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.")