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Merge branch 'hotfix-1.1.27'
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‎README.md‎

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# baseCode
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Data structures, math and statistics tools, and utilities that are often needed across projects.
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Used
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by [Gemma](https://github.com/PavlidisLab/Gemma), [ErmineJ](https://github.com/PavlidisLab/ermineJ), [GEOMMTx](https://github.com/PavlidisLab/GEOMMTx)
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and others.
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## R integration
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The R integration relies on native packages that needs to be installed in your local Maven repository in order to build
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baseCode.
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[rJava](https://rforge.net/rJava/) is usually available as a system package or it can be installed from source or using
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`install.packages("rJava")` in R.
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[Rserve](https://www.rforge.net/Rserve/) has to be installed from source with `install.packages("Rserve")`.
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```bash
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# You may need to adjust the path depending on your system.
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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
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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
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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
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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
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```

‎README.txt‎

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‎pom.xml‎

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<name>baseCode</name>
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<groupId>baseCode</groupId>
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<artifactId>baseCode</artifactId>
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<version>1.1.26</version>
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<version>1.1.27</version>
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<inceptionYear>2003</inceptionYear>
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<description>
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<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
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<artifactId>poi</artifactId>
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<version>5.4.1</version>
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<optional>true</optional>
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<exclusions>
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<exclusion>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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</exclusion>
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<exclusion>
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<groupId>commons-codec</groupId>
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<artifactId>commons-codec</artifactId>
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</exclusion>
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<exclusion>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-collections4</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<dependency>
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<groupId>commons-net</groupId>
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<artifactId>commons-net</artifactId>
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<version>3.11.1</version>
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<version>3.12.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.18.0</version>
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<version>2.20.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-collections4</artifactId>
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<version>4.4</version>
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<version>4.5.0</version>
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</dependency>
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<dependency>
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<groupId>commons-codec</groupId>
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<artifactId>commons-codec</artifactId>
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<version>1.18.0</version>
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<version>1.19.0</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-csv</artifactId>
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<version>1.14.0</version>
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<version>1.14.1</version>
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</dependency>
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<!-- R engine -->
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<!-- rJava -->
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<dependency>
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<groupId>org.rosuda.REngine</groupId>
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<artifactId>REngine</artifactId>
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<version>2.1.0</version>
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<version>${rJava.version}</version>
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<optional>true</optional>
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</dependency>
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<dependency>
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<groupId>org.rosuda.REngine</groupId>
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<artifactId>Rserve</artifactId>
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<version>1.8.1</version>
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<version>${rserve.version}</version>
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<optional>true</optional>
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</dependency>
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<!-- JRI is the engine implementation -->
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<dependency>
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<groupId>RoSuDA</groupId>
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<groupId>org.rosuda.REngine</groupId>
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<artifactId>JRI</artifactId>
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<version>0.5-0</version>
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<scope>runtime</scope>
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<version>${rJava.version}</version>
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<optional>true</optional>
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</dependency>
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<dependency>
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<groupId>RoSuDA</groupId>
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<groupId>org.rosuda.REngine</groupId>
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<artifactId>JRIEngine</artifactId>
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<version>0.5-0</version>
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<version>${rJava.version}</version>
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<optional>true</optional>
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</dependency>
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<!-- Sparse matrix library; lapack -->
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<dependency>
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<groupId>org.assertj</groupId>
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<artifactId>assertj-core</artifactId>
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<version>3.27.3</version>
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<version>3.27.4</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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<version>2.24.3</version>
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<version>${log4j.version}</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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<version>2.24.3</version>
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<version>${log4j.version}</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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<version>2.24.3</version>
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<version>${log4j.version}</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<includes>
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<include>**/*.owl.gz</include>
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<include>**/*.properties</include>
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<include>**/*.R</include>
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</includes>
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<filtering>false</filtering>
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</resource>
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<artifactId>maven-surefire-plugin</artifactId>
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<version>2.22.2</version>
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<configuration>
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<argLine>-enableassertions -Djava.awt.headless=true</argLine>
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<argLine>-enableassertions -Djava.awt.headless=true -Djava.library.path=${rJava.libDir}</argLine>
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<reportsDirectory>target/surefire-reports</reportsDirectory>
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<redirectTestOutputToFile>true</redirectTestOutputToFile>
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<includes>
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<configuration>
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<allowMajorUpdates>false</allowMajorUpdates>
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<ignoredVersions>.*-a.*,.*-b.*,.*-M.*</ignoredVersions>
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<dependencyExcludes>
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<dependencyExclude>org.rosuda.REngine:*:*</dependencyExclude>
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</dependencyExcludes>
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</configuration>
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</plugin>
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</plugins>
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<pavlab.server>frink.pavlab.msl.ubc.ca</pavlab.server>
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<pavlab.repoDir>/space/maven2</pavlab.repoDir>
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<pavlab.siteDir>/space/web/maven-sites</pavlab.siteDir>
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<log4j.version>2.25.1</log4j.version>
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<lucene.version>3.6.2</lucene.version>
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<!-- rJava -->
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<!-- You may override this in ~/.m2/settings.xml -->
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<rJava.version>1.0-13</rJava.version>
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<rJava.libDir>/usr/lib64/R/library/rJava/jri</rJava.libDir>
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<rserve.version>1.8-14</rserve.version>
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</properties>
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</project>

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