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

[Andreas Kahari]

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

-- 
a n d r e (  Andreas Kähäri                           ) 0 1 0 0 0
a s . k a  ) EMBL, European Bioinformatics Institute (  1 0 0 0 1
h a r i @ (  Wellcome Trust Genome Campus, Hinxton    ) 0 0 1 1 1
e b i . a  ) Cambridge, CB10 1SD                     (  0 0 1 0 0
c . u k   (  United Kingdom                           ) 0 0 0 1