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Update dependencies and fix pom.xml
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Lines changed: 186 additions & 257 deletions

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‎pom.xml‎

Lines changed: 75 additions & 139 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,14 @@
11
<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
3-
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
3+
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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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>1.0.32-SNAPSHOT</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.]]>
11+
<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
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</description>
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<url>https://github.com/pavlidisLab/basecode</url>
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<organization>
@@ -43,112 +43,108 @@
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<dependency>
4444
<groupId>org.apache.poi</groupId>
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<artifactId>poi</artifactId>
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<version>3.9</version>
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<version>5.0.0</version>
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</dependency>
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<dependency>
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<groupId>colt</groupId>
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<artifactId>colt</artifactId>
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<version>1.2.0</version>
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</dependency>
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<dependency>
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<groupId>xerces</groupId>
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<artifactId>xercesImpl</artifactId>
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<version>2.11.0</version>
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</dependency>
53+
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<!-- Apache Commons -->
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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>3.1</version>
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<version>3.8.0</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-math3</artifactId>
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<version>3.2</version>
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<version>3.6.1</version>
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</dependency>
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<dependency>
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<groupId>commons-configuration</groupId>
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<artifactId>commons-configuration</artifactId>
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<!-- special private build of snapshot until 2.0 is released officially -->
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<version>2.0-RCT</version>
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<exclusions>
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<exclusion>
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<groupId>javax.servlet</groupId>
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<artifactId>servlet-api</artifactId>
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</exclusion>
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</exclusions>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-configuration2</artifactId>
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<version>2.7</version>
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</dependency>
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<dependency>
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<groupId>commons-beanutils</groupId>
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<artifactId>commons-beanutils</artifactId>
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<version>1.8.3</version>
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<!-- needed by commons-configuration -->
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<scope>runtime</scope>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
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<version>3.12.0</version>
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</dependency>
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<dependency>
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<groupId>commons-collections</groupId>
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<artifactId>commons-collections</artifactId>
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<version>3.2.1</version>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.11.0</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-lang3</artifactId>
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<version>3.1</version>
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<artifactId>commons-collections4</artifactId>
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<version>4.4</version>
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</dependency>
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<!-- HTTP client -->
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpcore</artifactId>
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<version>4.4.14</version>
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</dependency>
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<dependency>
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<groupId>commons-dbcp</groupId>
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<artifactId>commons-dbcp</artifactId>
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<version>1.4</version>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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<version>4.5.13</version>
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</dependency>
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<!-- R engine -->
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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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</dependency>
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<dependency>
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<groupId>net.rforge</groupId>
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<groupId>org.rosuda.REngine</groupId>
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<artifactId>Rserve</artifactId>
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<version>0.6-8.1</version>
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<version>1.8.1</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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<artifactId>JRI</artifactId>
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<version>0.5-0</version>
112-
<optional>true</optional>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>RoSuDA</groupId>
116119
<artifactId>JRIEngine</artifactId>
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<version>0.5-0</version>
118121
</dependency>
122+
123+
<!-- Sparse matrix library; lapack -->
119124
<dependency>
120-
<groupId>net.sf.opencsv</groupId>
121-
<artifactId>opencsv</artifactId>
122-
<version>2.3</version>
123-
</dependency>
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<dependency><!-- Sparse matrix library; lapack -->
125125
<groupId>com.googlecode.matrix-toolkits-java</groupId>
126126
<artifactId>mtj</artifactId>
127-
<version>0.9.14</version>
127+
<version>1.0.4</version>
128128
</dependency>
129-
<dependency><!-- lapack -->
130-
<groupId>com.googlecode.netlib-java</groupId>
131-
<artifactId>netlib-java</artifactId>
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<version>0.9.3</version>
129+
<dependency>
130+
<groupId>net.sourceforge.f2j</groupId>
131+
<artifactId>arpack_combined_all</artifactId>
132+
<version>0.1</version>
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</dependency>
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<!-- Logging -->
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<dependency>
135137
<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
137-
<version>1.7.5</version>
139+
<version>1.7.32</version>
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</dependency>
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<!-- <dependency> <groupId>netlib-java</groupId> <artifactId>arpack-combo</artifactId> <version>0.1</version> <type>jar</type>
