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

Martin Morgan mtmorgan at fhcrc.org
Fri Oct 1 19:47:24 CEST 2010

On 10/01/2010 10:20 AM, Michael Lawrence wrote:
> In theory we should be able to back-port this change. I have no idea why it
> is not making it into the release. It was committed after the circular stuff
> (which breaks serialized object compatibility), but does not depend on it.

> Michael
> On Fri, Oct 1, 2010 at 9:00 AM, Steve Lianoglou <
> mailinglist.honeypot at gmail.com> wrote:
>> Hi,
>> On 09/14/2010 01:46 PM, Michael Lawrence wrote:
>>> I just checked in some changes to IRanges, that make this method work:
>> Sorry to bring up an old thread -- but I want to use the "fix"
>> parameter in resizing GRanges objects in some of my code.
>> I see that this change has been made to SVN, but if I'm not mistaken,
>> it seems to not be coming to the GRanges stuff that's scheduled to
>> land w/ BioC 2.7/R-2.12?

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


(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


(also from the Developers page) which suggests the Bioc 2.7 branch will
be cut Oct 15.


>> 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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