changeset 0:c012ba512834 draft

Uploaded
author brenninc
date Tue, 12 Apr 2016 04:13:24 -0400
parents
children 18ce5899a17a
files tool_dependencies.xml
diffstat 1 files changed, 115 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 12 04:13:24 2016 -0400
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<tool_dependency>
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+    </package>
+    <!--package name="R_extended" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
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+                        <package name="R" version="3.2.1" />
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