[Bioperl-l] failing tests and dubious warnings

Sun Apr 17 10:58:02 EDT 2005

On Apr 17, 2005, at 10:46 AM, Brian Osborne wrote:

> Hilmar,
>
> Cygwin 5.1, Perl 5.8.6.
>
> Index.t and LocationFactory.t pass, I don't see the errors you see.
>
> I see the same errors as you with PopGen.t. I also see those same  
> warnings
> with masta.t, FeatureIO, and primer3.
>
popgen error is due to something I changed in tree objects I'll fix the  
test soon.

> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: Saturday, April 16, 2005 8:36 PM
> To: Bioperl
> Subject: [Bioperl-l] failing tests and dubious warnings
>
>
> This is using a fresh checkout of the cvs HEAD of the main trunk. The
> following tests fail for me on Mac OSX 10.2.8 and perl 5.6.0.
>
> Could please somebody on another platform (likely many ;) check whether
> this is my setup that tickles it or whether it can be reproduced on
> other platforms. I'd rather not start hunting down peculiar problems
> restricted to perl 5.6.0 or something related to it.
>
> Failed Test           Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> -
> -------
> t/BioFetch_DB.t                     27    1   3.70%  8
> t/Index.t               79 20224    47    0   0.00%  ??
> t/LocationFactory.t                179    2   1.12%  178-179
> t/PopGen.t                          85    2   2.35%  82-83
>
> Details:
>
> t/BioFetch_DB.t: probably a time out, I won't bother for now. (even
> though I can reproduce this on every run!)
>
> t/Index.t:
>
> t/Index......................ok 18/47
> ------------- EXCEPTION  -------------
> MSG: Can't open 'DB_File' dbm file 'Wibbl4' : Inappropriate file type
> or format
> STACK Bio::Index::Abstract::open_dbm blib/lib/Bio/Index/Abstract.pm:385
> STACK Bio::Index::Abstract::new blib/lib/Bio/Index/Abstract.pm:149
> STACK Bio::Index::AbstractSeq::new blib/lib/Bio/Index/AbstractSeq.pm:91
> STACK toplevel t/Index.t:112
>
> --------------------------------------
> t/Index......................dubious
>          Test returned status 79 (wstat 20224, 0x4f00)
>          after all the subtests completed successfully
>
> Does this suggest anything to anyone? I've never had this test fail
> before.
>
> t/LocationFactory.t:
>
> t/LocationFactory............ok 177/179Use of uninitialized value in
> substitution (s///) at blib/lib/Bio/Factory/FTLocationFactory.pm line
> 169.
> Argument "complement(315036" isn't numeric in numeric gt (>) at
> blib/lib/Bio/Factory/FTLocationFactory.pm line 254.
> Argument "complement(315036" isn't numeric in numeric gt (>) at
> blib/lib/Bio/Location/Atomic.pm line 101.
> Argument "complement(315036" isn't numeric in numeric eq (==) at
> blib/lib/Bio/Location/Simple.pm line 315.
> t/LocationFactory............NOK 178Argument "complement(314652" isn't
> numeric in numeric gt (>) at blib/lib/Bio/Factory/FTLocationFactory.pm
> line 254.
> Argument "complement(314652" isn't numeric in numeric gt (>) at
> blib/lib/Bio/Location/Atomic.pm line 101.
> Argument "complement(314652" isn't numeric in numeric eq (==) at
> blib/lib/Bio/Location/Simple.pm line 315.
> t/LocationFactory............FAILED tests 178-179
>          Failed 2/179 tests, 98.88% okay
>
> t/PopGen.t:
>
> # Test 82 got: '89' (t/PopGen.t at line 432)
> #    Expected: '90'
> not ok 83
> # Test 83 got: 'NA07000' (t/PopGen.t at line 433)
> #    Expected: 'NA06994'
>
> Also, the following tests clutter the screen with various warnings that
> don't look entirely innocuous:
>
> t/FeatureIO..................ok 15/22
> -------------------- WARNING ---------------------
> MSG: '##feature-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: '##attribute-ontology' directive handling not yet implemented
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: '##source-ontology' directive handling not yet implemented
> ---------------------------------------------------
> t/FeatureIO..................ok 19/22
> -------------------- WARNING ---------------------
> MSG: Bio::SeqFeature::Annotated=HASH(0x863674) does not implement
> Bio::SeqFeatureI, ignoring.
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: Bio::SeqFeature::Annotated=HASH(0x855174) does not implement
> Bio::SeqFeatureI, ignoring.
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: Bio::SeqFeature::Annotated=HASH(0x8607c0) does not implement
> Bio::SeqFeatureI, ignoring.
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: Bio::SeqFeature::Annotated=HASH(0x85f82c) does not implement
> Bio::SeqFeatureI, ignoring.
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: Bio::SeqFeature::Annotated=HASH(0x8639f8) does not implement
> Bio::SeqFeatureI, ignoring.
> ---------------------------------------------------
> t/FeatureIO..................ok
>
> t/masta......................ok 3/16Use of uninitialized value in
> addition (+) at blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 222, <GEN1>
> line 10.
> Use of uninitialized value in addition (+) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 222, <GEN1> line 10.
> Use of uninitialized value in addition (+) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 222, <GEN1> line 10.
> Use of uninitialized value in numeric eq (==) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 226, <GEN1> line 10.
> # these are repeated many more times but cut here
> masta......................ok 14/16Use of uninitialized value in
> pattern match (m//) at blib/lib/Bio/Matrix/PSM/IO/masta.pm line 193,
> <GEN5> line 63.
> Use of uninitialized value in addition (+) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 222, <GEN5> line 63.
> Use of uninitialized value in addition (+) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 222, <GEN5> line 63.
> Use of uninitialized value in addition (+) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 222, <GEN5> line 63.
> Use of uninitialized value in numeric eq (==) at
> blib/lib/Bio/Matrix/PSM/SiteMatrix.pm line 226, <GEN5> line 63.
> # these are repeated many more times but cut here
> t/masta......................ok
>
> t/primer3....................ok 10/10Use of uninitialized value in
> pattern match (m//) at blib/lib/Bio/Seq/PrimedSeq.pm line 267, <GEN0>
> line 103.
> Use of uninitialized value in pattern match (m//) at
> blib/lib/Bio/Seq/PrimedSeq.pm line 267, <GEN0> line 103.
> Use of uninitialized value in pattern match (m//) at
> blib/lib/Bio/Seq/PrimedSeq.pm line 267, <GEN0> line 103.
> Use of uninitialized value in pattern match (m//) at
> blib/lib/Bio/Seq/PrimedSeq.pm line 267, <GEN0> line 103.
> Use of uninitialized value in pattern match (m//) at
> blib/lib/Bio/Seq/PrimedSeq.pm line 267, <GEN0> line 103.
> Use of uninitialized value in pattern match (m//) at
> blib/lib/Bio/Seq/PrimedSeq.pm line 267, <GEN0> line 103.
> t/primer3....................ok
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
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