[Bioperl-l] bioperl-1.5.0 RC2

[Nathan Haigh]

I'm a little confused about what your results are from. Obviously the failed test table was from an "nmake test".
However, it appears that you then did a "perl t\flat.t" why? Was it to get the full details of that particular test? If so you need
to run:
"perl -I. -w t\flat.t"
The -I. ensures you use the bioperl modules from the bioperl-1.5.0-RC2 not your installed version of bioperl (which may be 1.4 or
from the cvs). Also make sure that you are running from a path that contains no spaces - it appears as though you unpacked the
contents of bioperl-1.5.0-RC2 into a folder called "New Folder", this path contains a space, so may (and probably will) cause
unexpected effects/results.

Nathan

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Eric Just
> Sent: 13 January 2005 16:59
> To: Jason Stajich; Bioperl list
> Subject: Re: [Bioperl-l] bioperl-1.5.0 RC2
> 
> 
> 
> 
> activestate 5.8, windows XP
> 
> Failed Test  Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t\Registry.t  255 65280    13   11  84.62%  8-13
> t\flat.t        2   512    16   30 187.50%  2-16
> 4 subtests skipped.
> Failed 2/193 test scripts, 98.96% okay. 21/8916 subtests failed, 99.76% okay.
> 
> D:\tmp\New Folder\bioperl-1.5.0-RC2>perl t/flat.t
> 1..16
> ok 1
> 
> ------------- EXCEPTION  -------------
> MSG: flat file D:\tmp\New Folder\bioperl-1.5.0-RC2\tmpNew cannot be read:
> No such file or directory
> STACK Bio::DB::Flat::add_flat_file D:/Perl/site/lib/Bio/DB/Flat.pm:358
> STACK Bio::DB::Flat::_path2fileno D:/Perl/site/lib/Bio/DB/Flat.pm:519
> STACK Bio::DB::Flat::BDB::_index_file D:/Perl/site/lib/Bio/DB/Flat/BDB.pm:228
> STACK Bio::DB::Flat::BDB::build_index D:/Perl/site/lib/Bio/DB/Flat/BDB.pm:218
> STACK toplevel t/flat.t:70
> 
> --------------------------------------
> 
> D:\tmp\New Folder\bioperl-1.5.0-RC2>perl t/Registry.t
> 1..13
> ok 1
> ok 2
> ok 3 # DB_File or BerkeleyDB not found, skipping DB_File tests
> ok 4 # DB_File or BerkeleyDB not found, skipping DB_File tests
> This Perl doesn't implement function getpwuid(). Skipping...
> 
> -------------------- WARNING ---------------------
> MSG: Couldn't call new_from_registry on [Bio::DB::Flat]
> 
> ------------- EXCEPTION  -------------
> MSG: No flatfile fileid files in config - check the index has been made
> correctly
> STACK Bio::DB::Flat::BinarySearch::read_config_file
> D:/Perl/site/lib/Bio/DB/Flat/BinarySearch.pm:1297
> STACK Bio::DB::Flat::BinarySearch::new
> D:/Perl/site/lib/Bio/DB/Flat/BinarySearch.pm:280
> STACK Bio::DB::Flat::new D:/Perl/site/lib/Bio/DB/Flat.pm:181
> STACK Bio::DB::Flat::new_from_registry D:/Perl/site/lib/Bio/DB/Flat.pm:256
> STACK (eval) D:/Perl/site/lib/Bio/DB/Registry.pm:184
> STACK Bio::DB::Registry::_load_registry D:/Perl/site/lib/Bio/DB/Registry.pm:183
> STACK Bio::DB::Registry::new D:/Perl/site/lib/Bio/DB/Registry.pm:96
> STACK toplevel t/Registry.t:69
> 
> --------------------------------------
> 
> ---------------------------------------------------
> ok 5
> ok 6
> ok 7
> not ok 8
> # Failed test 8 in t/Registry.t at line 77
> Can't call method "seq" on an undefined value at t/Registry.t line 78.
> 
> D:\tmp\New Folder\bioperl-1.5.0-RC2>
> 
> 
> At 02:14 PM 1/12/2005, Jason Stajich wrote:
> >In preparation for Bioperl 1.5.0 developer release I have put up Release
> >Candidate 2.
> >
> >  http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.gz
> >  http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.bz2
> >  http://bioperl.org/DIST/bioperl-1.5.0-RC2.zip
> >
> >
> >We need people to test on this.  So download, run
> >  perl Makefile.PL
> >  make
> >  make test
> >
> >Let us know what breaks.  I've tested on OS X and few different linux
> >installs with different auxiliary modules installed.  Would be nice to
> >have a few more combinations of OS, perl versions, and suite of modules
> >installed before we make a release.
> >
> >Thanks for your help.
> >-jason
> >--
> >Jason Stajich
> >jason.stajich at duke.edu
> >http://www.duke.edu/~jes12/
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> ============================================
> 
> Eric Just
> e-just at northwestern.edu
> dictyBase Programmer
> Center for Genetic Medicine
> Northwestern University
> http://dictybase.org
> 
> ============================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
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