[BioPerl] Re: [Bioperl-l] load_gff.pl error

[Lincoln Stein]

Hi Mark,

Oh dear.  I maligned you.  I personally broke the code in order to satisfy 
your request that load_gff() handle tied filehandles.  Now we both have to 
spend time in purgatory.

Lincoln

On Thursday 09 October 2003 04:54 pm, Mark Wilkinson wrote:
> Uh... no, you threatened me with purgatory if I broke the way data
> loading from filehandles worked - you said nothing about messing with
> ARGV ;-)
>
> .besides, it doesn't look like this error is my fault??  I don't see
> any code in there that came from my fingers.  do you know what bit of
> code I wrote that is causing that error?
>
> M
>
> On Thu, 2003-10-09 at 14:26, Lincoln Stein wrote:
> > The issue is fixed in bioperl live.
> >
> > Lincoln
> >
> > PS: Mark, remember when I told you that your soul would be consigned to
> > purgatory if you broke anything when you changed the ARGV handling? 
> > Well, it happened.
> >
> > On Thursday 09 October 2003 03:23 pm, Vamsi wrote:
> > > Hi,
> > >
> > > I am trying to use the load_gff.pl located in the Bio-DB-GFF/scripts
> > > directory of the bioperl-1.2.3 distribution.
> > >
> > > When I try
> > > "perl load_gff.pl --dsn dbi:mysql:XXX --user XXX --pass XXX a.gff"
> > >
> > > I get the error
> > >
> > > Can't use string ("ARGV") as a symbol ref while "strict refs" in use at
> > > /usr/perl5/site_perl/5.005/Bio/DB/GFF.pm line 2130.
> > >
> > > When I modify sub do_load_gff in GFF.pm by having as the first line
> > > "no strict 'refs';"
> > > the error disappears.
> > >
> > > Is this something anyone else has faced?
> > >
> > > Thanks,
> > > Vamsi
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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