From b345b0ee923cd089a58feb8eeaba19cebd7f08c1 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 10:24:26 +0200
Subject: Making exec

---
 kernlab.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 kernlab.sh

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
old mode 100644
new mode 100755
-- 
cgit v1.2.3


From 5b5f068e2096ef86491887e773e2cf2349bb6344 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 12:03:59 +0200
Subject: Added Kernlab

---
 kernlab.sh | 39 +++++++++++++++++++++++++++++++++------
 1 file changed, 33 insertions(+), 6 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index db0c93d..d95b275 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -1,8 +1,35 @@
-#!/bin/sh
+#!/bin/bash
+#
+# Installs Kernlab.
+# Author: Christoph Helma, Andreas Maunz.
+#
 
-echo "Installing kernlab"
-. /etc/profile
+if [ "$(id -u)" = "0" ]; then
+  echo "This script must be run as non-root." 1>&2
+  exit 1
+fi
+
+# Utils
+R="`which R`"
+if [ ! -e "$R" ]; then
+  echo "'R' missing. Install 'R' first. Aborting..."
+  exit 1
+fi
+
+# Pkg
+VER="0.9-11"
+
+DIR="`pwd`"
+echo "This installs Kernlab."
+echo "Press <Return> to continue, or <Ctrl+C> to abort."
+read
 cd /tmp
-wget http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_0.9-11.tar.gz
-R CMD INSTALL kernlab_0.9-11.tar.gz
-cd -
+if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$VER.tar.gz">/dev/null 2>&1; then
+  echo "Download failed! Aborting..."
+  exit 1
+fi
+R CMD INSTALL kernlab_$VER.tar.gz
+cd "$DIR"
+
+echo
+echo "Kernlab Installation finished."
-- 
cgit v1.2.3


From e53c4f70598e403ba38c27a4637d540a10ee2075 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 12:07:43 +0200
Subject: Kernlab fix: Missing command

---
 kernlab.sh | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index d95b275..673c1f6 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -10,6 +10,12 @@ if [ "$(id -u)" = "0" ]; then
 fi
 
 # Utils
+WGET="`which wget`"
+if [ ! -e "$WGET" ]; then
+  echo "'wget' missing. Install 'wget' first. Aborting..."
+  exit 1
+fi
+
 R="`which R`"
 if [ ! -e "$R" ]; then
   echo "'R' missing. Install 'R' first. Aborting..."
-- 
cgit v1.2.3


From 6ba25c9cc51c285fdd1443057f61213668bb4a1b Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 12:24:28 +0200
Subject: Kernlab fix: Missing command

---
 kernlab.sh | 49 ++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 44 insertions(+), 5 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 673c1f6..56f3168 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -25,16 +25,55 @@ fi
 # Pkg
 VER="0.9-11"
 
-DIR="`pwd`"
+# Dest
+R_CONF=$HOME/.bash_R_ot
+DEST="$HOME/r-packages"
+if [ -n "$1" ]; then
+  DEST="$1"
+fi
+
+
 echo "This installs Kernlab."
 echo "Press <Return> to continue, or <Ctrl+C> to abort."
 read
-cd /tmp
-if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$VER.tar.gz">/dev/null 2>&1; then
-  echo "Download failed! Aborting..."
+
+DIR="`pwd`"
+
+R_DONE=false
+mkdir "$DEST" >/dev/null 2>&1
+if [ ! -d "$DEST" ]; then
+  echo "Install directory '$DEST' is not available! Aborting..."
   exit 1
+else
+  if ! rmdir "$DEST" >/dev/null 2>&1; then # if not empty this will fail
+    echo "Install directory '$DEST' is not empty. Skipping kernlab installation..."
+    R_DONE=true
+  fi
+fi
+if ! $R_DONE; then
+cd /tmp
+  if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$VER.tar.gz">/dev/null 2>&1; then
+    echo "Download failed! Aborting..."
+    exit 1
+  fi
+  export R_LIBS="$DEST"
+  $R CMD INSTALL "kernlab_$VER.tar.gz"
 fi
-R CMD INSTALL kernlab_$VER.tar.gz
+
+echo 
+echo "Preparing R..."
+if [ ! -f $R_CONF ]; then
+  echo "R_LIBS=\"$DEST\"" >> "$R_CONF"
+  echo "R package destination has been stored in '$R_CONF'."
+  echo -n "Decide if R configuration should be linked to your .bashrc ('y/n'): "
+  read ANSWER_R_CONF
+  if [ $ANSWER_R_CONF = "y" ]; then
+    echo "source \"$R_CONF\"" >> $HOME/.bashrc
+  fi
+else
+  echo "It seems R is already configured ('$R_CONF' exists)."
+fi
+
 cd "$DIR"
 
