Hi,
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
H.
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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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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