Release 1.6 Testing

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BioPerl Release 1.6.0 (BioPerl-core)

Links for installing BioPerl 1.6.0 can be found on the Release 1.6 page.

TODO

  • Change Log - will be corrected after the release. Not a top priority.
  • Need a better way of evaluating which tested modules have additional requirements (need to set up a utility method for dependencies.pl)
  • Work into Bio::Root::Build a way to preinstall required modules via CPANPLUS if called from the CPANPLUS shell. A ton of CPAN Tester cases are listed as UNKNOWN due to calling CPAN instead (dies from permissions issues). Maybe test off portal.open-bio.org?
    • For 1.5.2 I (--Senduran 18:03, 25 January 2009 (UTC)) tested CPAN stuff by uploading the .tar.gz to a named directory on ftp.open-bio and: 
 cpan> o conf urllist push ftp://ftp.open-bio.org/pub/bioperl/DIST/
 cpan> o conf commit
 cpan> install S/SE/SENDU/bioperl-live.tar.gz
    • I tried this with the various alphas and it didn't work, but it might for non-alpha releases. Worth a try, but we'll need to turn off any automated smoke tests (CPAN::Reporter) just in case. --Chris Fields 18:41, 25 January 2009 (UTC)
      • Not sure what you mean. It should have worked - all 1.5.2s were effectively 'alpha' after all. If you have difficulty getting it setup let me know and I'll do it. --Senduran 22:36, 25 January 2009 (UTC)
  • Further test cleansing...
    • Maybe split up some tests based on module (Annotation.t comes to mind).
    • Are we really using every file in t/data?

CPAN Tests

CPAN Testers

  • IRIX OS:6.5 arch:IP35-irix-64int
    • No idea why these are failing... 
 t/LocalDB/Index..............................
 ------------- EXCEPTION -------------
 MSG: Can't open 'DB_File' dbm file 'Wibbl4' : Invalid argument
 STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:386
 STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:150
 STACK Bio::Index::AbstractSeq::new Bio/Index/AbstractSeq.pm:81
 STACK toplevel t/LocalDB/Index.t:97
 -------------------------------------
 
 # Looks like you planned 64 tests but ran 33.
 # Looks like your test exited with 22 just after 33.
  Dubious, test returned 22 (wstat 5632, 0x1600)
  Failed 31/64 subtests
 ...
 t/SeqIO/asciitree............................
 #   Failed test at t/SeqIO/asciitree.t line 30.
 # Looks like you failed 1 test of 2.
  Dubious, test returned 1 (wstat 256, 0x100)
  Failed 1/2 subtests
  • Linux OS:2.6.9-22.18.bz155725.elsmp, arch: i386-linux-thread-multi
    • This is the same error that pops up when hitting the ulimit for the system. arch indicates threading is enabled, may be related to that. 
t/SeqFeature/SeqFeatCollection............... 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unable to tie DB_File handle
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::SeqFeature::Collection::new Bio/SeqFeature/Collection.pm:195
STACK: t/SeqFeature/SeqFeatCollection.t:122
-----------------------------------------------------------
# Looks like you planned 24 tests but ran 20.
# Looks like your test exited with 25 just after 20.
 Dubious, test returned 25 (wstat 6400, 0x1900)
 Failed 4/24 subtests
  • Linux OS:2.6.24-etchnhalf.1-amd64 arch:x86_64-linux-thread-multi-ld
    • Attempts to directly compare floating point fails some archs. Fixed in main trunk using float_is() instead of direct is(). 
 t/Assembly/ContigSpectrum....................
 #   Failed test at t/Assembly/ContigSpectrum.t line 79.
 #          got: '97.1153846153846154'
 #     expected: '97.1153846153846'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 80.
 #          got: '99.6394230769230769'
 #     expected: '99.6394230769231'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 81.
 #          got: '100.222222222222222'
 #     expected: '100.222222222222'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 146.
 #          got: '81.3333333333333333'
 #     expected: '81.3333333333333'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 147.
 #          got: '97.1153846153846154'
 #     expected: '97.1153846153846'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 148.
 #          got: '99.5192307692307692'
 #     expected: '99.5192307692308'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 167.
 #          got: '75.9285714285714286'
 #     expected: '75.9285714285714'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 168.
 #          got: '97.1153846153846154'
 #     expected: '97.1153846153846'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 169.
 #          got: '99.5879120879120879'
 #     expected: '99.5879120879121'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 170.
 #          got: '100.470588235294118'
 #     expected: '100.470588235294'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 182.
 #          got: '75.9285714285714286'
 #     expected: '75.9285714285714'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 183.
 #          got: '97.1153846153846154'
 #     expected: '97.1153846153846'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 184.
 #          got: '99.5879120879120879'
 #     expected: '99.5879120879121'
 
