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/2.12')
  18 mirrors <- c(mirrors,Omegahat="http://www.omegahat.org/R/src/contrib")
  19
  20 verbose<-TRUE
  21 debug<-FALSE
  22 package.filters <- c("OS_type","duplicates")
  23
  24 for (mirror.name in names(mirrors)) {
  25         mirror.url<-mirrors[mirror.name]
  26         message(paste("Updating list of available R packages from ",mirror.name," [",mirror.url,"].\n",sep=""))
  27         packages.retrieved <- NULL
  28         if ("CRAN" == mirror.name) {
  29                 packages.retrieved <- available.packages(contrib.url(mirror.url),filters=package.filters)
  30                 print(packages.retrieved[grep("SNP",rownames(packages.retrieved)),])
  31         } else if ("BioC" == mirror.name) {
  32                 repos <- c(
  33                         "bioc"
  34                         ,"data/annotation"
  35                         ,"data/experiment"
  36                         ,"extra"
  37                 )
  38                 for (s in repos) {
  39                         packages.retrieved <- rbind(
  40                                 packages.retrieved,
  41                                 available.packages(contrib.url(paste(mirror.url,s,sep="/")),filters=package.filters)
  42                         )
  43                 }
  44         } else {
  45                 packages.retrieved <- available.packages(mirror.url,filters=package.filters)
  46         }
  47         if (verbose) message(paste("Retrieved ",nrow(packages.retrieved)," package descriptions.\n",sep=""))
  48         available <- rbind(available, packages.retrieved)
  49         message('updating list of available R task views...')
  50         ctv.available <- rbind(ctv.available,available.views(repo=mirror.url))
  51 }
  52
  53 #available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
  54
  55 dupes <- duplicated(rownames(available), fromLast=T)
  56 if (sum(dupes)>0) {
  57         if (verbose) {
  58           cat("Found ",sum(dupes)," packages with the same name in different distributions. Those are now removed.\n",sep="")
  59           print(available[dupes,])
  60         }
  61
  62         available <- available[!dupes,,drop=F]
  63 } else {
  64         if (length(mirrors)>1) cat("All packages have different names.")
  65 }
  66
  67 # TODO: Check if not better a dedicated tool should be called for this
  68 message('updating list of base R packages...')
  69 base_pkgs <- c("base",
  70                "compiler",
  71                "datasets",
  72                "graphics",
  73                "grDevices",
  74                "grid",
  75                "methods",
  76                "parallel",
  77                "splines",
  78                "stats",
  79                "stats4",
  80                "tcltk",
  81                "tools",
  82                "utils")
  83 # readLines(pipe(paste('sudo pbuilder --execute --override-config --configfile'
  84 #                                  ,shQuote(pbuilder_config),'-- /usr/bin/R --vanilla 2>&1 >/dev/null <'
  85 #                                  ,shQuote(file.path(root,'exec/get_base_pkgs'))
  86 #                                  ,'| grep -v ^W:')))
  87
  88 if (any(grep("^E:",base_pkgs,value=FALSE))) {
  89         cat("Cannot continue, the following error occurred:\n")
  90         cat(paste(grep("^E:",base_pkgs,value=TRUE),collapse="\n"))
  91         cat("\n")
  92         q(save="no")
  93 }
  94
  95
  96 if (debug) {
  97         cat("The following base packages were determined:\n")
  98         print(base_pkgs)
  99 }
 100
 101 message('updating list of existing Debian packages...')
 102 debian_pkgs <- readLines(pipe('apt-cache rdepends r-base-core | sed -e "/^  r-cran/{s/^[[:space:]]*r/r/;p}" -e d | sort -u'))
 103
 104 if (any(grep("^E:",debian_pkgs,value=FALSE))) {
 105         cat("Cannot continue, the following error occurred:\n")
 106         cat(paste(grep("^E:",debian_pkgs,value=TRUE),collapse="\n"))
 107         cat("\n")
 108         q(save="no")
 109 }
 110
 111 if (verbose) {
 112         cat("The following packages were found to be available:\n")
 113         print(debian_pkgs)
 114 }
 115
 116 save(debian_pkgs, base_pkgs, available, ctv.available, file=file.path(cache_root,'cache.rda'),eval.promises=T)
 117
 118 message('synchronising database...')
 119 db_update_package_versions()