# HG changeset patch
# User iuc
# Date 1451904024 18000
# Node ID 73cd1d529330deeab1e9a37dc8a1c03e6c96c38d
# Parent  68077fb03d757bc257c07b671b1847e4072580e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_2 commit 630c0f1ac3419322998d92a1653f260c664283ab

diff -r 68077fb03d75 -r 73cd1d529330 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 19:34:39 2015 -0500
+++ b/tool_dependencies.xml	Mon Jan 04 05:40:24 2016 -0500
@@ -14,10 +14,10 @@
                         <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
                     </action>
                 </actions>
-                <actions architecture="x86_64" os="darwin">
+                <actions>
                     <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 changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="1007a3015bdb" 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 changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -32,10 +32,10 @@
                         <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 changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="47ad4d7ba9fe" 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 changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="1007a3015bdb" 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 changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
@@ -50,33 +50,11 @@
                         <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 changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="47ad4d7ba9fe" 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">
-                        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$READLINE_INCLUDE_PATH" &amp;&amp;
-                        ./configure --with-tcltk \
-                                    --with-blas \
-                                    --with-lapack \
-                                    --with-readline \
-                                    --with-cairo \
-                                    --with-libpng \
-                                    --without-x \
-                                    --enable-R-shlib \
-                                    --disable-R-framework \
-                                    --libdir=$INSTALL_DIR/lib \
-                                    --prefix=$INSTALL_DIR 
-                    </action>
-                    <action type="make_install" />
+                    <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</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>
                 </actions>