140-
</dependency> lapack -->
141+
142+
<!-- Jena -->
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<dependency>
142-
<groupId>org.slf4j</groupId>
143-
<artifactId>slf4j-log4j12</artifactId>
144-
<version>1.7.5</version>
145-
<scope>test</scope>
144+
<groupId>org.apache.jena</groupId>
145+
<artifactId>jena-core</artifactId>
146+
<version>2.7.4</version>
146147
</dependency>
147-
<!--java 8 only <dependency>
148-
<groupId>net.sourceforge.jdistlib</groupId>
149-
<artifactId>jdistlib</artifactId>
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<version>0.4.5</version>
151-
</dependency>-->
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<!-- Be careful with versions of lucene -->
153149
<!-- jena-text uses lucene 4.x.. Not ready for this. -->
154150
<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-text</artifactId> <version>1.0.0-SNAPSHOT</version>
@@ -157,108 +153,50 @@
157153
<groupId>org.apache.jena</groupId>
158154
<artifactId>jena-larq</artifactId>
159155
<version>1.0.0-incubating</version>
160-
<exclusions>
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<exclusion>
162-
<artifactId>slf4j-log4j12</artifactId>
163-
<groupId>org.slf4j</groupId>
164-
</exclusion>
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</exclusions>
166-
</dependency>
167-
<dependency>
168-
<groupId>log4j</groupId>
169-
<artifactId>log4j</artifactId>
170-
<version>1.2.17</version>
171-
<scope>test</scope>
172-
</dependency>
173-
<dependency>
174-
<groupId>org.slf4j</groupId>
175-
<artifactId>jcl-over-slf4j</artifactId>
176-
<version>1.7.5</version>
177-
</dependency>
178-
<dependency>
179-
<groupId>commons-logging</groupId>
180-
<artifactId>commons-logging</artifactId>
181-
<version>1.2</version>
182156
</dependency>
183157
<dependency>
184158
<groupId>org.apache.jena</groupId>
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<artifactId>jena-arq</artifactId>
186160
<version>2.9.4</version> <!-- latest release is 2.10.1, but not compatible with larq? -->
187-
<exclusions>
188-
<exclusion>
189-
<artifactId>slf4j-log4j12</artifactId>
190-
<groupId>org.slf4j</groupId>
191-
</exclusion>
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<exclusion>
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<artifactId>httpclient</artifactId>
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<groupId>org.apache.httpcomponents</groupId>
195-
</exclusion>
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<exclusion>
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<artifactId>httpcore</artifactId>
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<groupId>org.apache.httpcomponents</groupId>
199-
</exclusion>
200-
</exclusions>
201161
</dependency>
162+
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<!-- Lucene -->
202164
<dependency>
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<groupId>org.apache.lucene</groupId>
204166
<artifactId>lucene-core</artifactId>
205-
<version>3.6.2</version>
206-
</dependency>
207-
<dependency>
208-
<groupId>org.apache.lucene</groupId>
209-
<artifactId>lucene-queryparser</artifactId>
210-
<version>3.6.2</version>
167+
<version>${lucene.version}</version>
211168
</dependency>
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<dependency>
213170
<groupId>org.apache.lucene</groupId>
214171
<artifactId>lucene-analyzers</artifactId>
215-
<version>3.6.2</version>
172+
<version>${lucene.version}</version>
216173
</dependency>
174+
175+
<!-- Utilities -->
217176
<dependency>
218177
<groupId>jfree</groupId>
219178
<artifactId>jfreechart</artifactId>
220179
<version>1.0.13</version>
221180
</dependency>
181+
<!-- xml-apis is dependent on jena -->
222182
<dependency>
223-
<groupId>jfree</groupId>
224-
<artifactId>jcommon</artifactId>
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<version>1.0.16</version>
183+
<groupId>xml-apis</groupId>
184+
<artifactId>xml-apis</artifactId>
185+
<version>1.4.01</version>
226186
</dependency>
227187
<dependency>
228-
<groupId>org.apache.httpcomponents</groupId>
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<artifactId>fluent-hc</artifactId>
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<version>4.2.5</version>
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<groupId>com.opencsv</groupId>
189+
<artifactId>opencsv</artifactId>
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<version>5.5.2</version>
231191
</dependency>
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<!-- Testing utilities -->
232194
<dependency>
233195
<groupId>junit</groupId>
234196
<artifactId>junit</artifactId>
235-
<version>4.8.2</version>
197+
<version>4.13.2</version>
236198
<scope>test</scope>
237199
</dependency>
238-
<dependency>
239-
<groupId>mysql</groupId>
240-
<artifactId>mysql-connector-java</artifactId>
241-
<version>5.1.10</version>
242-
<scope>runtime</scope>
243-
<optional>true</optional>
244-
</dependency>
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<dependency>
246-
<groupId>commons-io</groupId>
247-
<artifactId>commons-io</artifactId>
248-
<version>2.4</version>
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</dependency>
250-
<dependency>
251-
<groupId>org.hsqldb</groupId>
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<artifactId>hsqldb</artifactId>
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<version>2.3.0</version>
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<scope>test</scope>
255-
</dependency>
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<dependency>
257-
<groupId>commons-codec</groupId>
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<artifactId>commons-codec</artifactId>
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<version>1.8</version>
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</dependency>
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262200
</dependencies>
263201
<build>
264202
<directory>target</directory>
@@ -320,8 +258,8 @@
320258
<artifactId>maven-compiler-plugin</artifactId>
321259
<version>3.8.1</version>
322260
<configuration>
323-
<source>1.7</source>
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<target>1.7</target>
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<source>1.8</source>
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<target>1.8</target>
325263
</configuration>
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</plugin>
327265
<plugin>
@@ -360,6 +298,7 @@
360298
<version>2.7</version>
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<configuration>
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<outputDirectory>${cobertura.outputDirectory}</outputDirectory>
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<check/>
363302
</configuration>
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</plugin>
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</plugins>
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398337
<version>3.3.0</version>
399338
<configuration>
400339
<quiet>true</quiet>
401-
<aggregate>false</aggregate>
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<source>7</source>
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<source>8</source>
403341
<doclint>none</doclint>
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</configuration>
405343
</plugin>
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429367
<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-report-plugin</artifactId>
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<version>2.22.2</version>
432-
<configuration>
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<argLine>-Xmx1024m</argLine>
434-
</configuration>
435370
</plugin>
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<plugin>
437372
<groupId>org.apache.maven.plugins</groupId>
@@ -563,5 +498,6 @@
563498
</profiles>
564499
<properties>
565500
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<lucene.version>3.6.2</lucene.version>
566502
</properties>
567503
</project>

‎src/ubic/basecode/dataStructure/matrix/SparseRaggedDoubleMatrix.java‎

Lines changed: 1 addition & 1 deletion
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@@ -22,7 +22,7 @@
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import java.util.List;
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import java.util.Vector;
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25-
import org.apache.commons.collections.CollectionUtils;
25+
import org.apache.commons.collections4.CollectionUtils;
2626
import org.apache.commons.lang3.ArrayUtils;
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import cern.colt.list.DoubleArrayList;

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