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

Laurent Gautier lgautier at gmail.com
Wed Jun 19 23:24:09 CEST 2013

I support this.

A notice that there is a newer version available is something a number 
of users would almost expect (since a number of the applications they 
use probably already do so), and would be in aligned with the 
bioconductor effort to reach the widest possible audience.

However, users should also be warned that updating R might break or 
change the behaviour of code they currently have working. A pointer to 
documentation about how to run several versions of R on a system would 
also be welcome. Otherwise the result could be that you just change the 
content of the annoying emails you receive to "my analysis scripts 
suddenly stopped working, what happened ?".


On 06/19/2013 11:07 PM, Simon Anders wrote:
> Hi
> I would like to suggest the floowing change to the biocLite.R script: 
> As soon as it is sourced, it should check whether the R interpreter it 
> is running in has at least the current major version number, and if 
> not, display a conspicious warning such as
> "WARNING: You are not using a current version of R.The 'biocLight' 
> script will there NOT install packages from the current Bioconductor 
> release but from the old release matched to your R version!
> Please consider updating R to version [current version] to ensure that 
> you are working with up-to-date packages."
> Background: More than two years ago, I changed the name of a function 
> in DESeq. Since then, and until today, I get an e-mail at least every 
> other week from a user asking why the function 'estimateDispersions' 
> mentioned in the vignette seem to be missing.
> This shows that there are huge numbers of users out there who use an 
> old R version and are unaware that biocLite will not give them current 
> package versions.
> I am sure I am not the only package maintainer battling with this. 
> Such a warning would not only reduce my ennui of having to explain 
> Bioconductor's versioning policy over and over but also keep many 
> users from unknowingly working with outdated software.
> Fortunately, the fact that users always source the biocLite.R script 
> right from the web server gives us the unique opportunity to make this 
> change such that it affects existing old R installations.
>   Simon
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list