From 9282f0715873f96cf43c23261a808dc00fb78914 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 31 Jan 2012 10:07:01 +0100
Subject: Fixed R lib install

---
 config.sh  | 2 --
 install    | 6 +++---
 kernlab.sh | 5 ++---
 packs.R    | 6 ++++++
 4 files changed, 11 insertions(+), 8 deletions(-)
 create mode 100644 packs.R

diff --git a/config.sh b/config.sh
index b553594..afe2012 100755
--- a/config.sh
+++ b/config.sh
@@ -16,7 +16,6 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-sun"
 # 3) What versions to install.
 RUBY_NUM_VER="1.8.7-2011.03"
 OB_NUM_VER="2.2.3"
-KL_NUM_VER="0.9-11"
 REDIS_NUM_VER="2.2.2"
 
 # 4) Server settings.
@@ -38,7 +37,6 @@ R_CONF="$OT_PREFIX/.sh_R_ot"
 
 RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
 OB_VER="openbabel-$OB_NUM_VER"
-KL_VER="$KL_NUM_VER"
 REDIS_VER="$REDIS_NUM_VER"
 
 RUBY_DEST="$OT_PREFIX/$RUBY_VER"
diff --git a/install b/install
index a486660..b0422b5 100755
--- a/install
+++ b/install
@@ -19,19 +19,19 @@ if [ -f "$HOME/.opentox-ui.sh" ]
 then
   mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE
 else
-  echo "$HOME/.opentox-ui.sh does not found (nothing to backup)."
+  echo "$HOME/.opentox-ui.sh not found (nothing to backup)."
 fi
 if [ -d "$HOME/.opentox" ]
 then
   mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE
 else
-  echo "$HOME/.opentox does not found (nothing to backup)."
+  echo "$HOME/.opentox not found (nothing to backup)."
 fi
 if [ -d "$HOME/opentox-ruby" ]
 then
   mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE
 else
-  echo "$HOME/opentox-ruby does not found (nothing to backup)."
+  echo "$HOME/opentox-ruby not found (nothing to backup)."
 fi 
 LOG="$HOME/tmp/`basename $0`-log.txt"
 . "./utils.sh"
diff --git a/kernlab.sh b/kernlab.sh
index 2df0b8e..aad125d 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -46,10 +46,9 @@ fi
 
 
 if ! $R_DONE; then
-  cd $HOME/tmp
   export R_LIBS="$R_DEST" # To install non-global
-  options(repos="http://mirrors.softliste.de/cran") # set mirror to avoid questioning the user
-  install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape"))
+  cmd="$R CMD BATCH packs.R" && run_cmd "$cmd" "R packages"
+  eval "$cmd"
 fi
 
 
diff --git a/packs.R b/packs.R
new file mode 100644
index 0000000..b130360
--- /dev/null
+++ b/packs.R
@@ -0,0 +1,6 @@
+# CRAN package installer for opentox-ruby
+# AM, 2012
+
+# set mirror to avoid questioning the user
+options(repos="http://mirrors.softliste.de/cran")
+install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape"))
-- 
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