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

Martin Morgan mtmorgan at fhcrc.org
Wed Jun 19 23:44:05 CEST 2013

On 06/19/2013 02:24 PM, Laurent Gautier wrote:
> 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 ?".

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

> L.
> 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 working with outdated software.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
> _______________________________________________
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