# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1415358294 -3600
# Node ID 16ad47f8751fdfa32252f25731b44c682fe46df3
# Parent  e6171a39dd049ab5651c9dff6884eed0aae39350
adding lib png and other options

diff -r e6171a39dd04 -r 16ad47f8751f INSTALL.r
--- a/INSTALL.r	Thu Nov 06 16:05:24 2014 +0100
+++ b/INSTALL.r	Fri Nov 07 12:04:54 2014 +0100
@@ -4,7 +4,7 @@
 source("http://bioconductor.org/biocLite.R")
 biocLite()
 
-# upgrage? Some packages are "old"  and can be upgraded with: biocLite("BiocUpgrade")
+# upgrade? Some packages are "old"  and can be upgraded with: biocLite("BiocUpgrade")
 
 
 #  install metaMS and multtest for differential analysis tool (from xcms)
diff -r e6171a39dd04 -r 16ad47f8751f tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 06 16:05:24 2014 +0100
+++ b/tool_dependencies.xml	Fri Nov 07 12:04:54 2014 +0100
@@ -7,13 +7,65 @@
       <install version="1.0">
           <actions_group>
                 <actions>
+                	<package name="readline" version="6.2">
+                      <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="libpng" version="1.6.7">
+                      <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="cairo" version="1.12.14">
+                      <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="pixman" version="0.32.4">
+                      <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="freetype" version="2.5.2">
+                      <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.3.tar.gz</action>
+                    <action type="set_environment_for_install">
+                      <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                          <package name="readline" version="6.2" />
+                        </repository>
+                        <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                          <package name="libpng" version="1.6.7" />
+                        </repository>
+                        <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                          <package name="cairo" version="1.12.14" />
+                        </repository>
+                        <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                          <package name="pixman" version="0.32.4" />
+                        </repository>
+                        <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                          <package name="freetype" version="2.5.2" />
+                        </repository>
+                    </action>
                     <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action>
                     <action type="move_directory_files">
 	                  	<source_directory>.</source_directory>
 	                    <destination_directory>$INSTALL_DIR</destination_directory>
 	                </action>
                     <action type="shell_command">
-                        cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR
+                        cd $INSTALL_DIR; 
+                        export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &amp;&amp;
+                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
+                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
+                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
+                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
+                        export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
+                        export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
+                        export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
+                        $INSTALL_DIR/configure  --with-tcltk \
+			                                    --with-blas \
+			                                    --with-lapack \
+			                                    --with-readline \
+			                                    --with-cairo \
+			                                    --with-libpng \
+			                                    --without-x \
+			                                    --enable-R-shlib \
+			                                    --disable-R-framework \
+			                                    --libdir=$INSTALL_DIR/lib \
+			                                    --prefix=$INSTALL_DIR
                     </action>
                     <action type="shell_command">make -C $INSTALL_DIR</action>
                 </actions>