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

On 06/19/2013 11:17 PM, Herv? Pag?s 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, Herv? Pag?s 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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