# HG changeset patch
# User brenninc
# Date 1460447614 14400
# Node ID 3f2e129aae278a92ab6049ea9779a0c22a219d78
# Parent  a010580cd2d4890f11ada3ea0524f0d6d5273341
Uploaded

diff -r a010580cd2d4 -r 3f2e129aae27 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Oct 09 06:52:41 2015 -0400
+++ b/tool_dependencies.xml	Tue Apr 12 03:53:34 2016 -0400
@@ -5,51 +5,63 @@
             <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="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <package name="readline" version="6.3">
-                    <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <package name="libpng" version="1.6.7">
-                    <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                    <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 name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" />
-                </package>
-                <package name="pixman" version="0.32.6">
-                    <repository name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" />
-                </package>
-                <package name="freetype" version="2.5.2">
-                    <repository name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" />
-                </package>
-                <package name="ncurses" version="6.0">
-                    <repository name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" />
+                <package name="cairo" version="1.14.2">
+                    <repository changeset_revision="66ad0cc12007" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                 </package>
                 <package name="fontconfig" version="2.11.1">
-                    <repository name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" />
-                </package-->
+                    <repository changeset_revision="e356ec1fdd7b" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                </package>
+                <package name="freetype" version="2.5.2">
+                    <repository changeset_revision="22887dea4683" name="package_freetype_2_5_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="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="492a5c665b59" name="package_libxml2_2_9_1" owner="iuc" 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="caf1e20aac98" 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="ac6ef08bf0e6" 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 name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" >
+                    <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>
-                    <repository name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" >
-                        <package name="pixman" version="0.32.6" />
+                    <repository changeset_revision="e356ec1fdd7b" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="fontconfig" version="2.11.1" />
                     </repository>
-                    <repository name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" >
+                    <repository changeset_revision="22887dea4683" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="freetype" version="2.5.2" />
                     </repository>
-                    <repository name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" >
+                    <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="492a5c665b59" name="package_libxml2_2_9_1" owner="iuc" 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 name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" >
-                        <package name="fontconfig" version="2.11.1" />
-                    </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;
@@ -79,6 +91,91 @@
                 <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">$ENV[ATLAS_LIB_DIR]/lib/atlas</environment_variable>
+
+                    <environment_variable action="set_to" name="ZLIB_ROOT_PATH">$ENV[ZLIB_ROOT_PATH]</environment_variable>
+                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$ENV[ZLIB_ROOT_PATH]/lib/pkgconfig</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ZLIB_ROOT_PATH]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="LIBRARY_PATH">$ENV[ZLIB_ROOT_PATH]/lib</environment_variable>
+                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$ENV[ZLIB_ROOT_PATH]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$ENV[ZLIB_ROOT_PATH]/include</environment_variable>
+
+                    <environment_variable action="set_to" name="LIBPNG_ROOT">$ENV[LIBPNG_ROOT]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[LIBPNG_ROOT]/bin</environment_variable>
+                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_ROOT]/lib</environment_variable>
+                    <environment_variable action="set_to" name="LIBPNG_INCLUDE_PATH">$ENV[LIBPNG_ROOT]/include</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$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">$ENV[PIXMAN_ROOT_PATH]/lib/pkgconfig</environment_variable>
+
+                    <environment_variable action="set_to" name="LIBXML2_ROOT_PATH">$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">$ENV[LIBXML2_ROOT_PATH]/include</environment_variable>
+
+                    <environment_variable action="set_to" name="FREETYPE_ROOT_PATH">$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">$ENV[FREETYPE_ROOT_PATH]/lib/pkgconfig</environment_variable>
+
+                    <environment_variable action="set_to" name="FONTCONFIG_ROOT_PATH">$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="DYLD_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">$ENV[CAIRO_ROOT_PATH]/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$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="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">$INSTALL_DIR/lib/R/include</environment_variable>
@@ -90,6 +187,7 @@
                     <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$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>