[Bioperl-l] Need Help: 0.7.2 and 0.9.1 tests and preparations

[Jason Eric Stajich]

Dennis- thanks for your input.

I will see about correcting the reference to tutorial.pl - I'm not sure
what that is referring to.

As for your errors regarding tests - these are all because of not having
certain modules installed - you should have gotten messages about this
when you ran % perl Makefile.PL.

The Compile/SW question is a common one - we need to update the README
regarding where to find the bioperl-ext distribution in order to build the
SW extension package.  I'll try and find someone to do that or else I'll
get it done myself before the release.

I did fix the error that is caused by the GDB test which is not handling
the missing LWP package very well.  Will push these corrections out into a
new candidate package tonight.

Thanks for your help!
-jason

 On Tue, 30 Oct 2001, Dennis V. Lavrov wrote:

> Hello Jason,
>
> I've installed bioperl 0.7.2 on MacOSX and got the following resuluts from
> the tests (Sorry, I'm new to perl and bioperl, so I'm not quite sure yet,
> what is important here).   I have a couple of other questions. I've tried
> to build the compilied extensions but could not find the directory
> Compile/SW.  I was also unable to find tutorial.pl script referred to
> in bptutorial.pl file: "A separate tutorial script (tutorial.pl - located
> in the top bioperl directory) with examples of many of methods described
> in the tutorial."
>
> Thanks,
> Dennis
>
[snip]
>
> **************************************************************************
> Dennis V. Lavrov, Ph.D.                       Dept. de Biochimie
> office: G314 Succ. Centre Ville               Universite de Montreal
> ph.  (514) 343-6111 ext. 5188                 2900 Boul. Edouard Montpetit
> fax: (514) 343-2210                           Montreal, Que H3T 1J4
> **************************************************************************
>
>
> On Mon, 29 Oct 2001, Jason Eric Stajich wrote:
>
> > I've put 0.7.2 candidate in
> > ftp://bioperl.org/pub/jason/bioperl-0.7.2-candidate.tar.gz
> >
> > Please download and test and help be part of the Bioperl development
> > process.  We need all platforms and environments tested although we should
> > hope to see no surprises from the 0.7.1 release.  Please note that we now
> > require perl >= 5.005.  We'll release and push to CPAN if all looks good.
> > Note this is different that the file in
> > ftp://bioperl.org/pub/DIST/bioperl-0.7.2.tar.gz (see footnote [1] for
> > reasons why) which is really not the 0.7.2 release.
> >
> > The 0.7.2 is a release from the 0.7 stable branch and so does not have
> > some of the functionality of the 0.9.x series (development head).  We will
> > plan to release another developer's release in the next few weeks which
> > will contain many new additions including Lincoln's GFF db, blastxml
> > parser, some improvements to BPlite & Variation modules, and
> > dna/rna->protein translation in 6 frames.
> >
> > For those interested in helping with the 0.9.1 release please checkout the
> > latest version from the head and run the tests.  Currently we have
> > the following tests breaking so no need to report them.
> >
> > Tempfile.t -- due to some changes in RootI, Ewan and I are sorting out
> > seqwithqual.t -- due to changes on my part, but I think I need Chad's help
> >                  to fix them back (if you're not completely pissed at me
> >                  for breaking things)
> > primaryqual.t -- ditto
> > csmscf.t      -- ditto
> >
> >
> > Yours,
> > -jason
> >
> > [1] (geeky developer CVS talk here)
> > It should be noted that due to an error on my part in the 0.7.1 release
> > there is already a release-0-7-2 tag on the repository - this is
> > essentially the same as the release-0-7-1 tag except for the MANIFEST and
> > Bio::SeqIO::genbank.  I plan to either nuke the 0-7-2 tag and readd it
> > when we tag this release or tag it as 0-7-2-1.  However I plan to call
> > this the 0.7.2 release to avoid any further confusion (if I haven't
> > already created it by mentioning all this).  I did push out a 0.7.2
> > tarball immedietly after the 0.7.1 error thinking we would use it to
> > replace the CPAN submission, but have thought better otherwise.  Thie
> > release will replace that file since it is identical to the corrected
> > 0.7.1 tarball.  If you have better ideas I am all ears.
> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu