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 I tried 'your out-of-date versions are...'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stick with an out-of-date version.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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