Hello, I have a couple of R questions. 1. When we have several aliases in a .Rd file is there a way to have only the first alias listed in the index for the package (00Index.html) I am asking this especially in the context of the marrayClasses package for the .Rd files for the classes. The index now lists both marrayLayout and marrayLayout-class. We added the alias marrayLayout because it's easier for people to use ? marrayLayout than ? marrayLayout- class. 2. I've installed the bundle Bioconductor. Is there a way to load all packages with one command in R, instead of going library(package1), library(package2), etc.? Thanks for your help. Sandrine ---------------------------------------------------------------------- --------- Sandrine Dudoit, Ph.D. E-mail: sandrine@stat.berkeley.edu Assistant Professor Tel: (510) 643-1108 Division of Biostatistics Fax: (510) 643-5163 School of Public Health http://www.stat.berkeley.edu/~sandrine University of California, Berkeley 140 Earl Warren Hall, #7360 Berkeley, CA 94720-7360 ---------------------------------------------------------------------- ---------

On Tue, 2 Apr 2002, Sandrine Dudoit wrote: > 2. I've installed the bundle Bioconductor. Is there a way to load all > packages with one command in R, instead of going library(package1), > library(package2), etc.? Do we need a dummy library, Bioconductor, with .First.lib <- function() { while (library in bioconductor.libraries) require(library) } It appears that there are numerous subsets that might be of interest, and might not be worth power-loading everything (but it might be worth some kind of "topic/activity" based loader of the above, i.e. Bioconductor.topic("cDNA"), Bioconductor.topic("affy"), or similar activity-sets. Comments? best, -tony A.J. Rossini Rsrch Asst Professor of Biostatistics rossini@u.washington.edu http://software.biostat.washington.edu/ Biostatistics/Univ. of Washington 206-543-1044 (3286=fax) (Thursdays) HIV Vaccine Trials Network/FHCRC 206-667-7025 (4812=fax) (M/Tu/W) (Friday location is generally unknown).

On Tue, Apr 02, 2002 at 12:48:53PM -0800, Anthony Rossini wrote: > On Tue, 2 Apr 2002, Sandrine Dudoit wrote: > > > > 2. I've installed the bundle Bioconductor. Is there a way to load all > > packages with one command in R, instead of going library(package1), > > library(package2), etc.? > > Do we need a dummy library, Bioconductor, with > > .First.lib <- function() { > while (library in bioconductor.libraries) > require(library) > } > > It appears that there are numerous subsets that might be of interest, and might not be worth power-loading everything (but it might be worth some kind of "topic/activity" based loader of the above, i.e. Bioconductor.topic("cDNA"), Bioconductor.topic("affy"), or similar activity-sets. > > Comments? These all seem reasonable, don't forget that if a package has a requires for something else that something else gets loaded with the package. For those of us working off of cvs there is an install target for the makefile in madman/Rpacks... > > best, > -tony > > > > A.J. Rossini Rsrch Asst Professor of Biostatistics > rossini@u.washington.edu http://software.biostat.washington.edu/ > Biostatistics/Univ. of Washington 206-543-1044 (3286=fax) (Thursdays) > HIV Vaccine Trials Network/FHCRC 206-667-7025 (4812=fax) (M/Tu/W) > (Friday location is generally unknown). > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B28 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+

>>>>> Sandrine Dudoit writes: > Hello, > I have a couple of R questions. > 1. When we have several aliases in a .Rd file is there a way to have only > the first alias listed in the index for the package (00Index.html) > I am asking this especially in the context of the marrayClasses package > for the .Rd files for the classes. The index now lists both > marrayLayout and marrayLayout-class. We added the alias marrayLayout because > it's easier for people to use ? marrayLayout than ? > marrayLayout-class. Sandrine, That's a limitation of the current Rd system: the INDEX file is generated from the info in the *name* and title slots of the Rd file. [This was not too bad in the old days but is really braindead now that we even say that the name is just an id which must be unique across the Rd objs in the package]. The \alias info is currently not used. R 1.6 should have a 3-arg \index command along the lines of \index{TOPIC}{TYPE}{DESCRIPTION} or \index[TYPE]{TOPIC}{DESCRIPTION} the latter being my pref, which will allow us to have a real index system. For the time being, all you can do is split into small pieces, or write good vignettes so that no one needs to look at the INDEX files. -k