# HG changeset patch
# User s-kaufmann
# Date 1408116405 14400
# Node ID 9914e0ec5a310a1acb44c1e23d71f7192c2103aa
# Parent  3208b7066844d225b58373c3244133b47ee3d8dc
Uploaded

diff -r 3208b7066844 -r 9914e0ec5a31 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 15 11:15:23 2014 -0400
+++ b/tool_dependencies.xml	Fri Aug 15 11:26:45 2014 -0400
@@ -32,99 +32,39 @@
 	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
 
- <package name="R_3_0_2" version="3.0.2">
+<package name="R_3_0_2" version="3.0.2">
         <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
-                        <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
-                    </action>
-                </actions>
-                <actions>
-                    <package name="readline" version="6.2">
-                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="libpng" version="1.6.7">
-                        <repository changeset_revision="833849e0ddfc" 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="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
-                    <action type="set_environment_for_install">
-                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="readline" version="6.2" />
-                        </repository>
-                        <repository changeset_revision="833849e0ddfc" 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_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;
-                        ./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 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
-                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
-                </actions>
+            <actions>
+                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="readline" version="6.2" />
+                    </repository>
+                    <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="5.9" />
+                    </repository>
+                    <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.6.7" />
+                    </repository>
+                </action>
+
+                <action type="shell_command">
+                    ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
+                </action>
+
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
                 <action type="set_environment">
-                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
                     <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
                     <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
+                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
                 </action>
-            </actions_group>
+            </actions>
         </install>
-        <readme>
-        The precompiled versions were built 2014-03-07.       
-        R is a free software environment for statistical computing and graphics. http://www.r-project.org/
-        </readme>
+        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
     </package>
-    
+
 </tool_dependency>