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

Hervé Pagès hpages at fhcrc.org
Thu Jun 20 00:27:18 CEST 2013


I support this too.

On 06/19/2013 02:44 PM, Martin Morgan wrote:
> 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

More important than new features, using the latest version of BioC gives
you the only version that is currently *supported*. I think the message
should stress that.

My $0.02


> 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
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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