[Bioperl-l] bioperl-1.5.0 RC2

Thu Jan 13 19:54:15 EST 2005

hey
It was the directory name.  I moved it up one directory and the tests 
worked.  My apologies.

Thanks for your responses.
Eric
At 01:49 PM 1/13/2005, Nathan Haigh wrote:
>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
>---
>avast! Antivirus: Outbound message clean.
>Virus Database (VPS): 0502-2, 11/01/2005
>Tested on: 13/01/2005 19:46:20
>avast! is copyright (c) 2000-2003 ALWIL Software.
>http://www.avast.com
>
>
>
>
>_______________________________________________
>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

============================================ 