[Bioperl-l] Temporary file names in Bio::Tools::Run::StandAlonwWUBlast

[Adam Sjøgren]

Brian writes:

> All tests pass with the patched code?

Well, I cannot claim that. What I can say, is that the number of tests
that pass/fail for me are unchanged.

Before (perl Build.sh && ./Build test):

  Files=83, Tests=1504, 50 wallclock secs ( 0.48 usr  0.12 sys + 45.10 cusr  6.33 csys = 52.03 CPU)
  Result: FAIL
  Failed 49/83 test programs. 14/1504 subtests failed.

After:

  Files=83, Tests=1504, 50 wallclock secs ( 0.45 usr  0.17 sys + 44.99 cusr  6.45 csys = 52.06 CPU)
  Result: FAIL
  Failed 49/83 test programs. 14/1504 subtests failed.

The test that mentions StandAloneWUBlast is
t/Tools/Run/StandAloneBlast.t, which for me ran like this before:

  $ prove -Ilib t/Tools/Run/StandAloneBlast.t 
  t/Tools/Run/StandAloneBlast.t .. 1/45 Use of uninitialized value $input1 in -e at /var/local/work/bioperl/bioperl-run/lib/Bio/Tools/Run/StandAloneBlast.pm line 474.
  Use of uninitialized value $input1 in concatenation (.) or string at /var/local/work/bioperl/bioperl-run/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm line 306.

  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG:  not Bio::Seq object or array of Bio::Seq objects or file name!
  STACK: Error::throw
  STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
  STACK: Bio::Tools::Run::StandAloneNCBIBlast::blastpgp /var/local/work/bioperl/bioperl-run/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm:306
  STACK: t/Tools/Run/StandAloneBlast.t:175
  -----------------------------------------------------------
  # Looks like you planned 45 tests but ran 43.
  # Looks like your test exited with 2 just after 43.
  t/Tools/Run/StandAloneBlast.t .. Dubious, test returned 2 (wstat 512, 0x200)
  Failed 2/45 subtests 
          (less 8 skipped subtests: 35 okay)

  Test Summary Report
  -------------------
  t/Tools/Run/StandAloneBlast.t (Wstat: 512 Tests: 43 Failed: 0)
    Non-zero exit status: 2
    Parse errors: Bad plan.  You planned 45 tests but ran 43.
  Files=1, Tests=43,  0 wallclock secs ( 0.02 usr  0.00 sys +  0.12 cusr  0.01 csys =  0.15 CPU)
  Result: FAIL

and like this (same result) after:

  $ prove -Ilib t/Tools/Run/StandAloneBlast.t 
  t/Tools/Run/StandAloneBlast.t .. 1/45 Use of uninitialized value $input1 in -e at /var/local/work/bioperl/bioperl-run/lib/Bio/Tools/Run/StandAloneBlast.pm line 474.
  Use of uninitialized value $input1 in concatenation (.) or string at /var/local/work/bioperl/bioperl-run/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm line 306.

  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG:  not Bio::Seq object or array of Bio::Seq objects or file name!
  STACK: Error::throw
  STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
  STACK: Bio::Tools::Run::StandAloneNCBIBlast::blastpgp /var/local/work/bioperl/bioperl-run/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm:306
  STACK: t/Tools/Run/StandAloneBlast.t:175
  -----------------------------------------------------------
  # Looks like you planned 45 tests but ran 43.
  # Looks like your test exited with 2 just after 43.
  t/Tools/Run/StandAloneBlast.t .. Dubious, test returned 2 (wstat 512, 0x200)
  Failed 2/45 subtests 
          (less 8 skipped subtests: 35 okay)

  Test Summary Report
  -------------------
  t/Tools/Run/StandAloneBlast.t (Wstat: 512 Tests: 43 Failed: 0)
    Non-zero exit status: 2
    Parse errors: Bad plan.  You planned 45 tests but ran 43.
  Files=1, Tests=43,  1 wallclock secs ( 0.02 usr  0.00 sys +  0.13 cusr  0.00 csys =  0.15 CPU)
  Result: FAIL


  Best regards,

    Adam

-- 
                                                          Adam Sjøgren
                                                    adsj at novozymes.com