[Bioperl-l] Package status for 1.5.2

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Sep 26 07:26:44 UTC 2006

Chris Fields wrote:
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
>> Sent: Monday, September 25, 2006 1:21 PM
>> To: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Package status for 1.5.2
>> Sendu Bala wrote:
>>> To what extent do we want a unified release for all the various
>>> packages? As I see it, here is the current status:
>>> Core
>>> ----
>>> P1 and P2 bugs remain in bugzilla, but nothing that need prevent the
>>> release. These only need to be resolved before 1.6.
>>> Test suite passes satisfactorily, though see
>>> http://www.bioperl.org/wiki/Release_1.5.2 for some minor issues (again,
>>> nothing that prevents release).
>>> Installation issues (ie. PPM, Windows) are being investigated by Nathan
>>> and Chris. Are they serious enough to prevent release? (Minimal Perl
>>> version will be 5.6.1)
>>> Conclusion: ok to be tagged bioperl-release-1-5-2-rc1 and released for
>>> testing.
>> Sorry, I had forgotten about the Bio::DB::SeqFeature failures on Windows
>> which need to be resolved before an RC is worth releasing. I've pushed
>> back RC1 release date to October 2nd; hopefully we can resolve the issue.
>> It will also give me time to resolve the bioperl-run problems that I
>> see, so I can do a unified release.
> I don't think you need to have all of the non-core distributions ready at
> the same time, especially if you want to have a few release candidates for
> the core before a final one.  I don't see the harm in getting it out there. 
> Anyway, I have worked out the BioDBSeqFeature_BDB.t issues on WinXP and have
> committed a fix; these now pass (though I can't get it to find my WinXP
> MySQL installation).  Essentially it was a path name issue; WinXP can't use
> names with '::' in paths, which the BDB adaptor was trying to make.  I added
> a workaround to check for $^O and modify the name of the tempfiles created.
> There is still a problem with the way Bioperl sets up tempfiles on WinXP (it
> creates them w/o problems, but runs into issues deleting them).  I'll draft
> up a quick test script and submit it to bugzilla.  My guess is that
> something changed in later versions of ActivePerl due to heightened
> (paranoiac?) security concerns regarding Windows.  There will probably need
> to be some updating of Root::IO to deal with this.  I'll see if Nathan Haigh
> can confirm this on his WinXP installation, so I know it's not just me ;>
I'll have a look.

> It's not a release killer, though, so I wouldn't worry too much about it.
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
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