#!/usr/bin/r -t

# Note: everything in the case needs to be system-independent!
library(cran2deb)
library(ctv)

#argv <- commandArgs()
#argv <- argv[-(1:match("--args", argv))]

#mirror <- 'http://cran.uk.r-project.org/'

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)
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:')))

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...')
db_update_package_versions()