Quoting Simon Urbanek <[EMAIL PROTECTED]>: > On May 23, 2006, at 10:31 PM, Herve Pages wrote: > > > I'm using R.app GUI 1.16-pre (3114) with R 2.3.0. > > The links defined in R.app for accessing the Bioconductor > > repositories need to be updated. > > > > This has been fixed in 3161 (and of all the people you should know, > actually ;)).
Simon, Point taken. In the future, I'll try to base my reports on the last Mac OS X GUI available here http://r.research.att.com/#GUI > > > but they should be (in this order): > > > > http://bioconductor.org/packages/bioc > > http://bioconductor.org/packages/data/annotation > > http://bioconductor.org/packages/data/experiment > > http://bioconductor.org/packages/omegahat > > http://bioconductor.org/packages/lindsey > > http://cran.fhcrc.org > > > > Should CRAN be really on that list? Well it depends what you are trying to achieve: if you want the GUI to show the user the list of Bioconductor packages only, then you don't need the 3 last repos. But if you also want the user to be able to install from this list and then to load the newly installed stuff, then you need 2 things: 1) provide a set of repos that is closed for the dependency relationship 2) provide the user with the option to have all the dependencies installed in addition to the packages s/he selected Since the GUI doesn't support 2), then I agree that we don't really need the 3 last repos (omegahat, lindsey and CRAN)... But I'd rather keep them anyway because: - Some users might want to do things like: install.packages('pkg', repos=getOption("BioC.Repos"), dep=TRUE) The only way to guarantee that this will work for _any_ Bioconductor package is to have all 5 repos returned by getOption("BioC.Repos") - Things are consistent with the biocLite() function that we provide for users of _all_ platforms http://bioconductor.org/docs/install-howto.html The inconvenient of this is that we end up with the GUI displaying a very long list... but this is not really a problem because I don't think many users actually browse the entire list: they'd rather use the search box instead. > Lindsey was omitted intentionally, because the packages are > constantly broken (0 of them compile on OS X to-date) and the > maintainer refuses to fix them despite instructions how to do so. > (His last response was that the users should fix it themselves...) That's sad :-/ > > Also, we have started to use a more consistent spelling for the > > project ( it's never too late ;-) ): please help us by using > > "Bioconductor" instead of "BioConductor". > > > > Oh, ok :). Are we allowed to use BioC or is it also Bioc? (The latter > looks rather boring ;)). Agreed :-), but OTOH, as Seth told me recently, "BioC" might suggest that we are using C instead of R. Anyway, let's stick to "BioC" for now... Thanks! H. _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
