# HG changeset patch
# User devteam
# Date 1393882284 18000
# Node ID 6d84e7988416ad1e6a8128a670b9130dc2ece95e
# Parent  4692358aa325a93c8e1e36d3b054c5a82b631cf1
Uploaded

diff -r 4692358aa325 -r 6d84e7988416 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 26 16:16:04 2013 -0400
+++ b/tool_dependencies.xml	Mon Mar 03 16:31:24 2014 -0500
@@ -2,27 +2,90 @@
 <tool_dependency>
     <package name="R" version="2.11.0">
         <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://cran.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action>
-                <action type="shell_command">
-                    ./configure --enable-R-shlib \
-                                --with-readline=no \
-                                --with-x=no \
-                                --prefix=$INSTALL_DIR \
-                                --libdir=$INSTALL_DIR/lib \
-                                --disable-R-framework
-                </action>
-                <action type="shell_command">make &amp;&amp; make install</action>
+            <actions_group>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-2.11.0-Darwin-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-2.11.0-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <package name="readline" version="6.2">
+                        <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="libpng" version="1.6.7">
+                        <repository changeset_revision="a0b0e0281cc4" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="cairo" version="1.12.14">
+                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="pixman" version="0.32.4">
+                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="freetype" version="2.5.2">
+                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="readline" version="6.2" />
+                        </repository>
+                        <repository changeset_revision="a0b0e0281cc4" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="libpng" version="1.6.7" />
+                        </repository>
+                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="cairo" version="1.12.14" />
+                        </repository>
+                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="pixman" version="0.32.4" />
+                        </repository>
+                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="freetype" version="2.5.2" />
+                        </repository>
+                    </action>
+                    <action type="shell_command">
+                        export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIBS" &amp;&amp;
+                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIBS" &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_INCLUDES" &amp;&amp;
+                        export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &amp;&amp;
+                        export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &amp;&amp;
+                        ./configure --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 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
+                </actions>
                 <action type="set_environment">
+                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
                     <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
                     <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
                 </action>
-            </actions>
+            </actions_group>
         </install>
         <readme>
+                The precompiled Linux version of this package was built 2014-02-28.
+                The precompiled OSX version of this package was built 2014-03-03.
                 R is a free software environment for statistical computing and graphics.
                 NOTE: See custom compilation options above 
         </readme>
     </package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>