[BioC] BiocInstaller on R-devel

[Martin Morgan]

On 04/10/2013 06:26 PM, Kasper Daniel Hansen wrote:
>
>
>
> On Wed, Apr 10, 2013 at 9:18 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     On 04/10/2013 05:43 PM, Kasper Daniel Hansen wrote:
>
>         Right now, I get that R-devel uses BiocInstaller 1.10.0 and points to
>         Bioconductor 2.12, the same as R-3.0.  Shouldn't it point to Bioconductor
>         2.13 for R-devel?
>
>
>     Hi Kasper -- remember that, because R is now on a yearly release cycle,
>     we're using R-3.0.x for both release and devel for the next ~6 months, see
>
>     http://bioconductor.org/__developers/useDevel/
>     <http://bioconductor.org/developers/useDevel/>
>
>     and after
>
>        source("http://bioconductor.__org/biocLite.R
>     <http://bioconductor.org/biocLite.R>")
>        useDevel()
>
>
> Point taken; Bioc devel should be using the R-3-0-branch.
>
> Nevertheless, if I use R-devel, I should be getting the Bioc devel version,
> which I don't.  I have
> R Under development (unstable) (2013-04-10 r62546) -- "Unsuffered Consequences"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin12.3.0 (64-bit)
>
> which is from right now.

If you're looking to correct this, then

   useDevel()

or remove.packages("BiocInstaller"); 
source("http://bioconductor.org/biocLite.R"). One would get the correct version 
if installing a new R-devel.

You do have an edge case and we'll fix it, thanks. Martin


>
> Kasper
>
>
>     But actually, I think your R-devel is a little out of date and that with
>     something more recent than
>
>     ------------------------------__------------------------------__------------
>     r62488 | ligges | 2013-04-03 16:12:25 -0700 (Wed, 03 Apr 2013) | 1 line
>
>     update BioC devel to 2.13
>     ------------------------------__------------------------------__------------
>
>     you'll get
>
>      > source("http://bioconductor.__org/biocLite.R
>     <http://bioconductor.org/biocLite.R>")
>     Installing package into
>     ‘/home/mtmorgan/R/x86_64-__unknown-linux-gnu-library/3.1’
>     (as ‘lib’ is unspecified)
>     trying URL
>     'http://www.bioconductor.org/__packages/2.13/bioc/src/__contrib/BiocInstaller_1.11.0.__tar.gz
>     <http://www.bioconductor.org/packages/2.13/bioc/src/contrib/BiocInstaller_1.11.0.tar.gz>'
>
>     ...
>
>     Martin
>
>
>
>         Best,
>         Kasper
>
>                  [[alternative HTML version deleted]]
>
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-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793