From 2e53016f91abb5af7e9cd24f336fce5f121c92ae Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 31 Jan 2012 09:04:16 +0100
Subject: Adjusted R installation

---
 config.sh  |  4 ++--
 kernlab.sh | 46 ++++++++++++++--------------------------------
 2 files changed, 16 insertions(+), 34 deletions(-)

diff --git a/config.sh b/config.sh
index 60dff2a..b553594 100755
--- a/config.sh
+++ b/config.sh
@@ -34,7 +34,7 @@ RUBY_CONF="$OT_PREFIX/.sh_ruby_ot"
 REDIS_CONF="$OT_PREFIX/.sh_redis_ot"
 NGINX_CONF="$OT_PREFIX/.sh_nginx_ot"
 OB_CONF="$OT_PREFIX/.sh_OB_ot"
-KL_CONF="$OT_PREFIX/.sh_R_ot"
+R_CONF="$OT_PREFIX/.sh_R_ot"
 
 RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
 OB_VER="openbabel-$OB_NUM_VER"
@@ -44,7 +44,7 @@ REDIS_VER="$REDIS_NUM_VER"
 RUBY_DEST="$OT_PREFIX/$RUBY_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
-KL_DEST="$OT_PREFIX/r-packages"
+R_DEST="$OT_PREFIX/r-packages"
 NGINX_DEST="$OT_PREFIX/nginx"
 REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER"
 
diff --git a/kernlab.sh b/kernlab.sh
index c4bafbd..2df0b8e 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -32,53 +32,35 @@ echo
 echo "Kernlab ('$LOG')."
 
 R_DONE=false
-mkdir "$KL_DEST" >/dev/null 2>&1
-if [ ! -d "$KL_DEST" ]; then
-  echo "Install directory '$KL_DEST' is not available! Aborting..."
+mkdir "$R_DEST" >/dev/null 2>&1
+if [ ! -d "$R_DEST" ]; then
+  echo "Install directory '$R_DEST' is not available! Aborting..."
   exit 1
 else
-  if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail
+  if ! rmdir "$R_DEST" >/dev/null 2>&1; then # if not empty this will fail
     R_DONE=true
   else
-    mkdir "$KL_DEST" >/dev/null 2>&1
+    mkdir "$R_DEST" >/dev/null 2>&1
   fi
 fi
 
 
 if ! $R_DONE; then
   cd $HOME/tmp
-  export R_LIBS="$KL_DEST" # To install non-global
-
-  URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download KL"
-  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL"
-
-
-  echo "Warning! If you already downloaded pls_2.3-0.tar.gz , robustbase_0.7-8.tar.gz and leaps_2.9.tar.gz from http://cran.r-project.org/src/contrib/ into $HOME/tmp/ press return, else <Ctrl+C> to stop installation."
-  read help_var2
-  echo 
-  #URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
-  #cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
-  cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
-
-  #URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz"
-  #cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
-  cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
-
-  #URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
-  #cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
-  cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS"
+  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"))
 fi
 
 
-if [ ! -f $KL_CONF ]; then
+if [ ! -f $R_CONF ]; then
 
-  echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
-  echo "if ! [ -d \"$KL_DEST\" ]; then echo \"\$0: '$KL_DEST' is not a directory!\"; fi" >> "$KL_CONF"
-  echo "R package destination has been stored in '$KL_CONF'."
+  echo "if echo \"\$R_LIBS\" | grep -v \"$R_DEST\">/dev/null 2>&1; then export R_LIBS=\"$R_DEST\"; fi" >> "$R_CONF"
+  echo "if ! [ -d \"$R_DEST\" ]; then echo \"\$0: '$R_DEST' is not a directory!\"; fi" >> "$R_CONF"
+  echo "R package destination has been stored in '$R_CONF'."
 
-  if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
-    echo ". \"$KL_CONF\"" >> $OT_UI_CONF
+  if ! grep "$R_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
+    echo ". \"$R_CONF\"" >> $OT_UI_CONF
   fi
 
 fi
-- 
cgit v1.2.3


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"))
-- 
cgit v1.2.3