[Bioperl-l] Build failure on upgrade using CPAN

[Warren Gallin]

Hi,

	I’ve been trying to upgrade to the latest BioPerl but I am getting test failures that prevent the installation of BioPerl-Run.

Here is the summary of test failures:

Test Summary Report
-------------------
t/Blat.t                    (Wstat: 65280 Tests: 40 Failed: 1)
  Failed test:  40
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 39 tests but ran 40.
t/Gumby.t                   (Wstat: 65280 Tests: 8 Failed: 1)
  Failed test:  1
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 124 tests but ran 8.
t/MCS.t                     (Wstat: 65280 Tests: 4 Failed: 2)
  Failed tests:  1-2
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 24 tests but ran 4.
t/Match.t                   (Wstat: 65280 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 7 tests but ran 1.
t/PhastCons.t               (Wstat: 65280 Tests: 6 Failed: 1)
  Failed test:  1
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 181 tests but ran 6.
t/SABlastPlus.t             (Wstat: 65280 Tests: 69 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 73 tests but ran 69.
t/Samtools.t                (Wstat: 7424 Tests: 37 Failed: 0)
  Non-zero exit status: 29
  Parse errors: Bad plan.  You planned 41 tests but ran 37.
Files=83, Tests=2309, 16 wallclock secs ( 0.39 usr  0.19 sys + 12.86 cusr  2.58 csys = 16.02 CPU)
Result: FAIL
Failed 7/83 test programs. 6/2309 subtests failed.
  CJFIELDS/BioPerl-Run-1.007001.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-Run-1.007001.tar.gz
Failed during this command:
 CJFIELDS/BioPerl-Run-1.007001.tar.gz         : make_test NO


So my question is, is the failure to build BioPerl-Run going to affect my ability to use the installed Distributions and Modules listed here:

Bundle    Bundle::BioPerl        (CJFIELDS/Bundle-BioPerl-2.1.9.tar.gz)
Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution    CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.25.tar.gz
Distribution    CJFIELDS/BioPerl-1.007001.tar.gz
Distribution    CJFIELDS/BioPerl-1.6.924.tar.gz
Distribution    CJFIELDS/BioPerl-DB-1.006900.tar.gz
Distribution    CJFIELDS/BioPerl-Network-1.006902.tar.gz
Distribution    CJFIELDS/BioPerl-Run-1.007001.tar.gz
Distribution    CJFIELDS/Bundle-BioPerl-2.1.9.tar.gz
Module  < Bio::Gonzales::Role::BioPerl::Constructor (JWB/Bio-Gonzales-0.062.tar.gz)
Module  < Bio::LiveSeq::IO::BioPerl (CJFIELDS/BioPerl-1.007001.tar.gz)
Module  < Dist::Zilla::PluginBundle::BioPerl (CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.25.tar.gz)
Module  < Fry::Lib::BioPerl      (BOZO/Fry-Lib-BioPerl-0.15.tar.gz)
Module  < Pod::Weaver::PluginBundle::BioPerl (CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.25.tar.gz)
Author          BIOPERLML ("Bioperl-l" <bioperl-l at lists.open-bio.org>)
15 items found

Sorry for what may be a question with an obvious answer, but these results seem too complex for me to interpret.

Warren Gallin