with
-----------> Bio::Tools::Run::StandAloneBlast.pm!
-----------> Probably no network access.
             Skipping Test


Check your network connections, preferably AFTER you update to CVS.  It's
possible that it's a proxy issue, but that should also be fixed in CVS.

Chris


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Dongsheng Che
> Sent: Thursday, July 13, 2006 1:55 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] remoteBlast problem
> 
> To whom it may concern:
> 
> I'm trying to do blast search remotely, so I downloaded bioperl-1.5, and
> followed the installation procedure, ie, perl Makefile.PL, make, make
> test. make install. I know there are some installation failure during the
> installation.
> 
> Since my main purpose is to get remoteBlast worked, I don't want bother to
> figure out all failures. but I run remote Blast, it gave me some erorrs
> from examples (bptutorial).
> -------------------------------------------------------------
> Beginning run_remoteblast example...
> Use of uninitialized value in numeric lt (<) at bptutorial.pl line 3303.
> 
> 
> **Warning**: Couldn't connect to NCBI with
> Bio::Tools::Run::StandAloneBlast.pm!
> Probably no network access.
> Skipping Test
> ----------------------------------------------------------------
> 
> I wondering what cause the problem.
> 
> Thanks in advance!
> 
> Dongsheng
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