# HG changeset patch
# User iuc
# Date 1450830879 18000
# Node ID 68077fb03d757bc257c07b671b1847e4072580e7
# Parent  41f43a2064ba0a836a5f0b2c2793e2b542395dee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_2 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5

diff -r 41f43a2064ba -r 68077fb03d75 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 10 22:39:35 2015 -0400
+++ b/tool_dependencies.xml	Tue Dec 22 19:34:39 2015 -0500
@@ -17,53 +17,53 @@
                 <actions architecture="x86_64" os="darwin">
                     <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action>
                     <package name="readline" version="6.2">
-                        <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" />
+                        <repository changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="libpng" version="1.6.7">
-                        <repository  name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" />
+                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="cairo" version="1.12.14">
-                        <repository name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" />
+                        <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="pixman" version="0.32.4">
-                        <repository name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" />
+                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="freetype" version="2.5.2">
-                        <repository name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" />
+                        <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="ncurses" version="5.9">
-                        <repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" />
+                        <repository changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <action type="set_environment_for_install">
-                        <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" >
+                        <repository changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="readline" version="6.2" />
                         </repository>
-                        <repository name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" >
+                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="libpng" version="1.6.7" />
                         </repository>
-                        <repository name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" >
+                        <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="cairo" version="1.12.14" />
                         </repository>
-                        <repository name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" >
+                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="pixman" version="0.32.4" />
                         </repository>
-                        <repository name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" >
+                        <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="freetype" version="2.5.2" />
                         </repository>
-                        <repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" >
+                        <repository changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="ncurses" version="5.9" />
                         </repository>
                     </action>
-                    <action type="shell_command"><![CDATA[
-                        export LDFLAGS="-L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &&
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" && 
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &&
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &&
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&
-                        export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &&
-                        export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &&
-                        export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &&
+                    <action type="shell_command">
+                        export LDFLAGS="-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,$PNG_LIB_PATH" &amp;&amp;
+                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
+                        export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
+                        export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
+                        export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
                         ./configure --with-tcltk \
                                     --with-blas \
                                     --with-lapack \
@@ -75,7 +75,7 @@
                                     --disable-R-framework \
                                     --libdir=$INSTALL_DIR/lib \
                                     --prefix=$INSTALL_DIR 
-                    ]]></action>
+                    </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>