 echo
-- 
cgit v1.2.3


From bf309f52283db539ca1f8d9c004cad7eb88b2de4 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 12:28:03 +0200
Subject: Kernlab fix: install dir

---
 kernlab.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 56f3168..0c7d7e8 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -26,7 +26,7 @@ fi
 VER="0.9-11"
 
 # Dest
-R_CONF=$HOME/.bash_R_ot
+R_CONF="$HOME/.bash_R_ot"
 DEST="$HOME/r-packages"
 if [ -n "$1" ]; then
   DEST="$1"
@@ -63,7 +63,7 @@ fi
 echo 
 echo "Preparing R..."
 if [ ! -f $R_CONF ]; then
-  echo "R_LIBS=\"$DEST\"" >> "$R_CONF"
+  echo "export R_LIBS=\"$DEST\"" >> "$R_CONF"
   echo "R package destination has been stored in '$R_CONF'."
   echo -n "Decide if R configuration should be linked to your .bashrc ('y/n'): "
   read ANSWER_R_CONF
-- 
cgit v1.2.3


From 0c926b09753901c446d9b5d82b8c3e9307fda887 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 12:57:21 +0200
Subject: nginx install

---
 kernlab.sh | 40 +++++++++++++++++++---------------------
 1 file changed, 19 insertions(+), 21 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 0c7d7e8..8da3ec6 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -23,13 +23,9 @@ if [ ! -e "$R" ]; then
 fi
 
 # Pkg
-VER="0.9-11"
-
-# Dest
-R_CONF="$HOME/.bash_R_ot"
-DEST="$HOME/r-packages"
+source ./config.sh
 if [ -n "$1" ]; then
-  DEST="$1"
+  KL_DEST="$1"
 fi
 
 
@@ -40,38 +36,40 @@ read
 DIR="`pwd`"
 
 R_DONE=false
-mkdir "$DEST" >/dev/null 2>&1
-if [ ! -d "$DEST" ]; then
-  echo "Install directory '$DEST' is not available! Aborting..."
+mkdir "$KL_DEST" >/dev/null 2>&1
+if [ ! -d "$KL_DEST" ]; then
+  echo "Install directory '$KL_DEST' is not available! Aborting..."
   exit 1
 else
-  if ! rmdir "$DEST" >/dev/null 2>&1; then # if not empty this will fail
-    echo "Install directory '$DEST' is not empty. Skipping kernlab installation..."
+  if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail
+    echo "Install directory '$KL_DEST' is not empty. Skipping kernlab installation..."
     R_DONE=true
+  else
+    mkdir "$KL_DEST" >/dev/null 2>&1
   fi
 fi
 if ! $R_DONE; then
 cd /tmp
-  if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$VER.tar.gz">/dev/null 2>&1; then
+  if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz">/dev/null 2>&1; then
     echo "Download failed! Aborting..."
     exit 1
   fi
-  export R_LIBS="$DEST"
-  $R CMD INSTALL "kernlab_$VER.tar.gz"
+  export R_LIBS="$KL_DEST"
+  $R CMD INSTALL "kernlab_$KL_VER.tar.gz"
 fi
 
