Merge pull request #73 from eric-vlaanderen/java_upgrade

Upgrade gradle configuration to support java 17+

Author: jbytecode

RCaller/build.gradle

@@ -11,16 +11,29 @@ group = 'com.github.jbytecode'
 version = '4.0.2'
 description = 'RCaller is a software library which simplifies performing data analysis and statistical calculations in Java using R. The details are hidden from users including transferring data between platforms, function calls, and retrieving results.'
 
+java.sourceCompatibility = JavaVersion.VERSION_11
+
 dependencies {
-    implementation 'org.apache.commons:commons-lang3:3.12.0'
-    compileOnly 'org.apache.arrow:arrow-vector:[5.0.0,)'
+    implementation 'org.apache.commons:commons-lang3:3.20.0'
+
+    compileOnly 'org.apache.arrow:arrow-vector:[19.0.0,20.0.0)'
 
     testImplementation 'junit:junit:4.13.2'
-    testImplementation 'org.apache.arrow:arrow-vector:[5.0.0,)'
-    testImplementation 'org.apache.arrow:arrow-memory-netty:[5.0.0,)'
+
+    testImplementation 'org.apache.arrow:arrow-vector:[19.0.0,)'
+    testImplementation 'org.apache.arrow:arrow-memory-netty:[19.0.0,)'
+    testImplementation 'org.apache.arrow:arrow-memory-unsafe:[19.0.0,)'
 }
 
-java.sourceCompatibility = JavaVersion.VERSION_11
+test {
+    jvmArgs '-Dio.netty.tryReflectionSetAccessible=true',
+            '-Dio.netty.noUnsafe=true',
+            // Force Apache Arrow to use standard Java APIs instead of Netty
+            '-Darrow.memory.allocation.manager.factory=org.apache.arrow.memory.unsafe.UnsafeAllocationManagerFactory',
+            // Correct the module open target syntax for standard classpaths
+            '--add-opens=java.base/java.nio=ALL-UNNAMED',
+            '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED'
+}
 
 java {
     withSourcesJar()

RCaller/gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.5-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

RCaller/src/main/java/com/github/rcaller/rstuff/ROutputParser.java

@@ -5,6 +5,7 @@
 import com.github.rcaller.io.ArrowBridge;
 import com.github.rcaller.io.ROutputParserArrow;
 import com.github.rcaller.io.ROutputParserXML;
+import org.apache.commons.lang3.NotImplementedException;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
 import java.io.*;
@@ -46,15 +47,15 @@ static ROutputParser create(RCallerOptions rCallerOptions) {
      * Returns parsed XML document.
      * @deprecated Do not use if you are not using XML consciously
      * @return parsed XML document
-     * @throw NotImplementedException if Arrow implementation is used
+     * @throws NotImplementedException if Arrow implementation is used
      */
     @Deprecated
     Document getDocument();
 
     /**
      * Inits parsed XML document.
      * @deprecated Do not use if you are not using XML consciously
-     * @throw NotImplementedException if Arrow implementation is used
+     * @throws NotImplementedException if Arrow implementation is used
      */
     @Deprecated
     void setDocument(Document document);
@@ -63,7 +64,7 @@ static ROutputParser create(RCallerOptions rCallerOptions) {
      * Returns XML file.
      * @deprecated Do not use if you are not using XML consciously. Can be replaced with {@link #getIPCResource}
      * @return XML file
-     * @throw NotImplementedException if Arrow implementation is used
+     * @throws NotImplementedException if Arrow implementation is used
      */
     @Deprecated
     File getXMLFile();
@@ -74,15 +75,15 @@ static ROutputParser create(RCallerOptions rCallerOptions) {
      * Returns raw XML document.
      * @deprecated Do not use if you are not using XML consciously
      * @return raw XML document
-     * @throw NotImplementedException if Arrow implementation is used
+     * @throws NotImplementedException if Arrow implementation is used
      */
     @Deprecated
     String getXMLFileAsString() throws IOException;
 
     /**
      * Inits XML file.
      * @deprecated Do not use if you are not using XML consciously. Can be replaced with {@link #setIPCResource}
-     * @throw NotImplementedException if Arrow implementation is used
+     * @throws NotImplementedException if Arrow implementation is used
      */
     @Deprecated
     void setXMLFile(File xmlFile);
@@ -101,7 +102,7 @@ static ROutputParser create(RCallerOptions rCallerOptions) {
      * Returns nodes from parsed XML document.
      * @deprecated Do not use if you are not using XML consciously
      * @return nodes from parsed XML document
-     * @throw NotImplementedException if Arrow implementation is used
+     * @throws NotImplementedException if Arrow implementation is used
      */
     @Deprecated
     NodeList getValueNodes(String name);