[Bioperl-l] failures on the stable branch

Tue Apr 20 12:52:56 EDT 2004

On Tue, 20 Apr 2004, Hilmar Lapp wrote:

> 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
> -------------------------------------------------------------
>
I'll take a look at some of these this week. I might have inadvertantly
caused some of them, not sure.

> 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

I've tried to fix these - but perl doesn't let you ask if an already
opened filehandle is opened for reading - I have a fix on the main trunk
which traps the error though.

>
> 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
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu