[Bioperl-l] plenty of tests fail on the main trunk

[Jason Stajich]

On Wed, 26 Feb 2003, Hilmar Lapp wrote:

> Failed Test           Stat Wstat Total Fail  Failed  List of Failed
> ------------------------------------------------------------------------
> -------
> t/BioGraphics.t                     17    1   5.88%  2
works for me as-is...
> t/Exception.t            2   512     8    8 100.00%  1-8
> t/LocusLink.t          255 65280    23   21  91.30%  3-23
> t/PhylipDist.t         255 65280    18    0   0.00%  ??
fixed
> t/PopGen.t               2   512    25    3  12.00%  23-25
fixed
> t/SeqFeatCollection.t              428   ??       %  ??
fixed
> t/flat.t                 2   512    13   13 100.00%  1-13
in progress - some more things are broken when I fix the initial bit

We should also really be testing the branch if we want to try and release
a 1.2.1 soon.

-j

>
> I am going to fix the failure in LocusLink.t, which is due to my local
> changes and shouldn't be visible to anyone else anyway. All others seem
> to be unrelated to what I'm hacking here:
>
> t/BioGraphics................FAILED test 2
>          Failed 1/17 tests, 94.12% okay
>
> t/Exception..................Can't locate TestObject.pm in @INC (@INC
> contains: t ./scripts/exceptions . blib/arch blib/lib
> /System/Library/Perl/darwin /System/Library/Perl /sw/lib/perl5/darwin
> /sw/lib/perl5 /Library/Perl/darwin /Library/Perl
> /Network/Library/Perl/darwin /Network/Library/Perl) at t/Exception.t
> line 35.
> BEGIN failed--compilation aborted at t/Exception.t line 35.
> t/Exception..................dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-8
>          Failed 8/8 tests, 0.00% okay
>
> (WTH is TestObject.pm??)
>
> t/PhylipDist.................Can't locate object method "_parse" via
> package "Bio::Matrix::PhylipDist" at blib/lib/Bio/Matrix/PhylipDist.pm
> line 118.
> t/PhylipDist.................dubious
>          Test returned status 255 (wstat 65280, 0xff00)
>          after all the subtests completed successfully
>
> t/PopGen.....................NOK 25
> ------------- EXCEPTION  -------------
> MSG: Could not open t/data/popgen_saureus.multidat for reading: No such
> file or directory
> STACK Bio::Root::IO::_initialize_io Bio/Root/IO.pm:260
> STACK Bio::Root::IO::new Bio/Root/IO.pm:206
> STACK Bio::PopGen::IO::new Bio/PopGen/IO.pm:108
> STACK Bio::PopGen::IO::new Bio/PopGen/IO.pm:121
> STACK toplevel t/PopGen.t:150
>
> --------------------------------------
> t/PopGen.....................dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 23-25
>          Failed 3/25 tests, 88.00% okay
>
> (someone forgot to commit a file??)
>
> t/SeqFeatCollection..........ok 432/428Don't know which tests failed:
> got 432 ok, expected 428
>
> t/flat.......................
> ------------- EXCEPTION  -------------
> MSG: Please supply a -dbname argument
> STACK Bio::DB::Flat::new blib/lib/Bio/DB/Flat.pm:135
> STACK toplevel t/flat.t:61
>
> --------------------------------------
> t/flat.......................dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-13
>          Failed 13/13 tests, 0.00% okay
>
> We've once had the rule that you only commit once tests pass, or you
> make an announcement on the list with good reasons why those tests are
> going to fail. Otherwise you owe beer. I don't know who's going to
> drink all that beer in Brisbane that accumulated over the last couple
> days, let alone who's going to buy it ...
>
> 	-hilmar
>

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