[Bioperl-l] bioperl-1.5.0 RC2

[Aaron J. Mackey]

To be pedantic, you should use "perl -Mblib t\flat.t" to ensure that  
all the right "build lib" files are being used.  But it looks like part  
of the problem is a mismatch between the expected number of tests and  
the number of tests actually run ...

-Aaron

On Jan 13, 2005, at 2:49 PM, 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
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--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
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