[Bioperl-l] bioperl-1.2.1 - Release Candidiate 2

[Jason Stajich]

> Also - Jason - there have been some recent commits about file closing on
> the head in bioperl-run - do these have a similar knockon effect to
> StandAloneBlast on the branch?
>

I fixed the StandAloneBlast on the branch yesterday in my flurry of
commits and it made it into the rc2.  I think we've fixed the past problem
by explicitly closing filehandles created by tempfile - setting them to
undef leaves them open.  We'll rethink this whole system later on now that
we know what the problem is.

Everything looks good for me on many OSes and perl versions (no 5.005
perl on any of the boxes to test on though).

bioperl-1.2.1-rc2 make test results:

OS X  (Bundle::BioPerl installed)
perl 5.6.1
All tests successful, 4 subtests skipped.
Files=137, Tests=6252, 412 wallclock secs (107.20 cusr + 15.18 csys = 122.38 CPU)

Sparc Solaris 5.8 (Bundle::BioPerl not installed)
perl 5.6.1
All tests successful, 25 subtests skipped.
Files=137, Tests=6116, 86 wallclock secs (72.67 cusr +  7.87 csys = 80.54 CPU)

Sparc Solaris 5.8 (Bundle::BioPerl not installed)
perl 5.8.0
All tests successful, 25 subtests skipped.
Files=137, Tests=6116, 190 wallclock secs (172.81 cusr +  8.79 csys = 181.60 CPU)

Alpha OSF1 4.0 (Bundle::BioPerl not installed)
perl 5.6.0
All tests successful, 5 subtests skipped.
Files=137, Tests=6116, 201 wallclock secs (99.90 cusr + 20.40 csys = 120.30 CPU)

IRIX64 (Bundle::BioPerl not installed)
perl 5.6.1
All tests successful, 6 subtests skipped.
Files=137, Tests=6116, 167 wallclock secs (147.99 cusr + 14.28 csys = 162.27 CPU)

i386 RHL 7.3 (Bundle::BioPerl installed)
perl 5.8.0
All tests successful, 4 subtests skipped.
Files=137, Tests=6252, 164 wallclock secs (92.76 cusr +  5.18 csys = 97.94 CPU)

i386 RHL 7.3 (Bundle::BioPerl installed)
perl 5.6.1
All tests successful, 4 subtests skipped.
Files=137, Tests=6252, 159 wallclock secs (90.89 cusr +  5.27 csys = 96.16 CPU)


-j

>
>
>
> Please, please, please - download and test this release. If everything is
> ok, I will release monday/tuesday.
>
>
>
> ewan
>
>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney at ebi.ac.uk>.
> -----------------------------------------------------------------
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu