trunk/exec/update_cache

   1 #!/usr/bin/r -t
   2
   3 # Note: everything in the case needs to be system-independent!
   4 library(cran2deb)
   5 library(ctv)
   6
   7 #argv <- commandArgs()
   8 #argv <- argv[-(1:match("--args", argv))]
   9
  10 #mirror <- 'http://cran.uk.r-project.org/'
  11
  12 available <- NULL
  13 ctv.available <- NULL
  14
  15 mirrors <- NULL
  16 mirrors <- c(mirrors,CRAN='http://cran.r-project.org')
  17 #mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.2')
  18 mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.7')
  19
  20 verbose<-TRUE
  21 debug<-FALSE
  22
  23 for (mirror.name in names(mirrors)) {
  24         mirror.url<-mirrors[mirror.name]
  25         message(paste("Updating list of available R packages from ",mirror.name," [",mirror.url,"].\n",sep=""))
  26         packages.retrieved <- NULL
  27         if ("CRAN" == mirror.name) {
  28                 packages.retrieved <- available.packages(contrib.url(mirror.url))
  29         } else if ("BioC" == mirror.name) {
  30                 repos <- c(
  31                         "bioc"
  32                         ,"data/annotation"
  33                         ,"data/experiment"
  34                         ,"extra"
  35                 )
  36                 for (s in repos) {
  37                         packages.retrieved <- rbind(
  38                                 packages.retrieved,
  39                                 available.packages(contrib.url(paste(mirror.url,s,sep="/")))
  40                         )
  41                 }
  42         } else {
  43                 packages.retrieved <- available.packages(mirror.url)
  44         }
  45         if (verbose) message(paste("Retrieved ",nrow(packages.retrieved)," package descriptions.\n",sep=""))
  46         available <- rbind(available, packages.retrieved)
  47         message('updating list of available R task views...')
  48         ctv.available <- rbind(ctv.available,available.views(repo=mirror.url))
  49 }
  50
  51 #available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
  52
  53 dupes <- duplicated(rownames(available), fromLast=T)
  54 if (sum(dupes)>0) {
  55         if (verbose) cat("Found ",sum(dupes)," packages with the same name in different distributions. Those are now removed.\n",sep="")
  56         available <- available[!dupes,,drop=F]
  57 } else {
  58         if (length(mirrors)>1) cat("All packages have different names.")
  59 }
  60
  61 # TODO: Check if not better a dedicated tool should be called for this
  62 message('updating list of base R packages...')
  63 base_pkgs <- c("base",
  64                "compiler",
  65                "datasets",
  66                "graphics",
  67                "grDevices",
  68                "grid",
  69                "methods",
  70                "parallel",
  71                "splines",
  72                "stats",
  73                "stats4",
  74                "tcltk",
  75                "tools",
  76                "utils")
  77 # readLines(pipe(paste('sudo pbuilder --execute --override-config --configfile'
  78 #                                  ,shQuote(pbuilder_config),'-- /usr/bin/R --vanilla 2>&1 >/dev/null <'
  79 #                                  ,shQuote(file.path(root,'exec/get_base_pkgs'))
  80 #                                  ,'| grep -v ^W:')))
  81
  82 if (any(grep("^E:",base_pkgs,value=FALSE))) {
  83         cat("Cannot continue, the following error occurred:\n")
  84         cat(paste(grep("^E:",base_pkgs,value=TRUE),collapse="\n"))
  85         cat("\n")
  86         q(save="no")
  87 }
  88
  89
  90 if (debug) {
  91         cat("The following base packages were determined:\n")
  92         print(base_pkgs)
  93 }
  94
  95 message('updating list of existing Debian packages...')
  96 debian_pkgs <- readLines(pipe('apt-cache rdepends r-base-core | sed -e "/^  r-cran/{s/^[[:space:]]*r/r/;p}" -e d | sort -u'))
  97
  98 if (any(grep("^E:",debian_pkgs,value=FALSE))) {
  99         cat("Cannot continue, the following error occurred:\n")
 100         cat(paste(grep("^E:",debian_pkgs,value=TRUE),collapse="\n"))
 101         cat("\n")
 102         q(save="no")
 103 }
 104
 105 if (verbose) {
 106         cat("The following packages were found to be available:\n")
 107         print(debian_pkgs)
 108 }
 109
 110 save(debian_pkgs, base_pkgs, available, ctv.available, file=file.path(cache_root,'cache.rda'),eval.promises=T)
 111
 112 message('synchronising database...')
 113 db_update_package_versions()