[Bioc-devel] Biobase 1.15.33 depends on ALL problem

Keith Satterley keith at wehi.EDU.AU
Fri Sep 7 02:46:16 CEST 2007

Hi Martin and Seth,

Thanks for your prompt responses. I downloaded a binary R-2.6.0alpha a couple of 
hours ago (about 15:00hours, Thursday, Seattle time). I then used biocLite to 
install all the packages I usually install and all works well now,



Seth Falcon wrote:
> Martin Morgan <mtmorgan at fhcrc.org> writes:
>> Thanks Keith for the report.
>> You've entered a bit of a twilight zone, and the sailing will be a bit
>> rough.
>> The underlying problem involves changes in R, not Biobase. I don't
>> know the details, but a series of changes between R r42739 and 42758
>> use a different way of representing package versions. It looks like
>> your R lies in the middle of this. I am speculating that the unusual
>> errors about package version mismatches relate to this; these problems
>> do not occur on more recent R on linux; there might be
>> windows-specific issues, which I will investigate later today.
>> Usually, the solution would be 'update R'. You'll want to be careful,
>> though, to update R to R-alpha, rather than R-devel, as R-devel has
>> branched in preparation for the release in October. The problem is
>> that R-alpha is available as *source*; if you are used to downloading
>> the binary version of R-devel, then you'll end up with R-2.7.0dev
>> (which we do not intend to be able to support with biocLite for at
>> least a couple of weeks).
> A Windows binary for R-alpha will be available Real Soon Now.  I
> expect it will be on our CRAN mirror http://cran.fhcrc.org sometime on
> Saturday if not before.
> + seth

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