# HG changeset patch
# User brenninc
# Date 1460544131 14400
# Node ID 1eda5afe26d0e02222482dbf371804fe4c33d9e4
# Parent  db02ab55306e9b6557a35a343904d27bb67a8c36
Uploaded

diff -r db02ab55306e -r 1eda5afe26d0 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 12 04:48:31 2016 -0400
+++ b/tool_dependencies.xml	Wed Apr 13 06:42:11 2016 -0400
@@ -35,6 +35,9 @@
                     <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                 </package>
                 <action type="set_environment_for_install">
+                    <repository changeset_revision="c47756a8136e" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="atlas" version="3.10.2" />
+                    </repository>
                     <repository changeset_revision="66ad0cc12007" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="cairo" version="1.14.2" />
                     </repository>
@@ -91,9 +94,9 @@
                 <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' $INSTALL_DIR/lib/R/bin/R</action>
                 <action type="set_environment">
+                    <environment_variable action="set_to" name="NCURSES_ROOT_PATH">$ENV[NCURSES_ROOT_PATH]</environment_variable>
                     <environment_variable action="set_to" name="NCURSES_INCLUDE_PATH">$ENV[NCURSES_ROOT_PATH]/include</environment_variable>
                     <environment_variable action="set_to" name="NCURSES_LIB_PATH">$ENV[NCURSES_ROOT_PATH]/lib/</environment_variable>
-                    <environment_variable action="set_to" name="NCURSES_ROOT_PATH">$ENV[NCURSES_ROOT_PATH]</environment_variable>
                     <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[NCURSES_ROOT_PATH]/lib</environment_variable>
                     <environment_variable action="prepend_to" name="LIBRARY_PATH">$ENV[NCURSES_ROOT_PATH]/lib</environment_variable>
                     <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[NCURSES_ROOT_PATH]/include</environment_variable>
@@ -101,12 +104,12 @@
                     <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[NCURSES_ROOT_PATH]/include/ncurses</environment_variable>
                     <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[NCURSES_ROOT_PATH]/include/ncurses</environment_variable>
 
+                    <environment_variable action="set_to" name="READLINE_ROOT_PATH">$ENV[READLINE_ROOT_PATH]</environment_variable>
                     <environment_variable action="set_to" name="READLINE_INCLUDE_PATH">$ENV[READLINE_ROOT_PATH]/include</environment_variable>
                     <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[READLINE_ROOT_PATH]/include</environment_variable>
                     <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[READLINE_ROOT_PATH]/include</environment_variable>
                     <environment_variable action="set_to" name="READLINE_LIB_PATH">$ENV[READLINE_ROOT_PATH]/lib</environment_variable>
                     <environment_variable action="set_to" name="READLINE_BIN_PATH">$ENV[READLINE_ROOT_PATH]/bin</environment_variable>
-                    <environment_variable action="set_to" name="READLINE_ROOT_PATH">$ENV[READLINE_ROOT_PATH]</environment_variable>
                     <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[READLINE_ROOT_PATH]/lib</environment_variable>
                     <!--environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[NCURSES_LIB_PATH]</environment_variable-->
                     <environment_variable action="prepend_to" name="LIBRARY_PATH">$ENV[READLINE_ROOT_PATH]/lib</environment_variable>
@@ -134,28 +137,27 @@
                     <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_ROOT]/lib</environment_variable>
                     <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[LIBPNG_ROOT]/lib/pkgconfig</environment_variable>
 
-                    <environment_variable action="set_to" name="PIXMAN_ROOT_PATH">$ENV[PIXMAN_ROOT_PATH]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PIXMAN_ROOT_PATH]/bin</environment_variable>
-                    <environment_variable action="set_to" name="PIXMAN_LIB_PATH">$ENV[PIXMAN_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[PIXMAN_ROOT_PATH]/lib/pkgconfig</environment_variable>
+                    <environment_variable action="set_to" name="PIXMAN_LIB_PATH">$ENV[PIXMAN_LIB_PATH]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PIXMAN_LIB_PATH]</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[PIXMAN_LIB_PATH]/pkgconfig</environment_variable>
 
