[Bioperl-l] installation problems

[Jason Stajich]

You upgraded your perl - did you reinstall Bioperl?

You might as well get bioperl 1.2.3 as well as it has several bugfixes.

-jason
On Wed, 15 Oct 2003, Richard Rouse wrote:

> Dear bioperl-db,
>
> I have mysql 3.23, slackware 8.1 and bioperl-1.2.2 I recently installed
> bioperl-db and it was working nicely until I updated perl from 5.8.0 to
> 5.8.1. Now I get errors when running make test and have problems with the
> load_seqdatabase.pl script:
>
> Using this command I get the following problem:
>
> perl ./load_seqdatabase.pl --host localhost --dbname biosql2 --dbuser
> richard --dbpass xxxx --lookup --safe --format genbank patent
> /home/richard/bioperl-1.2.2/bioperl-db/scripts/biosql/db/gbpat1.seq
>
>
>
> -------------------- WARNING ---------------------
> MSG: failed to load dbadaptor:
> ------------- EXCEPTION  -------------
> MSG: Failed to load module Bio::DB::BioSQL::DBAdaptor. Can't locate
> Bio/DB/DBAdaptorI.pm in @INC (@INC contains:
> /usr/local/lib/perl5/5.8.1/i686-linux /usr/local/lib/perl5/5.8.1
> /usr/local/lib/perl5/site_perl/5.8.1/i686-linux
> /usr/local/lib/perl5/site_perl/5.8.1 /usr/local/lib/perl5/site_perl .) at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioSQL/DBAdaptor.pm line 58.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioSQL/DBAdaptor.pm line 58.
> Compilation failed in require at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm line 407.
>
> STACK Bio::Root::Root::_load_module
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm:409
> STACK (eval) /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:155
> STACK Bio::DB::BioDB::_load_dbadaptor
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:154
> STACK Bio::DB::BioDB::new
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:121
> STACK toplevel ./load_seqdatabase.pl:353
>
> --------------------------------------
>
>
> ------------- EXCEPTION  -------------
> MSG: Failed to load module Bio::DB::BioSQL::dbadaptor. Can't locate
> Bio/DB/BioSQL/dbadaptor.pm in @INC (@INC contains:
> /usr/local/lib/perl5/5.8.1/i686-linux /usr/local/lib/perl5/5.8.1
> /usr/local/lib/perl5/site_perl/5.8.1/i686-linux
> /usr/local/lib/perl5/site_perl/5.8.1 /usr/local/lib/perl5/site_perl .) at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm line 407.
>
> STACK Bio::Root::Root::_load_module
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm:409
> STACK (eval) /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:155
> STACK Bio::DB::BioDB::_load_dbadaptor
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:154
> STACK Bio::DB::BioDB::new
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:121
> STACK toplevel ./load_seqdatabase.pl:353
>
> --------------------------------------
>
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: fatal: unable to load DBAdaptor for database:
> Bio::DB::BioSQL::{DBAdaptor,dbadaptor} all failed to load
> STACK Bio::DB::BioDB::new
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:122
> STACK toplevel ./load_seqdatabase.pl:353
>
> --------------------------------------
>
> Richard Rouse JD
> Rouse Patent Services
> USPTO Registered Patent Agent
> P.O. Box 948586
> La Jolla, CA 92037
> web: www.patentinformatics.com
> email: rjdrouse at patentinformatics.com
> phone: 619-846-8291
>
>
>
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> Bioperl-l at portal.open-bio.org
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu