[Bioperl-l] progress for 1.2.2 bugfix releae

Lincoln Stein lstein at cshl.org
Sat Jun 28 17:07:34 EDT 2003

This is good.  When is the expected date for the tarball release?


On Saturday 28 June 2003 03:46 pm, Jason Stajich wrote:
> I've cleaned up a load of things which had basically already been fixed on
> the main trunk by needed to be merged over.  A lot of things were revealed
> when running perl5.8.0 so I've tried to clean them up as well.
> The weirdness we saw with t/DB.t failing during make test (but succeeding
> when you run perl -w -I. t/DB.t) can be avoided by explicitly calling
> $seqio->close in the last test block.  Don't ask me why, I don't know.
> I've fixed this on the trunk and branch.
> Also merged the -noclose option for Bio::Root::IO (which when set will not
> close a filehandle upon object DESTROY) for the cases when we have shared
> filehandles.  This also prevents STDIN/OUT/ERR from being closed if they
> are used in an object which uses Bio::Root::IO for IO.  Without this we
> get some problems with some of the Indexing code and since it is an extra
> option not a major API change I decided it should be on the stable branch
> anways.
> I also fixed bugs 1458,1459 on both the main trunk and branch - thanks for
> the reports Mike Olsen!  Give it a try with current code in CVS and we'll
> close the bugs out if you agree they are fixed.
> Also added some notes in the Changes changelog. Checklist for the release
> need to make sure we up the version number- how are we doing that now.  I
> think the plan is to have all the changes in by Monday.  Once that happens
> we need to tag the release, do a clean cvs export checkout of the code, do
> a make manifest, and tar & zip up the whole thing.
> I also did some cleanup on Bio::DB::Flat::BinarySearch to make it more
> uniform between perl versions by ussing
> sysseek($fh,0,SEEK_END);
> $len = sysseek($fh,0,SEEK_CUR) instead of
> $len = tell($fh) in order to get the length of the file because tell
> deals with buffered io while sysseek does not.  I was having problems on
> 5.8.0 and applied the code replaced above where appropriate.
> Hilmar- I think there are still some warnings being spewed by some
> Ontology related code which we should probably get to before the code is
> released.
> t/GOterm.....................ok 1/59Use of uninitialized value in
> concatenation (.) or string at
> ./branch-1.2/blib/lib/Bio/Ontology/GOterm.pm line 285.
> t/OntologyEngine.............ok 2/22Use of uninitialized value in hash
> element at ./branch-1.2/blib/lib/Bio/Ontology/SimpleOntologyEngine.pm
> line 441.
> Also added some notes in the Changes changelog.
> Checklist for the release:
>   Need to make sure we up the version number in the right place. How are
>   we doing that now?
>   Brian will move the FAQ doc/faq/faq.xml and regenerate the FAQ
>   (bumping version number too - let me know if you can't do it).
>   Anything else?
> -jason
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
	1 Bungtown Road, Cold Spring Harbor, NY 11724

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