Remove system scope for rJava and Rserve dependencies

Add instructions in the README.md for how to install the JAR.

Author: arteymix

README.md

@@ -0,0 +1,25 @@
+# baseCode
+
+Data structures, math and statistics tools, and utilities that are often needed across projects.
+
+Used
+by [Gemma](https://github.com/PavlidisLab/Gemma), [ErmineJ](https://github.com/PavlidisLab/ermineJ), [GEOMMTx](https://github.com/PavlidisLab/GEOMMTx)
+and others.
+
+## R integration
+
+The R integration relies on native packages that needs to be installed in your local Maven repository in order to build
+baseCode.
+
+[rJava](https://rforge.net/rJava/) is usually available as a system package or it can be installed from source or using
+`install.packages("rJava")` in R.
+
+[Rserve](https://www.rforge.net/Rserve/) has to be installed from source with `install.packages("Rserve")`.
+
+```bash
+# You may need to adjust the path depending on your system.
+mvn install:install-file -DgroupId=org.rosuda.REngine -DartifactId=REngine -Dversion=1.0-13 -Dpackaging=jar -Dfile=/usr/lib64/R/library/rJava/jri/REngine.jar
+mvn install:install-file -DgroupId=org.rosuda.REngine -DartifactId=JRI -Dversion=1.0-13 -Dpackaging=jar -Dfile=/usr/lib64/R/library/rJava/jri/JRI.jar
+mvn install:install-file -DgroupId=org.rosuda.REngine -DartifactId=JRIEngine -Dversion=1.0-13 -Dpackaging=jar -Dfile=/usr/lib64/R/library/rJava/jri/JRIEngine.jar
+mvn install:install-file -DgroupId=org.rosuda.REngine -DartifactId=Rserve -Dversion=1.8-14 -Dpackaging=jar -Dfile=/usr/lib64/R/library/Rserve/java/Rserve.jar
+```

README.txt

@@ -122,32 +122,24 @@
 			<groupId>org.rosuda.REngine</groupId>
 			<artifactId>REngine</artifactId>
 			<version>${rJava.version}</version>
-			<scope>system</scope>
-			<systemPath>${rJava.REngine.jarPath}</systemPath>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.rosuda.REngine</groupId>
 			<artifactId>Rserve</artifactId>
 			<version>${rserve.version}</version>
-			<scope>system</scope>
-			<systemPath>${rserve.jarPath}</systemPath>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.rosuda.REngine</groupId>
 			<artifactId>JRI</artifactId>
 			<version>${rJava.version}</version>
-			<scope>system</scope>
-			<systemPath>${rJava.JRI.jarPath}</systemPath>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.rosuda.REngine</groupId>
 			<artifactId>JRIEngine</artifactId>
 			<version>${rJava.version}</version>
-			<scope>system</scope>
-			<systemPath>${rJava.JRIEngine.jarPath}</systemPath>
 			<optional>true</optional>
 		</dependency>
 
@@ -693,12 +685,7 @@
 		<!-- rJava -->
 		<!-- You may override this in ~/.m2/settings.xml -->
 		<rJava.version>1.0-13</rJava.version>
-		<rJava.prefix>/usr/lib64/R/library/rJava</rJava.prefix>
-		<rJava.libDir>${rJava.prefix}/jri</rJava.libDir>
-		<rJava.REngine.jarPath>${rJava.prefix}/jri/REngine.jar</rJava.REngine.jarPath>
-		<rJava.JRIEngine.jarPath>${rJava.prefix}/jri/JRIEngine.jar</rJava.JRIEngine.jarPath>
-		<rJava.JRI.jarPath>${rJava.prefix}/jri/JRI.jar</rJava.JRI.jarPath>
+		<rJava.libDir>/usr/lib64/R/library/rJava/jri</rJava.libDir>
 		<rserve.version>1.8-14</rserve.version>
-		<rserve.jarPath>/usr/lib64/R/library/Rserve/java/Rserve.jar</rserve.jarPath>
 	</properties>
 </project>