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

[Fields, Christopher J]

Hi Adam,

I have pulled this one in.  We could feasibly add tests for this (e.g. check whether the temp files exist in the format specified after the BLAST run) but IMO this might be a bit overkill, as this functionality is something that File::Temp provides and very likely tests for already.

chris

> On May 28, 2015, at 2:17 AM, Adam Sjøgren <adsj at novozymes.com> wrote:
> 
> 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
> 
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