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

[Chris Fields]

I don't get any issues (all tests pass), except a few warning messages which
is normal; some ontology handlind not implemented.  

Usually when running tests I use 'perl -I. t/test.t' to force it to use the
core directory first.  You might try that to see if it 'fixes' the problem.
If it does, there may be another bioperl installation in @INC being used
instead of your current directory.  

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Robert Buels
> Sent: Thursday, July 06, 2006 8:25 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] FeatureIO tests failing on linux debian sarge
> 
> 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
> 
> 
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