 echo 
 echo "Preparing R..."
-if [ ! -f $R_CONF ]; then
-  echo "export R_LIBS=\"$DEST\"" >> "$R_CONF"
-  echo "R package destination has been stored in '$R_CONF'."
+if [ ! -f $KL_CONF ]; then
+  echo "export R_LIBS=\"$KL_DEST\"" >> "$KL_CONF"
+  echo "R package destination has been stored in '$KL_CONF'."
   echo -n "Decide if R configuration should be linked to your .bashrc ('y/n'): "
-  read ANSWER_R_CONF
-  if [ $ANSWER_R_CONF = "y" ]; then
-    echo "source \"$R_CONF\"" >> $HOME/.bashrc
+  read ANSWER_KL_CONF
+  if [ $ANSWER_KL_CONF = "y" ]; then
+    echo "source \"$KL_CONF\"" >> $HOME/.bashrc
   fi
 else
-  echo "It seems R is already configured ('$R_CONF' exists)."
+  echo "It seems R is already configured ('$KL_CONF' exists)."
 fi
 
 cd "$DIR"
-- 
cgit v1.2.3


From 78a251a002390dafd1f26271e9b8a531fb9aea14 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 29 Mar 2011 13:06:32 +0200
Subject: Nginx fix: ENV variable

---
 kernlab.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 8da3ec6..91f6cb5 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -49,7 +49,7 @@ else
   fi
 fi
 if ! $R_DONE; then
-cd /tmp
+  cd /tmp
   if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz">/dev/null 2>&1; then
     echo "Download failed! Aborting..."
     exit 1
-- 
cgit v1.2.3


From 3dfa712a33df34c7d605abe36f4e7ff17f251162 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 31 Mar 2011 09:21:47 +0200
Subject: openbabel.sh

---
 kernlab.sh | 36 ++++++++++++++++++++++++------------
 1 file changed, 24 insertions(+), 12 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 91f6cb5..86f1503 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -24,12 +24,11 @@ fi
 
 # Pkg
 source ./config.sh
-if [ -n "$1" ]; then
-  KL_DEST="$1"
-fi
-
+source ./utils.sh
+LOG="/tmp`basename $0`-log.txt"
 
 echo "This installs Kernlab."
+echo "Log file is '$LOG'."
 echo "Press <Return> to continue, or <Ctrl+C> to abort."
 read
 
@@ -48,29 +47,42 @@ else
     mkdir "$KL_DEST" >/dev/null 2>&1
   fi
 fi
+
+
 if ! $R_DONE; then
   cd /tmp
-  if ! $WGET -O - "http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz">/dev/null 2>&1; then
-    echo "Download failed! Aborting..."
+  URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
+  if ! $WGET -O - "$URI">>$LOG 2>&1; then
+    printf "%25s%15s\n" "'Download'" "FAIL"
     exit 1
   fi
-  export R_LIBS="$KL_DEST"
-  $R CMD INSTALL "kernlab_$KL_VER.tar.gz"
+  printf "%25s%15s\n" "'Download'" "DONE"
+
+  export R_LIBS="$KL_DEST" # To install non-global
+
+  if ! $R CMD INSTALL "kernlab_$KL_VER.tar.gz">>$LOG 2>&1; then
+    printf "%25s%15s\n" "'Install'" "FAIL"
+  fi
+  printf "%25s%15s\n" "'Install'" "DONE"
 fi
 
+
 echo 
 echo "Preparing R..."
+
 if [ ! -f $KL_CONF ]; then
-  echo "export R_LIBS=\"$KL_DEST\"" >> "$KL_CONF"
+
+  echo "if ! [[ \"\$R_LIBS\" =~ \"$KL_DEST\" ]]; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
   echo "R package destination has been stored in '$KL_CONF'."
-  echo -n "Decide if R configuration should be linked to your .bashrc ('y/n'): "
-  read ANSWER_KL_CONF
-  if [ $ANSWER_KL_CONF = "y" ]; then
+
+  if ! grep "$KL_CONF" $HOME/.bashrc >/dev/null 2>&1 ; then
     echo "source \"$KL_CONF\"" >> $HOME/.bashrc
   fi
+
 else
   echo "It seems R is already configured ('$KL_CONF' exists)."
 fi
+source "$KL_CONF"
 
 cd "$DIR"
 
-- 
cgit v1.2.3


From 312d93bcc322fa5aca38f38cd266569aaf18b621 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 31 Mar 2011 11:56:47 +0200
Subject: all

---
 kernlab.sh | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 86f1503..5426744 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -25,12 +25,9 @@ fi
 # Pkg
 source ./config.sh
 source ./utils.sh
-LOG="/tmp`basename $0`-log.txt"
+LOG="/tmp/`basename $0`-log.txt"
 
-echo "This installs Kernlab."
-echo "Log file is '$LOG'."
-echo "Press <Return> to continue, or <Ctrl+C> to abort."
-read
+echo "Kernlab ('$LOG')."
 
 DIR="`pwd`"
 
@@ -41,7 +38,7 @@ if [ ! -d "$KL_DEST" ]; then
   exit 1
 else
   if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail
-    echo "Install directory '$KL_DEST' is not empty. Skipping kernlab installation..."
+    echo "Install directory '$KL_DEST' not empty. Skipping kernlab installation."
     R_DONE=true
   else
     mkdir "$KL_DEST" >/dev/null 2>&1
@@ -49,10 +46,13 @@ else
 fi
 
 
+echo 
+echo "Installing:"
+
 if ! $R_DONE; then
   cd /tmp
   URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
-  if ! $WGET -O - "$URI">>$LOG 2>&1; then
+  if ! $WGET "$URI" >>$LOG 2>&1; then
     printf "%25s%15s\n" "'Download'" "FAIL"
     exit 1
   fi
@@ -68,7 +68,7 @@ fi
 
 
 echo 
-echo "Preparing R..."
+echo "Preparing:"
 
 if [ ! -f $KL_CONF ]; then
 
@@ -82,9 +82,6 @@ if [ ! -f $KL_CONF ]; then
 else
   echo "It seems R is already configured ('$KL_CONF' exists)."
 fi
-source "$KL_CONF"
 
 cd "$DIR"
 
-echo
-echo "Kernlab Installation finished."
-- 
cgit v1.2.3


From 59f6d70df510eb5e009f71a15ccbf20053ec7975 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 31 Mar 2011 12:42:16 +0200
Subject: all

---
 kernlab.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 5426744..20aea16 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -4,6 +4,9 @@
 # Author: Christoph Helma, Andreas Maunz.
 #
 
+source ./config.sh
+source ./utils.sh
+
 if [ "$(id -u)" = "0" ]; then
   echo "This script must be run as non-root." 1>&2
   exit 1
@@ -23,8 +26,6 @@ if [ ! -e "$R" ]; then
 fi
 
 # Pkg
-source ./config.sh
-source ./utils.sh
 LOG="/tmp/`basename $0`-log.txt"
 
 echo "Kernlab ('$LOG')."
-- 
cgit v1.2.3


From 6bcb46de198aff22039eeb40f2a4392421c823d8 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 31 Mar 2011 13:56:31 +0200
Subject: all

---
 kernlab.sh | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 20aea16..b620ade 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -53,18 +53,10 @@ echo "Installing:"
 if ! $R_DONE; then
   cd /tmp
   URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
-  if ! $WGET "$URI" >>$LOG 2>&1; then
-    printf "%25s%15s\n" "'Download'" "FAIL"
-    exit 1
-  fi
-  printf "%25s%15s\n" "'Download'" "DONE"
+  cmd="$WGET $URI" && run_cmd "$cmd" "Download"
 
   export R_LIBS="$KL_DEST" # To install non-global
-
-  if ! $R CMD INSTALL "kernlab_$KL_VER.tar.gz">>$LOG 2>&1; then
-    printf "%25s%15s\n" "'Install'" "FAIL"
-  fi
-  printf "%25s%15s\n" "'Install'" "DONE"
+  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install"
 fi
 
 
-- 
cgit v1.2.3


From 7578e353de1cde367e7fd08235e23b6e499c1197 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 31 Mar 2011 14:44:24 +0200
Subject: all

---
 kernlab.sh | 8 --------
 1 file changed, 8 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index b620ade..9ab2556 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -47,9 +47,6 @@ else
 fi
 
 
-echo 
-echo "Installing:"
-
 if ! $R_DONE; then
   cd /tmp
   URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
@@ -60,9 +57,6 @@ if ! $R_DONE; then
 fi
 
 
-echo 
-echo "Preparing:"
-
 if [ ! -f $KL_CONF ]; then
 
   echo "if ! [[ \"\$R_LIBS\" =~ \"$KL_DEST\" ]]; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
@@ -72,8 +66,6 @@ if [ ! -f $KL_CONF ]; then
     echo "source \"$KL_CONF\"" >> $HOME/.bashrc
   fi
 
-else
-  echo "It seems R is already configured ('$KL_CONF' exists)."
 fi
 
 cd "$DIR"
-- 
cgit v1.2.3


From b69506cc0d7b3b2336444b6458cde7507388a8ca Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 1 Apr 2011 15:28:49 +0200
Subject: Removed sourcing of config.sh

---
 kernlab.sh | 1 -
 1 file changed, 1 deletion(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 9ab2556..73353a6 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -4,7 +4,6 @@
 # Author: Christoph Helma, Andreas Maunz.
 #
 
-source ./config.sh
 source ./utils.sh
 
 if [ "$(id -u)" = "0" ]; then
-- 
cgit v1.2.3


From 7dacb96c5c4c46f8fd0c76bd26e5d37319bb5eb1 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 1 Apr 2011 15:37:43 +0200
Subject: all

---
 kernlab.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 73353a6..2716b66 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -4,7 +4,8 @@
 # Author: Christoph Helma, Andreas Maunz.
 #
 
-source ./utils.sh
+source "`pwd`/utils.sh"
+DIR="`pwd`"
 
 if [ "$(id -u)" = "0" ]; then
   echo "This script must be run as non-root." 1>&2
@@ -29,8 +30,6 @@ LOG="/tmp/`basename $0`-log.txt"
 
 echo "Kernlab ('$LOG')."
 
-DIR="`pwd`"
-
 R_DONE=false
 mkdir "$KL_DEST" >/dev/null 2>&1
 if [ ! -d "$KL_DEST" ]; then
-- 
cgit v1.2.3


From dac77af34f7ed10223b1fe31d658df0c2b64c23f Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 1 Apr 2011 15:39:29 +0200
Subject: all

---
 kernlab.sh | 1 +
 1 file changed, 1 insertion(+)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 2716b66..21fc642 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -28,6 +28,7 @@ fi
 # Pkg
 LOG="/tmp/`basename $0`-log.txt"
 
+echo
 echo "Kernlab ('$LOG')."
 
 R_DONE=false
-- 
cgit v1.2.3


From aed19c4491d6713e4ea75d4a8febef57752203d9 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 1 Apr 2011 15:43:14 +0200
Subject: all

---
 kernlab.sh | 1 -
 1 file changed, 1 deletion(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 21fc642..395d49a 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -38,7 +38,6 @@ if [ ! -d "$KL_DEST" ]; then
   exit 1
 else
   if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail
-    echo "Install directory '$KL_DEST' not empty. Skipping kernlab installation."
     R_DONE=true
   else
     mkdir "$KL_DEST" >/dev/null 2>&1
-- 
cgit v1.2.3


From 6e15685c0992a720507209c2c9b43a9c561ade5e Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 1 Apr 2011 16:27:53 +0200
Subject: Removed bashismsh

---
 kernlab.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 395d49a..10141e2 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -1,10 +1,10 @@
-#!/bin/bash
+#!/bin/sh
 #
 # Installs Kernlab.
 # Author: Christoph Helma, Andreas Maunz.
 #
 
-source "`pwd`/utils.sh"
+. "`pwd`/utils.sh"
 DIR="`pwd`"
 
 if [ "$(id -u)" = "0" ]; then
@@ -61,7 +61,7 @@ if [ ! -f $KL_CONF ]; then
   echo "R package destination has been stored in '$KL_CONF'."
 
