# HG changeset patch
# User brenninc
# Date 1443705031 14400
# Node ID e5e60b114550f661caa0b9043d4ae669f66ca1a9
# Parent  304b62d6e6cf5953305c6fd05751a91271d8b094
Uploaded

diff -r 304b62d6e6cf -r e5e60b114550 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Oct 01 09:08:19 2015 -0400
+++ b/tool_dependencies.xml	Thu Oct 01 09:10:31 2015 -0400
@@ -1,102 +1,74 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R" version="3.2.1">
+    <package name="R" version="3.1.2">
+        <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="1d7f08f14e93" prior_installation_required="True" />
+    </package>
+    <package name="R_extend_level_one" version="0.0.1">
         <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="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="40f8ebe365e9" 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" />
-                </package>
-                <package name="cairo" version="1.14.2">
-                    <repository changeset_revision="9fe5875b0ede" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <package name="pixman" version="0.32.6">
-                    <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <package name="freetype" version="2.5.2">
-                    <repository changeset_revision="55f81025bcb0" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <package name="ncurses" version="6.0">
-                    <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <package name="fontconfig" version="2.11.1">
-                    <repository changeset_revision="e1df54930f90" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                </package>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="40f8ebe365e9" 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 changeset_revision="9fe5875b0ede" 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 changeset_revision="2db67636b074" 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="55f81025bcb0" 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 changeset_revision="9331b44bf167" 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="e1df54930f90" 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>
-                </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' $INSTALL_DIR/lib/R/bin/R</action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_DOC_DIR">$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">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
-                    <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="1d7f08f14e93" name="brenninc_r_sept32105" owner="brenninc" toolshed="https://testtoolshed.g2.bx.psu.edu/">
+                        <package name="R" version="3.1.2" />
+                        <!-- includes base, boot, 
+                                      class, cluster, codetools, compiler, 
+                                      datasets, 
+                                      foreign, 
+                                      graphics, grDevices, grid, 
+                                      KernSmooth, 
+                                      lattice, 
+                                      MASS, Matrix, methods, mgcv, 
+                                      nlme, nnet, 
+                                      parallel, 
+                                      rpart,
+                                      spatial, splines, stats, stats4, survival,
+                                      tcltk, tools,
+                                      utils-->
+
+                    </repository>  
+                    <!--No dependencies Not on https://bioarchive.galaxyproject.org -->
+                    <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> 
+                    <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package> 
+                        <!-- Imports graphics 
+                             Suggests: KernSmooth, MASS, kernlab, mvtnorm, vcd, dichromat, tcltk-->
+                    <package>https://cran.r-project.org/src/contrib/digest_0.6.8.tar.gz</package> 
+                    <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package> 
+                        <!-- Depends stats -->
+                    <package>https://cran.r-project.org/src/contrib/Formula_1.2-1.tar.gz</package> 
+                        <!-- Depends stats -->
+                    <package>https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz</package> 
+                        <!-- Depends grid 
+                             Suggests: testthat, plyr-->
+                    <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
+                        <!-- Suggests: 	testthat, knitr -->
+                    <package>https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz</package>
+                        <!-- Suggests: 	graph, Rgraphviz -->
+                    <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.0.tar.gz</package>
+                        <!-- Imports: 	methods, utils
+                             Suggests: 	RUnit, inline, rbenchmark, highlight, pkgKitten (≥ 0.1.2) -->
+                    <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/snow_0.3-13.tar.gz</package>
+                        <!-- Depends: R (≥ 2.12.1), utils
+                             Suggests: Rmpi, rpvm, rlecuyer, rsprng, nws -->
+                    <package>https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz</package>
+                        <!-- Depends: R (≥ 2.15), methods
+                             Imports: graphics, stats, utils -->
+                    <package>https://cran.r-project.org/src/contrib/stringi_0.5-5.tar.gz</package>
+                        <!-- Depends: R (≥ 2.13.1)
+                             Imports: tools, utils, stats -->
+                    <package>https://cran.r-project.org/src/contrib/XML_3.98-1.3.tar.gz</package>
+                        <!-- Depends: R (≥ 2.13.0), methods, utils
+                             Suggests: bitops, RCurl -->
+                    <package>https://cran.r-project.org/src/contrib/xtable_1.7-4.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz</package>
+                        <!-- Depends: R (≥ 2.14)
+                             Imports: stringi (≥ 0.4.1), magrittr
+                             Suggests: testthat, knitr -->
+                </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>
+
+