[Bioperl-l] indexing and accessing local database

[Qunfeng Dong]

> 
> What is the full version of perl i.e.
> % perl -v

 This is perl, v5.6.1 built for i386-linux

> 
> What version of bioperl?
> (if you don't know do this)
> % perldoc -m Bio::Seq | grep VERSION

use vars qw(@ISA $VERSION);
$VERSION = '1.0.1';


> 
> I'll guess that DB_File must not be installed correctly or something as
> this works on most linux+perl distributions out of the box.
> 
> What version of DB_File?
> (do this)
> % perldoc -m DB_File | grep VERSION
>

use vars qw($VERSION @ISA @EXPORT $AUTOLOAD $DB_BTREE $DB_HASH $DB_RECNO 
$VERSION = "1.75" ;
	BTREEVERSION
	HASHVERSION
  { XSLoader::load("DB_File", $VERSION)}
  { bootstrap DB_File $VERSION }


I installed the Bundle::Bioperl and Bioperl and the installation seemed to be
successful without any complains. 

 
> Are you getting a segfault or just an exception from bioperl?
> 
>


Just "Segmentational fault" without any other message

Qunfeng

 
> -jason
> 
> On Tue, 9 Jul 2002, Qunfeng Dong wrote:
> 
> > It's Linux and perl 5 (and when I install bioperl, perl is also installed)
> >
> >
> > > What operating system are you using and version of Perl?
> > >
> > > On Tue, 9 Jul 2002, Qunfeng Dong wrote:
> > >
> > > > Hi,
> > > >
> > > > I am trying to follow the sample code from
> > > >
http://bioperl.org/Core/POD/bptutorial.html#III_1_1_Accessing_remote_databas
> > > >
> > > > to build a local fasta sequence database
> > > >  #!/usr/bin/perl -w
> > > >  #scriptName - BuildIndex.pl
> > > >   use Bio::Index::Fasta; # using fasta file format
> > > >   $Index_File_Name = shift;
> > > >   $inx = Bio::Index::Fasta->new(
> > > >       -filename => $Index_File_Name,
> > > >       -write_flag => 1);
> > > >   $inx->make_index(@ARGV);
> > > >
> > > >
> > > > then I ran the script BuildIndex.pl as
> > > > % BuildIndex.pl indexName FastaSeqName
> > > > and I got Segmentation fault. Any idea why?
> > > >
> > > > Qunfeng Dong
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l@bioperl.org
> > > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > >
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason at cgt.mc.duke.edu
> > >
> > >
> >
> >
> > Qunfeng Dong, Ph.D
> > ZmDB Manager
> > 2104 Molecular Biology Building
> > Iowa State University
> > Ames, IA 50010
> >
> >
> >
> >
> >
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> 
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> Bioperl-l@bioperl.org
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> 


Qunfeng Dong, Ph.D
ZmDB Manager 
2104 Molecular Biology Building
Iowa State University
Ames, IA 50010