From e06845aa03a077579f3f571277461fe3d7f64a38 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Mon, 15 Aug 2016 17:43:49 -0400
Subject: [PATCH] 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 | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/cgi-updater-payload.sh b/cgi-updater-payload.sh
index 677cea8..628da9e 100755
--- a/cgi-updater-payload.sh
+++ b/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