[Bioc-sig-seq] Resizing a GRanges object with elements on the "*" strand

[Steve Lianoglou]

On Fri, Oct 1, 2010 at 1:47 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
<snip>
> I'm a little confused about what's being said here. If you're concerned
> that things in svn will not make it to Bioc 2.7, then... the Bioc 2.7
> branch has not been cut, so things in svn will definitely end up in Bioc
> 2.7. Packages that fail to pass R CMD build / check don't get pushed to
> the repository seen by biocLite(). From
> http://bioconductor.org/checkResults/devel/bioc-LATEST/

Ahh, cool ... I see. Thanks for the detailed explanation.

I mistakenly assumed that "the cut" had already been made since this
checkin happened quite a while ago and it hasn't been propagated
through to biocLite for v2.7.

I didn't realize there have been problems with building GenomicRanges
that was causing what I was seeing.

I'll read through more of the BioC-dev info stuff ...

Cheers,

-steve

>
> (see bioconductor.org -> Develoeprs -> Source Code & Build Reports) it
> seems like there are issues with GenomicRanges. When those are cleared
> up, the svn commits will get exposed. The issues will be cleared up
> before the release. The tentative release schedule is at
>
> http://bioconductor.org/developers/release-schedule/
>
> (also from the Developers page) which suggests the Bioc 2.7 branch will
> be cut Oct 15.
>
> Martin
>
>>>
>>> Is this intentional? If so, how come? I don't think it'll break
>>> backwards compatibility, right?
>>>
>>> Maybe an oversight? (perhaps on my part, or "yours" :-)?
>>>
>>> For now I think I'm just going to take this code and override the
>>> BioC-2.7 version of resize, since I'd like to use it but can't upgrad
>>> to svn GRanges since some of my stuff is getting hosed with the
>>> "circular" stuff that's starting to be introduced.
>>>
>>> Thanks,
>>> -steve
>>>
>>> --
>>> Steve Lianoglou
>>> Graduate Student: Computational Systems Biology
>>>  | Memorial Sloan-Kettering Cancer Center
>>>  | Weill Medical College of Cornell University
>>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
>>>
>>> _______________________________________________
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>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
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> Fred Hutchinson Cancer Research Center
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact