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

Martin Morgan mtmorgan at fhcrc.org
Thu Jun 20 08:50:41 CEST 2013

On 06/19/2013 11:17 PM, Hervé Pagès wrote:
> Martin,
> Just to make sure we are on the same page, we are talking about
> the message we get when we source http://bioconductor.org/biocLite.R
> (as Simon suggested), not the message we get when loading the
> BiocInstaller package and/or everytime we use biocLite().
> So it's a one time thing. IMO it can be loud. If people miss it, they
> won't see it again...

yes we're talking about the same thing. I suspect most people still 
source("http://bioconductor.org/biocLite.R"); biocLite() rather than 
BiocInstaller::biocLite() (that's what most of the documentation says, after 
all, and it's not an incorrect way of updating...), so it's not really a 
one-time thing. Certainly

   Bioconductor version 2.12 now available, see http://bioconductor.org/install

is a reasonable and more direct alternative.

> Almost any app those days (not only smart phone apps, but apps in
> general) will notify the user when a new version of the app is
> available. The wording is almost always the same (something like
> "a new version of the software is available") and everybody knows
> that this means less features, more bugs, a more restrictive
> license, more memory requirements, etc... ;-)
> H.
> On 06/19/2013 10:50 PM, Martin Morgan wrote:
>> 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.
>> Martin
>>> 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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