[Bioperl-l] Windows Testing

Tue, 3 Dec 2002 17:45:03 -0500 (EST)

Win2k
PERL 5.6.1 ActiveState
Today's CVS

Annotation.t
============
ok 58
ok 59
Use of uninitialized value in pattern match (m//) at
C:/Perl/site/lib/Bio/Cluste
r/UniGene.pm line 258.
ok 60

XEMBL_DB.t
==========
1..9
Unrecognized escape \d passed through at C:/Perl/site/lib/XML/DOM.pm line
136.
ok 1
ok 2 # server may be down

index.t
=======
Note: I do indeed have all three externals available.

ok 9
ok 10
ok 11
ok 12 # Bio::DB::FileCache not loaded because one or more of Storable,
DB_File or File::Temp not installed

simpleGOparser.t
================
not ok 13
# Test 13 got: 'GO:0015034' (t\simpleGOparser.t at line 80)
#    Expected: 'GO:0018895'
not ok 14
# Test 14 got: 'GO:0018895' (t\simpleGOparser.t at line 81)
#    Expected: 'GO:0015034'
ok 15
not ok 16
# Test 16 got: 'GO:0015034' (t\simpleGOparser.t at line 88)
#    Expected: 'GO:0018895'
not ok 17
# Test 17 got: 'GO:0018895' (t\simpleGOparser.t at line 89)
#    Expected: 'GO:0015034'
ok 18
not ok 19
# Test 19 got: 'GO:0015034' (t\simpleGOparser.t at line 102)
#    Expected: 'GO:0018895'
not ok 20
# Test 20 got: 'GO:0018895' (t\simpleGOparser.t at line 103)
#    Expected: 'GO:0015034'
ok 21
ok 22
not ok 23
# Test 23 got: 'GO:0015034' (t\simpleGOparser.t at line 118)
#    Expected: 'GO:0003673'
ok 24
not ok 25
# Test 25 got: 'GO:0003673' (t\simpleGOparser.t at line 120)
#    Expected: 'GO:0015034'
ok 26
not ok 27
# Test 27 got: 'GO:0015034' (t\simpleGOparser.t at line 127)
#    Expected: 'GO:0003673'
ok 28
not ok 29
# Test 29 got: 'GO:0003673' (t\simpleGOparser.t at line 129)
#    Expected: 'GO:0015034'
ok 30
ok 31
not ok 32
# Test 32 got: 'GO:0030481' (t\simpleGOparser.t at line 143)
#    Expected: 'GO:0005811'
not ok 33
# Test 33 got: 'GO:0005811' (t\simpleGOparser.t at line 144)
#    Expected: 'GO:0030481'
ok 34
not ok 35
# Test 35 got: 'GO:0005625' (t\simpleGOparser.t at line 154)
#    Expected: 'GO:0005623'
not ok 36
# Test 36 got: 'GO:0005938' (t\simpleGOparser.t at line 155)
#    Expected: 'GO:0005933'
not ok 37
# Test 37 got: 'GO:0005937' (t\simpleGOparser.t at line 156)
#    Expected: 'GO:0005935'
not ok 38
# Test 38 got: 'GO:0005935' (t\simpleGOparser.t at line 157)
#    Expected: 'GO:0005938'
not ok 39
# Test 39 got: 'GO:0005933' (t\simpleGOparser.t at line 158)
#    Expected: 'GO:0005937'
not ok 40
# Test 40 got: 'GO:0005623' (t\simpleGOparser.t at line 159)
#    Expected: 'GO:0005625'
ok 41
not ok 42
# Test 42 got: 'GO:0000667' (t\simpleGOparser.t at line 167)
#    Expected: 'GO:0000666'
not ok 43
# Test 43 got: 'polarisomeY' (t\simpleGOparser.t at line 168)
#    Expected: 'polarisomeX'
not ok 44
# Test 44 got: 'GO:0000666' (t\simpleGOparser.t at line 169)
#    Expected: 'GO:0000667'
not ok 45
# Test 45 got: 'polarisomeX' (t\simpleGOparser.t at line 170)
#    Expected: 'polarisomeY'
ok 46
ok 47
ok 48
not ok 49
# Test 49 got: 'GO:0000300' (t\simpleGOparser.t at line 185)
#    Expected: 'GO:0005792'
not ok 50
# Test 50 got: 'peripheral membrane protein of membrane fraction'
(t\simpleGOparser.t at line 186)
#    Expected: 'microsome'
not ok 51
# Test 51 got: 'GO:0019717' (t\simpleGOparser.t at line 187)
#    Expected: 'GO:0000299'
not ok 52
# Test 52 got: 'synaptosome' (t\simpleGOparser.t at line 188)
#    Expected: 'integral membrane protein of membrane fraction'
ok 53
ok 54
ok 55
ok 56
not ok 57
# Test 57 got: 'GO:0000299' (t\simpleGOparser.t at line 193)
#    Expected: 'GO:0000300'
not ok 58
# Test 58 got: 'integral membrane protein of membrane fraction'
(t\simpleGOparse
r.t at line 194)
#    Expected: 'peripheral membrane protein of membrane fraction'
not ok 59
# Test 59 got: 'GO:0005792' (t\simpleGOparser.t at line 195)
#    Expected: 'GO:0019717'
not ok 60
# Test 60 got: 'microsome' (t\simpleGOparser.t at line 196)
#    Expected: 'synaptosome'
ok 61

BioDBGFF.t
==========
ok 2
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 1.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 1.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 2.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 3.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 4.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 5.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 9.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 9.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 10.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 10.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 11.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 11.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 12.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 13.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 14.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 15.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 16.
<and many more>

game.t
======
ok 19
ok 20
Use of uninitialized value in pattern match (m//) at
C:/Perl/site/lib/XML/Writer.pm line 307.
Use of uninitialized value in print at C:/Perl/lib/IO/Handle.pm line 394.
ok 21
ok 22

Eponine.t
=========
Note: I don't have the software installed, just ran the test to see how it
handled the problem.  The "old java version" statement isn't accurate.

1..5
Use of uninitialized value in numeric lt (<) at t\Eponine.t line 52,
<PIPE> line
 2.
You need at least version 1.2 of JDK to run eponine
ok 1 # Skipping due to old java version

Pise.t
======
Note: I don't have the software installed, just ran the test to see how it
handled me.

1..10
Subroutine stdout redefined at C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm
line 53
4.
Subroutine stderr redefined at C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm
line 56
3.
defined(%hash) is deprecated at C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm
line 9
83.
        (Maybe you should just omit the defined()?)
ok 1
ok 2
ok 3
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
Use of uninitialized value in concatenation (.) or string at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 1019.
Use of uninitialized value in concatenation (.) or string at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 1100.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125.
Use of uninitialized value in hash element at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
Use of uninitialized value in hash element at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 131.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125.
Use of uninitialized value in hash element at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125.
Use of uninitialized value in hash element at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
ok 4
ok 5
ok 6
ok 7
ok 8
Odd number of elements in hash assignment at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 982, <GEN8> line 290.
Use of uninitialized value in concatenation (.) or string at
C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 1100, <GEN8> line 290.
Use of uninitialized value in string eq at
C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125, <GEN8> line 290.
<many times>