[Bioc-devel] upgrading

[Morgan, Martin]

Technically, prior to the release we were using R-3.2 for both release and devel. Only after the release did we 'support' R-devel, implying a new installation of BiocInstaller.

I guess you were using R-devel prior to the release and had an unsupported installation of BiocInstaller. Alternatively, you updated R over an existing library. Apparently at least one of these scenarios (probably the former) is somehow common amongst Bioc developers. I guess in general our approach has been to realize that there are many incorrect ways to skin a cat, and we cannot possibly anticipate all of them, so we will only support the approved way. 

Sorry for the frustration.

Martin

> -----Original Message-----
> From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
> Kasper Daniel Hansen
> Sent: Tuesday, October 20, 2015 10:55 AM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] upgrading
> 
> 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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