[Bioperl-l] failures on the stable branch

Wed Apr 21 23:43:15 EDT 2004

Thanks for your fixes Jason.

The DB.t failures were in fact sort-of my fault as I just realized, 
because I had forgotten to merge my fix for the range query from the 
main trunk to the branch (NCBI indeed changed the accepted date format).

In fact I had hesitated because I hoped part of the fixes would be 
temporary only (any change to the query result caused by changed data 
in the databank will cause some of the tests to fail), but given that 
nobody has time to come up with a more permanent solution for testing 
the range query I guess it is better to at least get rid of the error 
for the time being. So, I just did that. DB.t passes for me on the 
branch.

	-hilmar

On Wednesday, April 21, 2004, at 07:01  AM, Jason Stajich wrote:

> These are due to problems with Bio::DB::Query::GenBank
>
> setting the env variable BIOPERLDEBUG=1 will give more information.
>
>> ok 62 # could not connect to Genbank
>> ok 63 # could not connect to Genbank
>> ok 64 # could not connect to Genbank
>> ok 65 # could not connect to Genbank
>> ok 66 # could not connect to Genbank
>> ok 67 # could not connect to Genbank
>> ok 68 # could not connect to Genbank
>> ok 69 # could not connect to Genbank
>> ok 70 # could not connect to Genbank
>> ok 71 # could not connect to Genbank
>> ok 72 # could not connect to Genbank
>> ok 73 # could not connect to Genbank
>> ok 74 # could not connect to Genbank
>> ok 75 # could not connect to Genbank
>> ok 76 # could not connect to Genbank
>> ok 77 # could not connect to Genbank
>> ok 78 # could not connect to Genbank
>>
>>
>> t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta
>> cannot be found
>> Exception
>> ------------- EXCEPTION  -------------
>> MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate
>> Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t blib/arch
>> blib/lib /System/Library/Perl/darwin /System/Library/Perl
>> /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin
>> /sw/lib/perl5 /Library/Perl/darwin /Library/Perl
>> /Network/Library/Perl/darwin /Network/Library/Perl .) at
>> blib/lib/Bio/AlignIO/largemultifasta.pm line 69, <GEN32> line 28.
>> BEGIN failed--compilation aborted at
>> blib/lib/Bio/AlignIO/largemultifasta.pm line 69, <GEN32> line 28.
>> Compilation failed in require at blib/lib/Bio/Root/Root.pm line 394,
>> <GEN32> line 28.
>>
>> STACK Bio::Root::Root::_load_module blib/lib/Bio/Root/Root.pm:396
>> STACK (eval) blib/lib/Bio/AlignIO.pm:420
>> STACK Bio::AlignIO::_load_format_module blib/lib/Bio/AlignIO.pm:419
>> STACK Bio::AlignIO::new blib/lib/Bio/AlignIO.pm:347
>> STACK toplevel t/AlignIO.t:283
>>
>> --------------------------------------
>>
>> For more information about the AlignIO system please see the AlignIO
>> docs.
>> This includes ways of checking for formats at compile time, not run 
>> time
>> Can't call method "next_aln" on an undefined value at t/AlignIO.t line
>> 285, <GEN32> line 28.
>> t/AlignIO....................dubious
>>          Test returned status 2 (wstat 512, 0x200)
>> DIED. FAILED tests 76-80
>>          Failed 5/80 tests, 93.75% okay
>>
>> t/cigarstring................Can't use an undefined value as an ARRAY
>> reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, <GEN1>
>> line 434.
>> t/cigarstring................dubious
>>          Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 1-3
>>          Failed 3/3 tests, 0.00% okay
>>
> fixed
>>
>>
>> (* note: these are only warnings, although they don't leave you with
>> comfort *)
>> t/GFF........................ok 1/32Filehandle Symbol::GEN0 opened 
>> only
>> for output at blib/lib/Bio/Root/IO.pm line 440.
>> t/GFF........................ok 2/32Filehandle Symbol::GEN1 opened 
>> only
>> for output at blib/lib/Bio/Root/IO.pm line 440.
>> t/GFF........................ok
>>
> Added code from main trunk to quiet this
> local $^W=0;
>
> unless some has another way to see if fh is readable.
>
>> t/GeneCoordinateMapper.......ok 71/113
>> -------------------- WARNING ---------------------
>> MSG: sorted sublocation array requested but root location doesn't
>> define seq_id (at least one sublocation does!)
>> ---------------------------------------------------
>>
>> -------------------- WARNING ---------------------
>> MSG: sorted sublocation array requested but root location doesn't
>> define seq_id (at least one sublocation does!)
>> ---------------------------------------------------
>> t/GeneCoordinateMapper.......ok 98/113Use of uninitialized value in
>> concatenation (.) at blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
>> t/GeneCoordinateMapper.......ok
>
> fixed - this was a problem on main trunk too.
>>
>> _______________________________________________
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>> Bioperl-l at portal.open-bio.org
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>>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------