[Bioperl-l] FeatureIO tests failing on linux debian sarge

[Robert Buels]

I am stumped.  On a fresh checkout from cvs (as of like 10 seconds ago):


rob at rubisco:/usr/local/lib/site_perl/bioperl-live$ perl -v

This is perl, v5.8.4 built for i386-linux-thread-multi

Copyright 1987-2004, Larry Wall

Perl may be copied only under the terms of either the Artistic License 
or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using `man perl' or `perldoc perl'.  If you have access to the
Internet, point your browser at http://www.perl.com/, the Perl Home Page.

rob at rubisco:/usr/local/lib/site_perl/Bio$ perl t/FeatureIO.t
1..22
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
Can't locate object method "get_Annotations" via package 
"Bio::SeqFeature::Annotated" at 
/usr/local/lib/site_perl/Bio/SeqFeature/Annotated.pm line 292, <GEN1> 
line 2.
ok 7 # Cannot complete FeatureIO tests
ok 8 # Cannot complete FeatureIO tests
ok 9 # Cannot complete FeatureIO tests
ok 10 # Cannot complete FeatureIO tests
ok 11 # Cannot complete FeatureIO tests
ok 12 # Cannot complete FeatureIO tests
ok 13 # Cannot complete FeatureIO tests
ok 14 # Cannot complete FeatureIO tests
ok 15 # Cannot complete FeatureIO tests
ok 16 # Cannot complete FeatureIO tests
ok 17 # Cannot complete FeatureIO tests
ok 18 # Cannot complete FeatureIO tests
ok 19 # Cannot complete FeatureIO tests
ok 20 # Cannot complete FeatureIO tests
ok 21 # Cannot complete FeatureIO tests
ok 22 # Cannot complete FeatureIO tests

However, same code runs fine on my debian unstable machine (perl 
5.8.8).  Perhaps this is a bug in debian stable's perl?

I did some poking around through the code, changing @ISA = qw/.../ to 
use base, switching the order of inclusion in the ISA at the top of 
Bio::SeqFeature::Annotated, no dice.

Anybody able to reproduce this?  Anyone have any ideas?

Rob

-- 
Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu