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

Martin Morgan mtmorgan at fhcrc.org
Thu Jun 20 02:21:21 CEST 2013

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.


> 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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