On May 24, 2006, at 1:21 PM, Paul Roebuck wrote: > On Wed, 24 May 2006 Herve Pages wrote: > >> Quoting Simon Urbanek <[EMAIL PROTECTED]>: >> >>> On May 23, 2006, at 10:31 PM, Herve Pages wrote: >>> >>> [SNIP] >>> >>>> 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") > > Forgive, but if that's the case, why can't it be specified as such: > > whole.enchilda.repos <- c(getOption("BioC.Repos"), > "http://bioconductor.org/packages/omegahat";, > "http://cran.fhcrc.org";) # getOption > ("repos")? > install.packages('pkg', repos = whole.enchilda.repos, depend = TRUE) > >> - Things are consistent with the biocLite() function that we >> provide >> for users of _all_ platforms >> http://bioconductor.org/docs/install-howto.html > > Since the above would be an internal change to the install > script, the above would be even less effort. > >> 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. > > I don't. There may be others as well... I'd rather BioC > packages be kept separate from CRAN packages in the > listing...
I second that. While I am indifferent to what goes on under the hood, the Gui (as it stands right now) should only list Bioconductor packages when selecting either "Bioconductor (sources)" or "Bioconductor (binaries)". /Kasper > ---------------------------------------------------------- > SIGSIG -- signature too long (core dumped) > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
