[Bioperl-l] Tons of test failing in bioperl-live

[Chris Fields]

All,

Just updated to the latest live today (both Mac OS X and Ubuntu 9.10) and found a ton of tests failing due to recent commits.  This isn't to say the commits were wrong or bad, as failures could just as easily indicate bad regression tests, but they do indicate *something* needs to be addressed.  We still have a lot of users unfortunately pulling from svn due to GBrowse2 bug fixes. Please make sure to run tests prior to committing to trunk, particularly if you are making changes to commonly used modules (SeqIO, LocatableSeq, etc), and address problems if they pop up.  If tests are failing, having a discussion on list as to the reasons why is a good thing.

Also, with this in mind, please make sure to retain the previous API as much as possible.  The recent commits to SeqIO re: optionally returning a PrimarySeq now fundamentally change the returned object to a Bio::PrimarySeq by default (i.e. is-not-a Bio::SeqI).  A significant subset of the trunk failures are due to this fundamental change in behavior.  Running tests prior to the commit would have caught this out, and we could have discussed it more on list.  

These, and other failed tests, should be addressed in some way so tests pass accordingly (and new tests for the optional Bio::PrimarySeq behavior would be a good thing too).  I'll do my best to dig in and fix a few as well.

chris

Latest test run on bioperl-live (Mac OS X):

Test Summary Report
-------------------
t/Assembly/Assembly.t                      (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: No plan found in TAP output
t/Assembly/ContigSpectrum.t                (Wstat: 1024 Tests: 188 Failed: 4)
  Failed tests:  153, 155, 168, 170
  Non-zero exit status: 4
t/LocalDB/Flat.t                           (Wstat: 6400 Tests: 4 Failed: 1)
  Failed test:  4
  Non-zero exit status: 25
  Parse errors: Bad plan.  You planned 24 tests but ran 4.
t/LocalDB/Index/Index.t                    (Wstat: 1024 Tests: 64 Failed: 4)
  Failed tests:  10, 12, 14, 20
  Non-zero exit status: 4
t/LocalDB/Registry.t                       (Wstat: 2304 Tests: 13 Failed: 1)
  Failed test:  13
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 14 tests but ran 13.
t/LocalDB/transfac_pro.t                   (Wstat: 65280 Tests: 67 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 115 tests but ran 67.
t/Map/Map.t                                (Wstat: 1536 Tests: 267 Failed: 6)
  Failed tests:  249, 262-264, 266-267
  Non-zero exit status: 6
t/Perl.t                                   (Wstat: 768 Tests: 29 Failed: 3)
  Failed tests:  3, 7-8
  Non-zero exit status: 3
t/RemoteDB/BioFetch.t                      (Wstat: 1024 Tests: 36 Failed: 4)
  Failed tests:  18, 21-23
  Non-zero exit status: 4
t/RemoteDB/HIV/HIVQuery.t                  (Wstat: 2304 Tests: 35 Failed: 0)
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 41 tests but ran 35.
t/SearchIO/SimilarityPair.t                (Wstat: 65280 Tests: 10 Failed: 1)
  Failed test:  4
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 12 tests but ran 10.
t/SearchIO/Tiling.t                        (Wstat: 256 Tests: 1097 Failed: 1)
  Failed test:  1095
  Non-zero exit status: 1
t/Seq/PrimedSeq.t                          (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 10 tests but ran 2.
t/SeqFeature/SeqAnalysisParser.t           (Wstat: 2304 Tests: 5 Failed: 0)
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 14 tests but ran 5.
t/SeqFeature/SeqFeature.t                  (Wstat: 256 Tests: 222 Failed: 1)
  Failed test:  86
  Non-zero exit status: 1
t/SeqIO/seqxml.t                           (Wstat: 2304 Tests: 45 Failed: 2)
  Failed tests:  15, 36
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 58 tests but ran 45.
t/SeqTools/GuessSeqFormat.t                (Wstat: 256 Tests: 52 Failed: 1)
  Failed test:  12
  Non-zero exit status: 1
t/Tools/Run/WBCommandExts.t                (Wstat: 256 Tests: 22 Failed: 1)
  Failed test:  22
  Non-zero exit status: 1
t/Tools/ePCR.t                             (Wstat: 2304 Tests: 7 Failed: 0)
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 27 tests but ran 7.
Files=341, Tests=21416, 439 wallclock secs ( 3.52 usr  1.67 sys + 133.53 cusr 16.14 csys = 154.86 CPU)
Result: FAIL
Failed 19/341 test programs. 30/21416 subtests failed.