[Bioperl-l] failures on the stable branch

[Hilmar Lapp]

On the latest update of the stable branch if you run the test suite you  
get a number of failures, some of them looking troubling to the  
uninitiated.

Given that we point people at downloading the current stable branch as  
a means of getting bug fixes early, in my opinion we should not aim any  
lower than that on the stable branch *all* tests pass at *any* time,  
with no exceptions. Also, modules should not be added on the stable  
branch, let alone an API be altered.

If you feel your module is warranted for being added to the branch as  
an exception, please *always* ask on the mailing list before adding it  
to the branch.

	-hilmar
--  
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

The failures:

Failed Test     Stat Wstat Total Fail  Failed  List of Failed
------------------------------------------------------------------------ 
-------
t/AlignIO.t        2   512    80   10  12.50%  76-80
t/DB.t                        78    9  11.54%  79-87
t/SearchIO.t                1145    9   0.79%  1146-1154
t/cigarstring.t  255 65280     3    6 200.00%  1-3

I fixed the AlignIO failure by removing the failing format as it is an  
added one, as opposed to adding the missing module on the branch. I  
also fixed the SearchIO failures by fixing the number of tests.

DB.t fails because it encounters more tests than announced. I don't  
know whether this is due to a query response having changed, or due to  
the connection failures. Note that unlike before these connection  
failures are reproducible and not intermittent.

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



(* 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

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