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

Chris Fields cjfields at uiuc.edu
Fri Oct 26 08:51:26 EDT 2007

On Oct 26, 2007, at 5:10 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>> I was looking at the Gumby runnable, which is pretty cool. But I got
>> an error 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...
> No, most likely this is another thing broken by the SeqFeature  
> changes.
> I'm going to go ahead and try out some of my proposals in the
> 'Bio::SeqFeature::Annotated API change' thread.

I was able to repeat it on my end.  If you have a fix for it  
involving B::SF::A then definitely go ahead.


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