[Bioc-devel] biocLite should warn when called from a non-current R version

Simon Anders anders at embl.de
Thu Jun 20 00:01:23 CEST 2013


On 19/06/13 23:44, Martin Morgan wrote:
> As a message (not warning or error), how about
>    New features are available in Bioconductor version 2.12, R version
> 3.0.1.
>    See http://bioconductor.org/install
> and if the instructions / dire consequences at
> http://bioconductor.org/install are not sufficient then we can update that

I see Laurent's point, but this message would not be helpful. The fact 
that biocLite.R does not pull the newest package version available is 
unusual, surprising, and a policy rather unique to Bioconductor. Hence 
it is something that even an otherwise computer-savvy user will 
appreciate being warned about. The fact that updating a system can break 
things, however, is common. Furthermore, any user attempting to update 
his R version will nearly automatically discover that his old R does not 
disappear if he does not actively delete it.

So, what about removing the advice to update but leaving in the warning:

"Warning: The biocLite function will NOT install the most recent release 
versions of Bioconductor packages because you are not using a current R 
version. Please see http://... for more information."

This brings me to another issue: How should a newcomer to Bioconductor 
know that Bioconductor releases are tied to R versions and that biocLite 
will always pull packages from the Bioconductor release matched to the 
used R version rather than from the current Bioconductor release?

The page at http://bioconductor.org/install/ does _not_ mention this 
important fact! Could somebody please fix this?


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