# HG changeset patch
# User brenninc
# Date 1444397165 14400
# Node ID f37472daa3a8531eca68868314f79d97aa685134
# Parent  38b5b5e6905abbca6056fceb1c0f7aced51b4c07
Uploaded

diff -r 38b5b5e6905a -r f37472daa3a8 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Oct 09 09:25:03 2015 -0400
+++ b/tool_dependencies.xml	Fri Oct 09 09:26:05 2015 -0400
@@ -1,9 +1,5 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R" version="3.2.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action>
                 <package name="atlas" version="3.10.2">
                     <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                 </package>
@@ -28,7 +24,19 @@
                 <package name="fontconfig" version="2.11.1">
                     <repository changeset_revision="204a8c713d82" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                 </package>
+                <package name="libmxl2" version="2.9.1">
+                    <repository changeset_revision="df7589f53a88" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>                
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="c609d39e063f" name="brenninc_r_sept32105" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R_cairo" version="0.0.3">
+        <install version="1.0">
+            <actions>
                 <action type="set_environment_for_install">
+                    <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="atlas" version="3.10.2" />
+                    </repository>
                     <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="readline" version="6.3" />
                     </repository>
@@ -50,53 +58,31 @@
                     <repository changeset_revision="204a8c713d82" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="fontconfig" version="2.11.1" />
                     </repository>
-                </action>
-                <action type="shell_command">
-                    export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
-                    export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_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="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &amp;&amp;
-                    export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
-                    export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" &amp;&amp;
-                    export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" &amp;&amp;
-                    export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
-                    export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
-                    export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
-                    ./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="make_install" />
-                <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
-                <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
-                    <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
-                    <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
-                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
+                    <repository changeset_revision="df7589f53a88" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="libmxl2" version="2.9.1" />
+                    </repository>
+                </action>            
+                <action type="setup_r_environment">
+                    <repository changeset_revision="c609d39e063f" name="brenninc_r_sept32105" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.2.1" />
+                        <!-- includes base, boot, 
+                                      class, cluster, codetools, compiler, 
+                                      datasets, 
+                                      foreign, 
+                                      graphics, grDevices, grid, 
+                                      KernSmooth, 
+                                      lattice, 
+                                      MASS, Matrix, methods, mgcv, 
+                                      nlme, nnet, 
+                                      parallel, 
+                                      rpart,
+                                      spatial, splines, stats, stats4, survival,
+                                      tcltk, tools,
+                                      utils-->
+                    </repository>  
+                    <package>https://cran.r-project.org/src/contrib/Archive/Cairo/Cairo_1.5-8.tar.gz</package>
+                </action>            
             </actions>
         </install>
-        <readme>
-                The precompiled versions of this package were built 2015-07-27.
-                R is a free software environment for statistical computing and graphics.
-                NOTE: See custom compilation options above.
-        </readme>
     </package>
 </tool_dependency>