[Bioc-devel] upgrading

[Ramon Diaz-Uriarte]

Dear Daniel,

I was just doing the same thing, and things worked fine for me (I am on Linux):

- download and compile R-devel

- get biocLite

source("http://bioconductor.org/biocLite.R")

which tells me

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocInstaller_1.21.1.tar.gz'

(...[stuff omitted here])

Bioconductor version 3.3 (BiocInstaller 1.21.1)



- Then, I always do (since I run all of this from an automated script)

try(useDevel(devel = TRUE))

which sure enough tells me

Error : 'devel' version already in use


but things work fine, and I have installed a bunch of packages from devel.



R.

On Tue, 20-10-2015, at 16:55, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:
> So I have an R-devel where I have a previous (pre-bioc-3.2) installed
> version of BiocInstaller.
>
> 1) I re-compile R-devel today.
> 2) I run
>   source("http://www.bioconductor.org/biocLite.R")
> which gives me BiocInstaller 1.20.0.  However, the current one for
> Bioc-devel is 1.21.1.
>
> When I try to push to a higher level version, by doing
>   library(BiocInstaller)
>   useDevel(TRUE)
> I get
>
>> useDevel(TRUE)
> Error: 'devel' version requires a more recent R
>
> If I now try to upgrade I get
>> biocLite("BiocUpgrade")
> Error: Bioconductor version 3.2 cannot be upgraded with R version 3.3.0
>
> This all looks problematic.  How to I upgrade to Bioc-devel using R-devel?
> Btw. there are no instructions anymore at
>   https://www.bioconductor.org/developers/how-to/useDevel/
>
> Best,
> Kasper
>
> 	[[alternative HTML version deleted]]
>
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-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz