[Bioperl-l] installation problems

[Richard Rouse]

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