BUG: Fix R updater function

- For some reason the exported bash function has trouble scoping the
  exported variable, so pass it explicitly as a function parameter.

- Create R_LIBS_USER directory if necessary.

- Correct printf expansion of R packages.

- Fix various typos.

- Use setwd() because we are spawning R in the /root directory.  This
  more robust that relying on `su - $user`.

- Enable echo for debugging.

cgi-updater-payload.sh

@@ -34,10 +34,15 @@ python_install_packages() {
 }
 
 r_install_packages() {
-    local pkgs=\"$(sprintf "\",%s\"" "${r_pkgs[@]}")\"
-    R --quiet -vanilla -e <<EOF
+    local pkgs=$@
+    pkgs=\"$(printf "\",\"%s" $pkgs)\"
+    Rscript --vanilla - <<EOF
+options(echo = TRUE)
+dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)
+.libPaths(Sys.getenv("R_LIBS_USER"))
+setwd(paste(Sys.getenv("R_HOME")))
 source("https://bioconductor.org/biocLite.R")
-biocLite(c(${pkgs:3})
+biocLite(c(${pkgs:3}))
 EOF
 }
 
@@ -50,10 +55,9 @@ main () {
     # Install R libraries in the user home directory so that updating
     # the libraries later on does not triggering the "unwritable
     # directory" warning.
-    export r_pkgs
-    export -f r_install packages
-    su cgi_user -c "bash -c r_install_packages"
-    unset r_pkgs r_install_packages
+    export -f r_install_packages
+    su cgi_user -c "bash -c \"r_install_packages ${r_pkgs[*]}\""
+    unset r_install_packages
 }
 
 main