[Bioc-devel] biocLite should warn when called from a non-current R version
On 06/19/2013 03:01 PM, Simon Anders wrote:
Hi 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."
I moved a little on the wording New features require Bioconductor version 2.12, R version 3.0.1; your versions are 2.11 and 2.15.3. See http://bioconductor.org/install. but won't elevate this to a warning or include language about what is supported (although I appreciate the value of both of these suggestions, thanks). The install page tries to be more explicit about the connection between R / Bioc version (remember that R is on a yearly release cycle, so it's no longer one-R one-Bioc). I haven't incorporated text about how to manage multiple R instances (I don't think I could do justice to this, and it's more of an R issue anyway; probably there should at least be a caution). I'm wondering why my iphone hasn't told me to update my nytimes app. Thanks for the suggestions. Martin
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? Simon
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