[Bioperl-l] bioperl-run gumby tests fail for me

Albert Vilella avilella at gmail.com
Fri Oct 26 05:33:09 EDT 2007

Hi all,

I was looking at the Gumby runnable, which is pretty cool. But I got an
when running the tests (see below). Can other people reproduce this?

It seems to me that the runnable is expecting a tree object, not the
filename for a tree...

avilella at magneto:~/bioperl/vanilla/bioperl-run$ perl t/Gumby.t
ok 1 - use Bio::Tools::Run::Phylo::Gumby;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::TreeIO;
ok 4 - use Bio::DB::Taxonomy;
ok 5 - use Bio::Tools::GFF;
ok 6 - Found input alignment file
ok 7 - Found input tree file
ok 8 - Found input gff file
ok 9 - The object isa Bio::Tools::Run::Phylo::Gumby
ok 10 - has a created method not in args
ok 11 - quiet was set
ok 12 - program_dir returned correct default
ok 13 - Correct exe default name
Can't call method "value" without a package or object reference at
/home/avilella/bioperl/vanilla/bioperl-live/Bio/Tools/Phylo/Gumby.pm line
136, <GEN2> line 6.
# Looks like you planned 124 tests but only ran 13.
# Looks like your test died just after 13.

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