[Bioperl-l] failing tests and dubious warnings

[Hilmar Lapp]

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
-------------------------------------------------------------