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

Martin Morgan mtmorgan at fhcrc.org
Thu Jun 20 07:50:07 CEST 2013

On 06/19/2013 09:15 PM, Hervé Pagès wrote:
> 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,

Thanks Herve for your comments. I tried 'your out-of-date versions are...' and 
similar, but to me that (also flagging this as a 'warning') sounded too 
heavy-handed; there are good reasons (e.g., consistency) why one might want to 
stick with an out-of-date version. Also I used 'available' (hence the trifecta 
'new', 'version', 'available') initially (also 'Bioconductor version 2.12 now 
available, see...', I think this would be a reasonable alternative to the 
current message), but 'require' seemed to be more forceful and to address 
Simon's concern (without saying 'n.b. to users of DESeq, estimateDispersions 
requires Bioconductor version...' ;) that users mistakenly expect new features 
to exist in old releases.

It's easy to make changes to the message, so keep the suggestions coming. I 
might not say no to all of them.


> I mean, maybe the message is just suggesting me to install a
> devel/alpha/beta/unstable version of BioC or something like that.
> H.
>> 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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