 #   Failed test at t/Assembly/ContigSpectrum.t line 185.
 #          got: '100.470588235294118'
 #     expected: '100.470588235294'
 # Looks like you failed 14 tests of 134.
  Dubious, test returned 14 (wstat 3584, 0xe00)
  Failed 14/134 subtests
 ...
 t/Tools/pICalculator.........................
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.9990522675830216'
 #     expected: '12.999052267583'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.9970039353900433'
 #     expected: '12.99700393539'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.9905348815880837'
 #     expected: '12.9905348815881'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.9701609055248109'
 #     expected: '12.9701609055248'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.9065486239061606'
 #     expected: '12.9065486239062'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.7131376670492343'
 #     expected: '12.7131376670492'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '12.1681721433832016'
 #     expected: '12.1681721433832'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '10.8960154975974819'
 #     expected: '10.8960154975975'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '8.82939162036317199'
 #     expected: '8.82939162036317'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '6.81329734996811944'
 #     expected: '6.81329734996812'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '5.58311842185451827'
 #     expected: '5.58311842185452'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '4.87361913724595923'
 #     expected: '4.87361913724596'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '4.11053952923424807'
 #     expected: '4.11053952923425'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '3.0064471148474131'
 #     expected: '3.00644711484741'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '1.91237900622079392'
 #     expected: '1.91237900622079'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '1.19755236429121406'
 #     expected: '1.19755236429121'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '0.669596284738211824'
 #     expected: '0.669596284738213'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '0.0571988207175853551'
 #     expected: '0.0571988207175853'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-0.584285455699190851'
 #     expected: '-0.584285455699191'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-1.14218959353988718'
 #     expected: '-1.14218959353989'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-1.79865831607401865'
 #     expected: '-1.79865831607402'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-2.74360327055111622'
 #     expected: '-2.74360327055112'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-3.87361697725167578'
 #     expected: '-3.87361697725167'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-4.91494976791444694'
 #     expected: '-4.91494976791445'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-6.01005299841695587'
 #     expected: '-6.01005299841696'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-7.43711791135299539'
 #     expected: '-7.43711791135299'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-8.77859455006781631'
 #     expected: '-8.77859455006782'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-9.53905973773057685'
 #     expected: '-9.53905973773058'
 
 #   Failed test at t/Tools/pICalculator.t line 25.
 #          got: '-9.84470802408586165'
 #     expected: '-9.84470802408586'
 # Looks like you failed 29 tests of 38.
  Dubious, test returned 29 (wstat 7424, 0x1d00)
  Failed 29/38 subtests

BioPerl-run Release 1.5.9_1

Initial alpha release.

TODO

  • Update Changes, BUGS, etc.
  • TCoffee test failures

CPAN Tests

BioPerl-db Release 1.5.9_1

Initial alpha release.

TODO

  • Update Changes, BUGS, etc.

CPAN Tests

BioPerl-network Release 1.5.9_1

Initial alpha release.

TODO

  • Update Changes, BUGS, etc.

CPAN Tests

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