On 06/19/2013 03:01 PM, Simon Anders wrote:
Hi
On 19/06/13 23:44, Martin Morgan wrote:
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
I see Laurent's point, but this message would not be helpful. The fact that
biocLite.R does not pull the newest package version available is unusual,
surprising, and a policy rather unique to Bioconductor. Hence it is something
that even an otherwise computer-savvy user will appreciate being warned about.
The fact that updating a system can break things, however, is common.
Furthermore, any user attempting to update his R version will nearly
automatically discover that his old R does not disappear if he does not actively
delete it.
So, what about removing the advice to update but leaving in the warning:
"Warning: The biocLite function will NOT install the most recent release
versions of Bioconductor packages because you are not using a current R version.
Please see http://... for more information."
I moved a little on the wording
New features require Bioconductor version 2.12, R version 3.0.1; your
versions are 2.11 and 2.15.3. See http://bioconductor.org/install.
but won't elevate this to a warning or include language about what is supported
(although I appreciate the value of both of these suggestions, thanks). The
install page tries to be more explicit about the connection between R / Bioc
version (remember that R is on a yearly release cycle, so it's no longer one-R
one-Bioc). I haven't incorporated text about how to manage multiple R instances
(I don't think I could do justice to this, and it's more of an R issue anyway;
probably there should at least be a caution).
I'm wondering why my iphone hasn't told me to update my nytimes app.
Thanks for the suggestions.
Martin
This brings me to another issue: How should a newcomer to Bioconductor know that
Bioconductor releases are tied to R versions and that biocLite will always pull
packages from the Bioconductor release matched to the used R version rather than
from the current Bioconductor release?
The page at http://bioconductor.org/install/ does _not_ mention this important
fact! Could somebody please fix this?
Simon
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