mirrors <- NULL
mirrors <- c(mirrors,CRAN='http://cran.r-project.org')
-#mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.2')
-mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.7')
+mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.11')
+mirrors <- c(mirrors,Omegahat="http://www.omegahat.org/R/src/contrib")
verbose<-TRUE
debug<-FALSE
+package.filters <- c("OS_type","duplicates")
for (mirror.name in names(mirrors)) {
mirror.url<-mirrors[mirror.name]
message(paste("Updating list of available R packages from ",mirror.name," [",mirror.url,"].\n",sep=""))
packages.retrieved <- NULL
if ("CRAN" == mirror.name) {
- packages.retrieved <- available.packages(contrib.url(mirror.url))
+ packages.retrieved <- available.packages(contrib.url(mirror.url),filters=package.filters)
+ print(packages.retrieved[grep("SNP",rownames(packages.retrieved)),])
} else if ("BioC" == mirror.name) {
repos <- c(
"bioc"
for (s in repos) {
packages.retrieved <- rbind(
packages.retrieved,
- available.packages(contrib.url(paste(mirror.url,s,sep="/")))
+ available.packages(contrib.url(paste(mirror.url,s,sep="/")),filters=package.filters)
)
}
} else {
- packages.retrieved <- available.packages(mirror.url)
+ packages.retrieved <- available.packages(mirror.url,filters=package.filters)
}
if (verbose) message(paste("Retrieved ",nrow(packages.retrieved)," package descriptions.\n",sep=""))
available <- rbind(available, packages.retrieved)
dupes <- duplicated(rownames(available), fromLast=T)
if (sum(dupes)>0) {
- if (verbose) cat("Found ",sum(dupes)," packages with the same name in different distributions. Those are now removed.\n",sep="")
+ if (verbose) {
+ cat("Found ",sum(dupes)," packages with the same name in different distributions. Those are now removed.\n",sep="")
+ print(available[dupes,])
+ }
+
available <- available[!dupes,,drop=F]
} else {
if (length(mirrors)>1) cat("All packages have different names.")
# TODO: Check if not better a dedicated tool should be called for this
message('updating list of base R packages...')
-base_pkgs <- readLines(pipe(paste('sudo pbuilder --execute --override-config --configfile'
- ,shQuote(pbuilder_config),'-- /usr/bin/R --vanilla 2>&1 >/dev/null <'
- ,shQuote(file.path(root,'exec/get_base_pkgs'))
- ,'| grep -v ^W:')))
+base_pkgs <- c("base",
+ "compiler",
+ "datasets",
+ "graphics",
+ "grDevices",
+ "grid",
+ "methods",
+ "parallel",
+ "splines",
+ "stats",
+ "stats4",
+ "tcltk",
+ "tools",
+ "utils")
+# readLines(pipe(paste('sudo pbuilder --execute --override-config --configfile'
+# ,shQuote(pbuilder_config),'-- /usr/bin/R --vanilla 2>&1 >/dev/null <'
+# ,shQuote(file.path(root,'exec/get_base_pkgs'))
+# ,'| grep -v ^W:')))
if (any(grep("^E:",base_pkgs,value=FALSE))) {
cat("Cannot continue, the following error occurred:\n")