[Bioperl-l] Version bug in GFF, bioperl 1.2.2

[Lincoln Stein]

Very unfortunate.  This will be fixed in bioperl 1.3, or I can change ldas now 
to ignore the version string.  Should I do that?

Lincoln


On Wednesday 16 July 2003 06:30 am, Andreas Kahari wrote:
> Hi list,
>
> When installing LDasServer-1.11, and using bioperl 1.2.2, you
> will get
>
> Warning: prerequisite Bio::DB::GFF 1.02 not found. We have unknown version.
>
> .. which also prevents the DAS server from running (apache error log):
>
> Bio::DB::GFF does not define $Bio::DB::GFF::VERSION--version check failed
> at /var/www/cgi-bin/das line 15. BEGIN failed--compilation aborted at
> /var/www/cgi-bin/das line 15. [Wed Jul 16 10:19:11 2003] [error] [client
> 127.0.0.1] Premature end of script headers: /var/www/cgi-bin/das
>
>
> This is because the $VERSION string was taken out of GFF.pm.
>
> The following patch to the GFF.pm module solves it (version 1.04
> was the version of GFF in bioperl 1.2.1):
>
>
> --- GFF.pm.orig    Sat Jul  5 01:52:30 2003
> +++ GFF.pm      Wed Jul 16 11:21:15 2003
> @@ -455,8 +455,10 @@
>  use Bio::DasI;
>  use Bio::Root::Root;
>
> -use vars qw(@ISA);
> +use vars qw(@ISA $VERSION);
>  @ISA = qw(Bio::Root::Root Bio::DasI);
> +
> +$VERSION = 1.04;
>
>  my %valid_range_types = (overlaps     => 1,
>                          contains     => 1,
>
>
> Cheers,
> Andreas

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