#!/usr/bin/r -t
+
# Note: everything in the case needs to be system-independent!
library(cran2deb)
library(ctv)
#argv <- argv[-(1:match("--args", argv))]
#mirror <- 'http://cran.uk.r-project.org/'
-mirror <- 'http://cran.r-project.org/'
-message('updating list of available R packages...')
-available <- available.packages(contrib.url(mirror))
+available <- NULL
+ctv.available <- NULL
+
+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')
+
+verbose<-TRUE
+debug<-FALSE
+
+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))
+ } else if ("BioC" == mirror.name) {
+ repos <- c(
+ "bioc"
+ ,"data/annotation"
+ ,"data/experiment"
+ ,"extra"
+ )
+ for (s in repos) {
+ packages.retrieved <- rbind(
+ packages.retrieved,
+ available.packages(contrib.url(paste(mirror.url,s,sep="/")))
+ )
+ }
+ } else {
+ packages.retrieved <- available.packages(mirror.url)
+ }
+ if (verbose) message(paste("Retrieved ",nrow(packages.retrieved)," package descriptions.\n",sep=""))
+ available <- rbind(available, packages.retrieved)
+ message('updating list of available R task views...')
+ ctv.available <- rbind(ctv.available,available.views(repo=mirror.url))
+}
#available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
-#dupes <- duplicated(rownames(available), fromLast=T)
-#available <- available[!dupes,]
-message('updating list of available R task views...')
-ctv.available <- available.views(repo=mirror)
+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="")
+ 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:')))
-#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 <- ''
+if (any(grep("^E:",base_pkgs,value=FALSE))) {
+ cat("Cannot continue, the following error occurred:\n")
+ cat(paste(grep("^E:",base_pkgs,value=TRUE),collapse="\n"))
+ cat("\n")
+ q(save="no")
+}
+
+
+if (debug) {
+ cat("The following base packages were determined:\n")
+ print(base_pkgs)
+}
message('updating list of existing Debian packages...')
debian_pkgs <- readLines(pipe('apt-cache rdepends r-base-core | sed -e "/^ r-cran/{s/^[[:space:]]*r/r/;p}" -e d | sort -u'))
+if (any(grep("^E:",debian_pkgs,value=FALSE))) {
+ cat("Cannot continue, the following error occurred:\n")
+ cat(paste(grep("^E:",debian_pkgs,value=TRUE),collapse="\n"))
+ cat("\n")
+ q(save="no")
+}
+
+if (verbose) {
+ cat("The following packages were found to be available:\n")
+ print(debian_pkgs)
+}
+
save(debian_pkgs, base_pkgs, available, ctv.available, file=file.path(cache_root,'cache.rda'),eval.promises=T)
message('synchronising database...')