Hi I second improving the awareness of users about new Bioc releases and also personally do not mind loud messages while I am installing/upgrading packages, even if it is each time I source/run biocLite(). Indeed for old releases that I maintain for old projects very rarely have to install a new package.
Cheers, Diego On Thu, Jun 20, 2013 at 3:50 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: > 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 >>>>> >>>>> >>>>> >>>> >>> >>> >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
