[Bioperl-l] For CVS developers-potentialpitfall with "return undef"

Wed Jun 7 17:03:01 UTC 2006

Hi,

Just did a make test on bioperl-live on AIX 5.2.0.0 and perl 5.8.7 and I had a few 
failures:

Failed Test         Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/Annotation.t                    89    2  79 88
t/Biblio.t                        24    1  2
t/LocusLink.t                     23    1  23
t/PhysicalMap.t                   14    2  11-12
t/RepeatMasker.t                   6    3  1-2 6
t/StandAloneBlast.t               18    4  19-22
t/TaxonTree.t                     17   30  11 18-42
t/alignUtilities.t                 9    1  9
t/psm.t              255 65280    48   35  29 32-48
t/tutorial.t                      21   15  7-21

Not sure if any of these are related to the "return undef" changes, or are known.  I also 
had some warnings running BioGraphics.t

t/BioGraphics................Use of uninitialized value in numeric lt (<) at Bio/Graphics/
FeatureFile.pm line 547, <GEN0> line 61.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureFile.pm line 548, 
<GEN0> line 61.
Use of uninitialized value in numeric le (<=) at Bio/Graphics/FeatureFile.pm line 568, 
<GEN0> line 61.
Use of uninitialized value in numeric le (<=) at Bio/Graphics/FeatureFile.pm line 568, 
<GEN0> line 61.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureFile.pm line 569, 
<GEN0> line 61.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureFile.pm line 569, 
<GEN0> line 61.
Use of uninitialized value in numeric lt (<) at Bio/Graphics/FeatureBase.pm line 170, 
<GEN0> line 61.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureBase.pm line 171, 
<GEN0> line 61.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureFile.pm line 548, 
<GEN0> line 62.
Use of uninitialized value in numeric le (<=) at Bio/Graphics/FeatureFile.pm line 568, 
<GEN0> line 62.
Use of uninitialized value in numeric le (<=) at Bio/Graphics/FeatureFile.pm line 568, 
<GEN0> line 62.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureFile.pm line 569, 
<GEN0> line 62.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureFile.pm line 569, 
<GEN0> line 62.
Use of uninitialized value in numeric lt (<) at Bio/Graphics/FeatureBase.pm line 170, 
<GEN0> line 62.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureBase.pm line 171, 
<GEN0> line 62.
Use of uninitialized value in numeric lt (<) at Bio/Graphics/FeatureBase.pm line 170, 
<GEN0> line 62.
Use of uninitialized value in numeric gt (>) at Bio/Graphics/FeatureBase.pm line 171, 
<GEN0> line 62.
t/BioGraphics................ok

I also ran the tests manually and below I've attached what came out (doesn't always agree 
with the results of make test, and in a few cases (e.g. tutorial.t or StandAloneBlast.t) 
there were no errors running the tests manually.
Paul

Annotation.t
============
not ok 8
# Test 8 got: '' (t/Annotation.t at line 59)
#   Expected: '0'

not ok 71
# Test 71 got: 'dumpster|test case|Ann:00001' (t/Annotation.t at line 187)
#    Expected: 'dumpster|test case|'

not ok 79
# Failed test 79 in t/Annotation.t at line 217

ok 85
Use of uninitialized value in concatenation (.) or string at /db2blast/Paul/perl5.8.7/lib/
site_perl/5.8.7/Bio/Annotation/Annot
ationFactory.pm line 236.

------------- EXCEPTION  -------------
MSG: Bio::AnnotationI implementation Bio::Annotation:: failed to load:
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::Annotation::. Can't locate Bio/Annotation/.pm in @INC 
(@INC contains: t /db2blast/Paul/perl5.8
.7/lib/5.8.7/aix /db2blast/Paul/perl5.8.7/lib/5.8.7 /db2blast/Paul/perl5.8.7/lib/
site_perl/5.8.7/aix /db2blast/Paul/perl5.8.7/
lib/site_perl/5.8.7 /db2blast/Paul/perl5.8.7/lib/site_perl .) at /db2blast/Paul/perl5.8.7/
lib/site_perl/5.8.7/Bio/Root/Root.pm
 line 396.

