[Bioc-devel] biocLite should warn when called from a non-current R version
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
> 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?
More information about the Bioc-devel