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

Hervé Pagès hpages at fhcrc.org
Thu Jun 20 06:15:22 CEST 2013

Hi Martin,

On 06/19/2013 05:21 PM, Martin Morgan wrote:
> 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.

I think people want to make sure they're using the latest version.
Using the latest version of course means new features, bug fixes, speed
improvements, changes in the API, a new shinny color scheme, etc...
If you really want to keep this message as short and discrete as
possible (I wonder why you'd want that), then I think it's important
to mention those 3 words: new version available.

 From the above message I can guess that this means I won't be
installing the latest version but why not be straightforward and just
say it? Also I'm not totally sure those new features are ready yet,
I mean, maybe the message is just suggesting me to install a
devel/alpha/beta/unstable version of BioC or something like that.


> 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

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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list