Build failure on upgrade using CPAN

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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" <[hidden email]>)
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





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Re: Build failure on upgrade using CPAN

Fields, Christopher J
This shouldn’t affect other BioPerl code that I know of.

BioPerl-Run modules are always a bit more difficult to test, primarily b/c they wrap executables but don’t have an easy way to evaluate support versions of software within tests (Samtools for instance I’m sure isn’t updated for the 1.x releases).  Do you have the below tools (BLAT, Bumby, etc) installed?

chris

On 5/6/17, 4:30 PM, "Bioperl-l on behalf of Warren Gallin" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:

    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" <[hidden email]>)
    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
   
   
   
   
   
    _______________________________________________
    Bioperl-l mailing list
    [hidden email]
    http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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