[Bioperl-l] progress for 1.2.2 bugfix releae
heikki at nildram.co.uk
Sun Jun 29 20:51:14 EDT 2003
On Sun, 2003-06-29 at 00:07, Lincoln Stein wrote:
> This is good. When is the expected date for the tarball release?
The first test tarball should be out (I have not done it before so the
there might be surprises) on Tuesday and the final one by early next
week (aiming at Tuesday).
> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
More information about the Bioperl-l