[Bioperl-l] Can't locate object method "is_compatible" via package "Bio::Tree::Tree"

Chris Fields cjfields at uiuc.edu
Thu Jan 17 08:25:41 EST 2008


Probably need to file this as a bug.  There is a similar issue with  
Bio::TreeIO::nexus, but it probably isn't related unless it is using  
the same parsing logic:

http://bugzilla.open-bio.org/show_bug.cgi?id=2356

chris

On Jan 17, 2008, at 5:18 AM, Sendu Bala wrote:

> viping wrote:
>> Hi Everyone,
>>
>> I'm using ActivePerl-5.8.8.822-MSWin32-x86-280952 + bioperl-1.5.2 +
>> Windows XP SP2. When running example codes(attched below as t.pl)
>> within Bio\Tree\Compatible.pm , I got this error:
>>
>> Can't locate object method "is_compatible" via package
>> "Bio::Tree::Tree"
>>
>> I replaced "$t1->is_compatible($t2)" with "is_compatible
>> Bio::Tree::Compatible ($t1,$t2)",
>
> Yup, you had the right idea; unfortunately the synopsis code for
> Bio::Tree::Compatible is wrong.
> I've now fixed it in svn.
>
>
>> the error changed: Can't locate object method "get_nodes" via package
>> "Bio::Tree::Compatible" at i:/Perl/site/lib/Bio/Tree/Compatible.pm
>> line 252, <GEN1> line 1.
>
> I didn't get quite that error; instead I had an issue with TreeIO: for
> whatever reason it is only returning one tree from your input file  
> (ie.
> $t2 is undefined).
>
> I therefore got "Can't call method "get_nodes" on an undefined value  
> [...]"
>
> Can someone look into/confirm that?
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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