/usr/lib/R/site-library/Biobase/scripts/getBioCPkgNames.R is in r-bioc-biobase 2.38.0-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | # This function provides a widget for users to select packages to
# download from Bioconductor.
#
getBioCWidget <- function(bundle = TRUE){
nameList <- list()
popList <- function(toPut){
nameList[[toPut]] <<- "BioC Package"
}
if(bundle)
pkgNames <- getBioCBundle()
else
pkgNames <- getBioCPkgNames()
trash <- sapply(pkgNames, popList)
selected <- listSelect(nameList, "Select packages from the list",
NULL, NULL)
toGet <- NULL
for(i in names(selected)){
if(selected[[i]]){
toGet <- c(toGet, i)
}
}
getBioC(libName = toGet, destdir = NULL, isDevel = FALSE,
verbose = TRUE, bundle = bundle)
}
getBioCPkgNames <- function(){
pkgNames <- NULL
biocURL <- getDefaultRep(bioCOnly = TRUE)
repository <- getRep(biocURL[[1]])
for(i in repository){
if(isPak(i)){
pkgNames <- c(pkgNames, gsub("^Package: *(.*)", "\\1", i))
}
}
return(unique(pkgNames))
}
getBioCBundle <- function(){
return(c("exprs", "affy", "cdna"))
}
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