# HG changeset patch
# User brenninc
# Date 1444390279 14400
# Node ID 7bd7b7f98a91bfecbf33e4d40ad27b6037f67c3e
# Parent  980c02545efc203d274b1962f6e777c8812f7a9a
Uploaded

diff -r 980c02545efc -r 7bd7b7f98a91 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 04 08:10:52 2015 -0400
+++ b/tool_dependencies.xml	Fri Oct 09 07:31:19 2015 -0400
@@ -1,51 +1,102 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="pixman" version="0.32.4">
-      <repository changeset_revision="873f53f1abcd" name="package_pixman_0_32_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="libpng" version="1.6.7">
-      <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="freetype" version="2.5.2">
-      <repository changeset_revision="8999860ddf69" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="cairo" version="1.12.14">
-      <install version="1.0">
-          <actions>
-              <action type="download_by_url">http://depot.galaxyproject.org/package/source/cairo/cairo-1.12.14.tar.bz2</action>
+    <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>
+                <package name="readline" version="6.3">
+                    <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="libpng" version="1.6.7">
+                    <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <!--package name="cairo" version="1.14.2">
+                    <repository name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" />
+                </package>
+                <package name="pixman" version="0.32.6">
+                    <repository name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" />
+                </package>
+                <package name="freetype" version="2.5.2">
+                    <repository name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" />
+                </package>
+                <package name="ncurses" version="6.0">
+                    <repository name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" />
+                </package>
+                <package name="fontconfig" version="2.11.1">
+                    <repository name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" />
+                </package-->
                 <action type="set_environment_for_install">
-                  <repository changeset_revision="873f53f1abcd" name="package_pixman_0_32_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                      <package name="pixman" version="0.32.4" />
+                    <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>
                     <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                      <package name="libpng" version="1.6.7" />
+                        <package name="libpng" version="1.6.7" />
+                    </repository>
+                    <!--repository name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" >
+                        <package name="cairo" version="1.14.2" />
+                    </repository>
+                    <repository name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" >
+                        <package name="pixman" version="0.32.6" />
                     </repository>
-                    <repository changeset_revision="8999860ddf69" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                      <package name="freetype" version="2.5.2" />
+                    <repository name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" >
+                        <package name="freetype" version="2.5.2" />
                     </repository>
+                    <repository name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" >
+                        <package name="ncurses" version="6.0" />
+                    </repository>
+                    <repository name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" >
+                        <package name="fontconfig" version="2.11.1" />
+                    </repository-->
                 </action>
                 <action type="shell_command">
-                    export LDFLAGS="-Wl,-rpath,$PIXMAN_LIB_PATH -Wl,-rpath,$LIBPNG_ROOT/lib -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp; \ 
-                    ./configure --prefix=$INSTALL_DIR \
-                        --with-x=no \
-                        --enable-ft=yes \
-                        --enable-xcb-shm=no \
-                        --enable-xlib-xcb=no \
-                        --enable-xcb=no \
-                        --enable-xlib-xrender=no
+                    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" />
-                <!-- Create an empty cairo-xlib.h file, because R's configure script explicitly includes it even if X is disabled. -->
-                <action type="shell_command">touch $INSTALL_DIR/include/cairo/cairo-xlib.h</action>
+                <action type="shell_command">sed -i.bak -e 's;$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' $INSTALL_DIR/lib/R/bin/R</action>
                 <action type="set_environment">
-                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$INSTALL_DIR/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="CAIRO_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
+                    <environment_variable action="set_to" name="R_DOC_DIR">$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>
             </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>