-                    <environment_variable action="set_to" name="LIBXML2_ROOT_PATH">$ENV[LIBXML2_ROOT_PATH]</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[LIBXML2_ROOT_PATH]/lib/pkgconfig</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[LIBXML2_ROOT_PATH]/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$ENV[LIBXML2_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBXML2_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="LIBRARY_PATH">$ENV[LIBXML2_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[LIBXML2_ROOT_PATH]/include</environment_variable>
-                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[LIBXML2_ROOT_PATH]/include</environment_variable>
+                    <environment_variable action="set_to" name="LIBXML2_ROOT_DIR">$ENV[LIBXML2_ROOT_DIR]</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[LIBXML2_ROOT_DIR]/lib/pkgconfig</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[LIBXML2_ROOT_DIR]/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$ENV[LIBXML2_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBXML2_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="LIBRARY_PATH">$ENV[LIBXML2_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[LIBXML2_ROOT_DIR]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[LIBXML2_ROOT_DIR]/include</environment_variable>
 
-                    <environment_variable action="set_to" name="FREETYPE_ROOT_PATH">$ENV[FREETYPE_ROOT_PATH]</environment_variable>
-                    <environment_variable action="set_to" name="FREETYPE_LIB_PATH">$ENV[FREETYPE_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[FREETYPE_ROOT_PATH]/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[FREETYPE_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$ENV[FREETYPE_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[FREETYPE_ROOT_PATH]/include</environment_variable>
-                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[FREETYPE_ROOT_PATH]/include</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[FREETYPE_ROOT_PATH]/lib/pkgconfig</environment_variable>
+                    <environment_variable action="set_to" name="FREETYPE_ROOT_DIR">$ENV[FREETYPE_ROOT_DIR]</environment_variable>
+                    <environment_variable action="set_to" name="FREETYPE_LIB_PATH">$ENV[FREETYPE_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[FREETYPE_ROOT_DIR]/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[FREETYPE_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$ENV[FREETYPE_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[FREETYPE_ROOT_DIR]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[FREETYPE_ROOT_DIR]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[FREETYPE_ROOT_DIR]/lib/pkgconfig</environment_variable>
 
                     <environment_variable action="set_to" name="FONTCONFIG_ROOT_PATH">$ENV[FONTCONFIG_ROOT_PATH]</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$ENV[FONTCONFIG_ROOT_PATH]/bin</environment_variable>
@@ -166,15 +168,15 @@
                     <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[FONTCONFIG_ROOT_PATH]/include/</environment_variable>
                     <environment_variable action="prepend_to" name="CPP_INCLUDE_PATH">$ENV[FONTCONFIG_ROOT_PATH]/include/</environment_variable>
 
-                    <environment_variable action="set_to" name="CAIRO_ROOT_PATH">$ENV[CAIRO_ROOT_PATH]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[CAIRO_ROOT_PATH]/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$ENV[CAIRO_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="CAIRO_INCLUDE_PATH">$ENV[CAIRO_ROOT_PATH]/include</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[CAIRO_ROOT_PATH]/lib/pkgconfig</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[CAIRO_ROOT_PATH]/lib</environment_variable>
-                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[CAIRO_ROOT_PATH]//include</environment_variable>
-                    <environment_variable action="set_to" name="CAIRO_CFLAGS">-I$ENV[CAIRO_ROOT_PATH]/include/cairo</environment_variable>
-                    <environment_variable action="set_to" name="CAIRO_LIBS">"-L$ENV[CAIRO_ROOT_PATH]/lib -lcairo"</environment_variable>
+                    <environment_variable action="set_to" name="CAIRO_ROOT_DIR">$ENV[CAIRO_ROOT_DIR]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[CAIRO_ROOT_DIR]/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$ENV[CAIRO_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="CAIRO_INCLUDE_PATH">$ENV[CAIRO_ROOT_DIR]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[CAIRO_ROOT_DIR]/lib/pkgconfig</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[CAIRO_ROOT_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[CAIRO_ROOT_DIR]//include</environment_variable>
+                    <environment_variable action="set_to" name="CAIRO_CFLAGS">-I$ENV[CAIRO_ROOT_DIR]/include/cairo</environment_variable>
+                    <environment_variable action="set_to" name="CAIRO_LIBS">"-L$ENV[CAIRO_ROOT_DIR]/lib -lcairo"</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>