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

[Jason Stajich]

On Mon, 15 Dec 2003, Koen van der Drift wrote:

> 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
 fixed - changed the test to be more lenient
> t/ESEfinder.t                12    4  33.33%  4-5 8 11
 i dunno - works fine for me right now - this depending on your network
  connection working
> t/RefSeq.t                   13    5  38.46%  4-7 9
  this also depends on network connection and the remote servers being up,
  worked for me
> t/Scansite.t    255 65280    12    0   0.00%  ??

  this one seems to hang for me - but gets to test 6 for me. also need
network connection

> t/game.t        255 65280    23   44 191.30%  2-23
  removed this now that sheldon has updated to apollo game
  and fixed the module - the old tests will not work.

For the devs:

We may need to think about how to set a flag for tests which should not
run when no network connecion is found (or perhaps not be run as part of
the default tests no matter what unless someone asks for them specifically
- this might save a lot of future pain).


> 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.
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu