[Bioc-devel] biocLite should warn when called from a non-current R version
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
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from unknowingly working with outdated software.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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