# HG changeset patch
# User brenninc
# Date 1460110466 14400
# Node ID 1e0df89a18e95cbcbf70fe93a3858bd9db0ecf73

Uploaded

diff -r 000000000000 -r 1e0df89a18e9 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Apr 08 06:14:26 2016 -0400
@@ -0,0 +1,196 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <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="c47756a8136e" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="cairo" version="1.14.2">
+                    <repository changeset_revision="83f00b68affb" name="package_cairo_1_14_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="fontconfig" version="2.11.1">
+                    <repository changeset_revision="93cd49855fe1" name="package_fontconfig_2_11_1" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="freetype" version="2.5.2">
+                    <repository changeset_revision="d39e2eb401ec" name="package_freetype_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="libpng" version="1.6.7">
+                    <repository changeset_revision="d1a409e4f67d" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="libxml2" version="2.9.1">
+                    <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>                
+                <package name="ncurses" version="6.0">
+                    <repository changeset_revision="15e2190c87ca" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="pixman" version="0.32.6">
+                    <repository changeset_revision="82d1a680686f" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="readline" version="6.3">
+                    <repository changeset_revision="de22495ddf2b" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="zlib" version="1.2.8">
+                    <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="83f00b68affb" name="package_cairo_1_14_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="cairo" version="1.14.2" />
+                    </repository>
+                    <repository changeset_revision="93cd49855fe1" name="package_fontconfig_2_11_1" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="fontconfig" version="2.11.1" />
+                    </repository>
+                    <repository changeset_revision="d39e2eb401ec" name="package_freetype_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="freetype" version="2.5.2" />
+                    </repository>
+                    <repository changeset_revision="d1a409e4f67d" 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" />
+                    </repository>
+                    <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="libxml2" version="2.9.1" />
+                    </repository>
+                    <repository changeset_revision="15e2190c87ca" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="6.0" />
+                    </repository>
+                    <repository changeset_revision="82d1a680686f" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="pixman" version="0.32.6" />
+                    </repository>
+                    <repository changeset_revision="de22495ddf2b" 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="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
+                <action type="shell_command">
+                    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" />
+                <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' $INSTALL_DIR/lib/R/bin/R</action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="NCURSES_INCLUDE_PATH">$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">$ENV[NCURSES_ROOT_PATH]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[NCURSES_ROOT_PATH]/include</environment_variable>
+                    <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_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">$ENV[READLINE_ROOT_PATH]/lib</environment_variable>
+                    <environment_variable action="append_to" name="PATH">$ENV[READLINE_ROOT_PATH]/bin</environment_variable>
+
+                    <environment_variable action="set_to" name="ATLAS_LIB_DIR">$ENV[ATLAS_LIB_DIR]/lib</environment_variable>
+                    <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$ENV[ATLAS_LIB_DIR]/include</environment_variable>
+                    <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$ENV[ATLAS_LIB_DIR]/lib/atlas</environment_variable>
+                    <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$ENV[ATLAS_LIB_DIR]/lib/atlas</environment_variable>
+                    <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$ENV[ATLAS_LIB_DIR]</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]/lib/atlas</environment_variable>
+  
+                    <environment_variable action="set_to" name="ZLIB_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable>
+                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable>
+
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="LIBPNG_ROOT">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable action="set_to" name="LIBPNG_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
+
+                    <environment_variable action="set_to" name="PIXMAN_ROOT_PATH">$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">$ENV[PIXMAN_ROOT_PATH]/lib/pkgconfig</environment_variable>
+
+                    <environment_variable action="set_to" name="LIBXML2_ROOT_PATH">$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="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="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]/freetype/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[FREETYPE_ROOT_PATH]/freetype/include</environment_variable>
+                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[FREETYPE_ROOT_PATH]/freetype/include</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[FREETYPE_ROOT_PATH]/lib/pkgconfig</environment_variable>
+
+                    <environment_variable action="set_to" name="FONTCONFIG_ROOT_PATH">$ENV[FONTCONFIG_ROOT_PATH]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[FONTCONFIG_ROOT_PATH]/bin</environment_variable>
+                    <environment_variable action="set_to" name="FONTCONFIG_FILE">$ENV[FONTCONFIG_ROOT_PATH]/etc/fonts/fonts.conf</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[FONTCONFIG_ROOT_PATH]/lib/pkgconfig</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[FONTCONFIG_ROOT_PATH]/lib/</environment_variable>
+                    <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="set_to" name="CAIRO_LIB_PATH">$ENV[CAIRO_ROOT_PATH]/lib</environment_variable>
+                    <environment_variable action="set_to" name="CAIRO_INCLUDE_PATH">$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="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="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>