STACK Bio::Root::Root::_load_module /db2blast/Paul/perl5.8.7/lib/site_perl/5.8.7/Bio/Root/
Root.pm:398
STACK (eval) /db2blast/Paul/perl5.8.7/lib/site_perl/5.8.7/Bio/Annotation/
AnnotationFactory.pm:149
STACK Bio::Annotation::AnnotationFactory::create_object /db2blast/Paul/perl5.8.7/lib/
site_perl/5.8.7/Bio/Annotation/Annotation
Factory.pm:148
STACK toplevel t/Annotation.t:237
--------------------------------------

STACK Bio::Annotation::AnnotationFactory::create_object /db2blast/Paul/perl5.8.7/lib/
site_perl/5.8.7/Bio/Annotation/Annotation
Factory.pm:152
STACK toplevel t/Annotation.t:237
--------------------------------------

PhysicalMap.t
=============
not ok 11
# Test 11 got: <UNDEF> (t/PhysicalMap.t at line 55)
#    Expected: '0' (code holds and returns a string, definition requires a boolean)
not ok 12
# Test 12 got: '3' (t/PhysicalMap.t at line 56)
#    Expected: '1' (code holds and returns a string, definition requires a boolean)

TaxonTree.t
===========
ok 10
Use of uninitialized value in string eq at /db2blast/Paul/perl5.8.7/lib/site_perl/5.8.7/
Bio/Taxonomy/Taxon.pm line 559.
not ok 11
# Test 11 got: <UNDEF> (t/TaxonTree.t at line 35)
#    Expected: 'species'
ok 12 # foo is not a rank, class variable @RANK not initialised
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
Can't use string ("this could be anything") as a HASH ref while "strict refs" in use at /
db2blast/Paul/perl5.8.7/lib/site_perl
/5.8.7/Bio/Taxonomy/Taxon.pm line 452.

alignUtilities.t
================
ok 6

-------------------- WARNING ---------------------
MSG: Replacing one sequence [n1/1-36]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Replacing one sequence [n1/1-36]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Replacing one sequence [n1/1-36]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Replacing one sequence [n1/1-36]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Replacing one sequence [n1/1-36]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Replacing one sequence [n1/1-36]
---------------------------------------------------
ok 7
ok 8
not ok 9
# Test 9 got: '1' (t/alignUtilities.t at line 53)
#   Expected: '3'

RepeatMasker.t
==============
t/RepeatMasker...............FAILED tests 1-2, 6
        Failed 3/6 tests, 50.00% okay

StandAloneBlast.t
=================
t/StandAloneBlast............FAILED tests 19-22
        Failed 4/18 tests, 77.78% okay

psm.t
=====
t/Pseudowise.................ok
t/psm........................NOK 29Illegal division by zero at t/psm.t line 147, <GEN1> 
line 36.
t/psm........................dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 29, 32-48
        Failed 18/48 tests, 62.50% okay
t/QRNA.......................ok

tutorial.t
==========
t/tutorial...................ok 5/21
The following numeric arguments can be passed to run the corresponding demo-script.
1  => sequence_manipulations
2  => seqstats_and_seqwords
3  => restriction_and_sigcleave
4  => other_seq_utilities
5  => run_perl
6  => searchio_parsing
8  => hmmer_parsing
9  => simplealign
10 => gene_prediction_parsing
11 => access_remote_db
12 => index_local_db
13 => fetch_local_db    (NOTE: needs to be run with demo 12)
14 => sequence_annotation
15 => largeseqs
16 => liveseqs
17 => run_struct
18 => demo_variations
19 => demo_xml
20 => run_tree
21 => run_map
22 => run_remoteblast
23 => run_standaloneblast
24 => run_clustalw_tcoffee
25 => run_psw_bl2seq

In addition the argument "100" followed by the name of a single
bioperl object will display a list of all the public methods
available from that object and from what object they are inherited.

Using the parameter "0" will run all the tests that do not require
external programs (i.e. tests 1 to 22).
Using any other argument (or no argument) will run this display.

So typical command lines might be:
To run all core demo scripts:
 > perl -w  bptutorial.pl 0
or to just run the local indexing demos:
 > perl -w  bptutorial.pl 12 13
or to list all the methods available for object Bio::Tools::SeqStats -
 > perl -w  bptutorial.pl 100 Bio::Tools::SeqStats

t/tutorial...................FAILED tests 7-21
        Failed 15/21 tests, 28.57% okay

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho
> Sent: Wednesday, June 07, 2006 4:58 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] For CVS developers-
> potentialpitfallwith"returnundef"
> 
> Committed.
> 
> Please report any surprising changes in functionality to the list.
> 
> -Heikki
> 