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working with outdated software.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
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