# HG changeset patch
# User bgruening
# Date 1372681305 14400
# Node ID 1d5580f2ece03b8f2e3c641775358ebb2098d124
# Parent  b16fa4edfe55690c4f307e17cd64b6abba59fb3e
Uploaded

diff -r b16fa4edfe55 -r 1d5580f2ece0 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 01 08:19:37 2013 -0400
+++ b/tool_dependencies.xml	Mon Jul 01 08:21:45 2013 -0400
@@ -1,35 +1,44 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="91076df3471b" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="lapack" version="3.4.2">
+        <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="atlas" version="3.10.1">
+        <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="readline" version="6.2">
         <repository changeset_revision="b936498ae90c" name="package_readline_6_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="rpy2_2_3_6" version="2.3.6">
+
+    <package name="R_3_0_1" version="3.0.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.6.tar.gz</action>
+                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
                 <action type="set_environment_for_install">
+                    <repository changeset_revision="25dc49b0d6d5" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="atlas" version="3.10.1" />
+                    </repository>
+                    <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="lapack" version="3.4.2" />
+                    </repository>
                     <repository changeset_revision="b936498ae90c" name="package_readline_6_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="readline" version="6.2" />
                     </repository>
-                    <repository changeset_revision="91076df3471b" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="R_3_0_1" version="3.0.1" />
-                    </repository>
                 </action>
 
                 <action type="shell_command">
-                export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                export LDFLAGS=-L$READLINE_LIB_PATH &amp;&amp; 
-                python setup.py build --r-home $R_HOME --r-home-lib $R_HOME/lib install --home $INSTALL_DIR</action>
+                    export LDFLAGS=-L$READLINE_LIB_PATH &amp;&amp; 
+                    export CPPFLAGS=-I$READLINE_INCLUDE_PATH &amp;&amp; 
+                    ./configure --with-lapack="-L$ATLAS_LIB_DIR -llapack -lcblas" --with-blas="$LAPACK_LIB_DIR" --enable-R-shlib  --with-x=no --with-readline=yes --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install
+                </action>
                 <action type="set_environment">
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="set_to" name="R_HOME">$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>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.
-        http://rpy.sourceforge.net/rpy2.html
-        </readme>
+        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
     </package>
 </tool_dependency>