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

Simon Anders anders at embl.de
Wed Jun 19 23:07:19 CEST 2013


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from unknowingly working with outdated software.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.


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