   if ! grep "$KL_CONF" $HOME/.bashrc >/dev/null 2>&1 ; then
-    echo "source \"$KL_CONF\"" >> $HOME/.bashrc
+    echo ". \"$KL_CONF\"" >> $HOME/.bashrc
   fi
 
 fi
-- 
cgit v1.2.3


From c3496282449215855acb5c083c20a1782803617a Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Sat, 2 Apr 2011 15:32:29 +0200
Subject: Replaced substring matching by grep

---
 kernlab.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 10141e2..4267a86 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -57,7 +57,7 @@ fi
 
 if [ ! -f $KL_CONF ]; then
 
-  echo "if ! [[ \"\$R_LIBS\" =~ \"$KL_DEST\" ]]; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
+  echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
   echo "R package destination has been stored in '$KL_CONF'."
 
   if ! grep "$KL_CONF" $HOME/.bashrc >/dev/null 2>&1 ; then
-- 
cgit v1.2.3


From 112bb64ae66c852797d5c305df7e1823bca10117 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Sat, 2 Apr 2011 07:41:39 -0700
Subject: Fixed link to libgfortran

---
 kernlab.sh | 1 +
 1 file changed, 1 insertion(+)
 mode change 100755 => 100644 kernlab.sh

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
old mode 100755
new mode 100644
index 4267a86..20ebaca
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -51,6 +51,7 @@ if ! $R_DONE; then
   cmd="$WGET $URI" && run_cmd "$cmd" "Download"
 
   export R_LIBS="$KL_DEST" # To install non-global
+  sudo ln -s /usr/lib/libgfortran.so.3 /usr/lib/libgfortran.so>$LOG 2>&1 # may fail, but nevermind
   cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install"
 fi
 
-- 
cgit v1.2.3


From d1cda0647404a6a83e5a9b93e3c2789cc5123537 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Sat, 2 Apr 2011 08:49:05 -0700
Subject: removed ln -s again

---
 kernlab.sh | 1 -
 1 file changed, 1 deletion(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 20ebaca..4267a86 100644
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -51,7 +51,6 @@ if ! $R_DONE; then
   cmd="$WGET $URI" && run_cmd "$cmd" "Download"
 
   export R_LIBS="$KL_DEST" # To install non-global
-  sudo ln -s /usr/lib/libgfortran.so.3 /usr/lib/libgfortran.so>$LOG 2>&1 # may fail, but nevermind
   cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install"
 fi
 
-- 
cgit v1.2.3


From e8dc762a04a5559392ec6fa8bdd055bd6557acc7 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 7 Apr 2011 08:42:19 +0200
Subject: Using separate rc file for installer

---
 kernlab.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index 4267a86..a49635f 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -60,8 +60,8 @@ if [ ! -f $KL_CONF ]; then
   echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
   echo "R package destination has been stored in '$KL_CONF'."
 
-  if ! grep "$KL_CONF" $HOME/.bashrc >/dev/null 2>&1 ; then
-    echo ". \"$KL_CONF\"" >> $HOME/.bashrc
+  if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
+    echo ". \"$KL_CONF\"" >> $OT_UI_CONF
   fi
 
 fi
-- 
cgit v1.2.3


From e2da541cecd308ee314267b33476c052f31e3204 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 11 Apr 2011 09:10:00 +0200
Subject: Guarding dirs, Linking OB LIB to site_ruby

---
 kernlab.sh | 1 +
 1 file changed, 1 insertion(+)

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
index a49635f..2fba2a8 100644
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -58,6 +58,7 @@ fi
 if [ ! -f $KL_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'."
 
   if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
-- 
cgit v1.2.3


From d5044c3a4ff041da62e144496fb6ef9e5969804e Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 27 Apr 2011 14:59:49 +0200
Subject: Changed exec status

---
 kernlab.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 kernlab.sh

(limited to 'kernlab.sh')

diff --git a/kernlab.sh b/kernlab.sh
old mode 100644
new mode 100755
-- 
cgit v1.2.3