[Bioperl-l] some tests fail on Mac OS X

[Koen van der Drift]

Hi,

I checked out bioperl-live this afternoon (EST), so I would get the  
latest and greatest. However, I still get some tests that fail. Note  
that I did the tests while offline (I only have a modem at home).  
Here's some output:


Failed Test    Stat Wstat Total Fail  Failed  List of Failed
------------------------------------------------------------------------ 
-------
t/Coalescent.t               11    1   9.09%  9
t/ESEfinder.t                12    4  33.33%  4-5 8 11
t/RefSeq.t                   13    5  38.46%  4-7 9
t/Scansite.t    255 65280    12    0   0.00%  ??
t/game.t        255 65280    23   44 191.30%  2-23
17 subtests skipped.
Failed 5/179 test scripts, 97.21% okay. 32/8135 subtests failed, 99.61%  
okay.
make: *** [test_dynamic] Error 2
[ModusOperandi:~/Desktop/bioperl-live] koen%


When I am online, ESEFinder.t and RefSeq.t pass, the others still fail.



>>> % perl -I. -w t/ESEfinder.t

Using the command above I got more info on each failing tests:


[ModusOperandi:~/Desktop/bioperl-live] koen% perl -w -I. t/Coalescent.t
1..11
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
not ok 9
# Test 9 got: '' (t/Coalescent.t at line 67)
#   Expected: '1' (fu and li D*)
ok 10
ok 11

[ModusOperandi:~/Desktop/bioperl-live] koen% perl -w -I. t/game.t
1..23
Parameterless "use IO" deprecated at /sw/lib/perl5/XML/Writer.pm line 16
ok 1
Can't locate object method "next_primary_seq" via package  
"Bio::SeqIO::game" at t/game.t line 65.

[ModusOperandi:~/Desktop/bioperl-live] koen% perl -w -I. t/ESEfinder.t
1..12
ok 1
ok 2

-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::DNA::ESEfinder Request Error:
500 (Internal Server Error) Can't connect to exon.cshl.org:80 (Bad  
hostname 'exon.cshl.org')
Client-Date: Tue, 16 Dec 2003 00:48:44 GMT


---------------------------------------------------
ok 3
not ok 4
# Failed test 4 in t/ESEfinder.t at line 72
not ok 5
# Failed test 5 in t/ESEfinder.t at line 73
ok 6
ok 7
not ok 8
# Test 8 got: <UNDEF> (t/ESEfinder.t at line 76)
#   Expected: '41'
ok 9 # No network access - could not connect to ESEfinder server
ok 10
Use of uninitialized value in join or string at Bio/Seq/Meta/Array.pm  
line 434.
Use of uninitialized value in join or string at Bio/Seq/Meta/Array.pm  
line 434.
not ok 11
# Test 11 got: ' ' (t/ESEfinder.t at line 84)
#    Expected: '-3.221149 -1.602223'
ok 12

[ModusOperandi:~/Desktop/bioperl-live] koen% perl -w -I. t/RefSeq.t
1..13
ok 1
ok 2
ok 3
sleeping for 3 seconds
not ok 4
# Failed test 4 in t/RefSeq.t at line 78
not ok 5
# Failed test 5 in t/RefSeq.t at line 79
not ok 6
# Failed test 6 in t/RefSeq.t at line 80
not ok 7
# Failed test 7 in t/RefSeq.t at line 81
ok 8

-------------------- WARNING ---------------------
MSG: acc (NM_006732) does not exist
---------------------------------------------------
not ok 9
# Failed test 9 in t/RefSeq.t at line 97
ok 10 # Unable to RefSeq test - probably no network connection.
ok 11 # Unable to RefSeq test - probably no network connection.
ok 12 # Unable to RefSeq test - probably no network connection.
ok 13 # Unable to RefSeq test - probably no network connection.

[ModusOperandi:~/Desktop/bioperl-live] koen% perl -w -I. t/Scansite.t
1..12
Transliteration pattern not terminated at  
Bio/Tools/Analysis/Protein/Scansite.pm line 372.
Compilation failed in require at t/Scansite.t line 44.
ok 1 # unable to run all of the tests depending on web access
ok 2 # unable to run all of the tests depending on web access
ok 3 # unable to run all of the tests depending on web access
ok 4 # unable to run all of the tests depending on web access
ok 5 # unable to run all of the tests depending on web access
ok 6 # unable to run all of the tests depending on web access
ok 7 # unable to run all of the tests depending on web access
ok 8 # unable to run all of the tests depending on web access
ok 9 # unable to run all of the tests depending on web access
ok 10 # unable to run all of the tests depending on web access
ok 11 # unable to run all of the tests depending on web access
ok 12 # unable to run all of the tests depending on web access

[ModusOperandi:~/Desktop/bioperl-live] koen% perl -w -I. t/game.t
1..23
Parameterless "use IO" deprecated at /sw/lib/perl5/XML/Writer.pm line 16
ok 1
Can't locate object method "next_primary_seq" via package  
"Bio::SeqIO::game" at t/game.t line 65.


thanks,

- Koen.