[Bioperl-l] Small bug in Bio::Tools::GFF.pm - Target output

Sendu Bala bix at sendu.me.uk
Thu Apr 19 08:17:19 EDT 2007


Don Gilbert wrote:
> Dear Bioperl list,
> 
> There is a small bug in what I think is the current Bio::Tools::GFF.pm,
> that blocks output of Target attributes (in gff3 at least).  See a patch
> here
> 
> http://wiki.gmod.org/index.php/Load_BLAST_Into_Chado#Convert_BLAST_analysis_to_GFF

The patch was applied by Brian but is currently generating this warning:

./Build test --test_files t/GbrowseGFF.t --verbose
t/GbrowseGFF....1..5
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::GbrowseGFF;
ok 3 - use Bio::Root::IO;
ok 4
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
Use of uninitialized value in sprintf at 
/.../core/blib/lib/Bio/Tools/GFF.pm line 1020, <GEN1> line 193.
ok 5
ok
All tests successful.

Can this patch be looked at again and rolled-back if the problem can't 
be fixed?


Cheers,
Sendu.


More information about the Bioperl-l mailing list