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

Sendu Bala bix at sendu.me.uk
Thu Jan 17 06:18:56 EST 2008


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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