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

Hervé Pagès hpages at fhcrc.org
Thu Jun 20 08:17:14 CEST 2013


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...

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... ;-)


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

Hervé Pagès

Program in Computational Biology
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