Strip out javadoc support. Ignore warnings for the moment.

Author: tomwhite

build.gradle

@@ -57,7 +57,7 @@ repositories {
     mavenLocal()
 }
 
-final requiredJavaVersion = "8"
+final requiredJavaVersion = "11"
 final htsjdkVersion = System.getProperty('htsjdk.version','2.20.2')
 final picardVersion = System.getProperty('picard.version','2.20.5')
 final barclayVersion = System.getProperty('barclay.version','2.1.0')
@@ -129,11 +129,11 @@ def resolveLargeResourceStubFiles(largeResourcesFolder, buildPrerequisitesMessag
 // resource files that are needed to run the build but are still lfs stub files.
 def ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPrerequisitesMessage) {
     // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.
-    if (ToolProvider.getSystemToolClassLoader() == null) {
-        throw new GradleException(
-                "The ClassLoader obtained from the Java ToolProvider is null. "
-                + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
-    }
+//    if (ToolProvider.getSystemToolClassLoader() == null) {
+//        throw new GradleException(
+//                "The ClassLoader obtained from the Java ToolProvider is null. "
+//                + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
+//    }
     if (!file(".git").isDirectory()) {
         throw new GradleException("The GATK Github repository must be cloned using \"git clone\" to run the build. "
                 + "$buildPrerequisitesMessage")
@@ -169,7 +169,7 @@ configurations.all {
 }
 
 tasks.withType(JavaCompile) {
-  options.compilerArgs = ['-proc:none', '-Xlint:all', '-Werror', '-Xdiags:verbose']
+  options.compilerArgs = ['-proc:none', '-Xlint:all', '-Xdiags:verbose']
   options.encoding = 'UTF-8'
 }
 
@@ -215,12 +215,12 @@ configurations {
 // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,
 // test execution, and gatkDoc generation, but we don't want them as part of the runtime
 // classpath and we don't want to redistribute them in the uber jar.
-final javadocJDKFiles = files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())
+final javadocJDKFiles = null // files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())
 
 dependencies {
     // javadoc utilities; compile/test only to prevent redistribution of sdk jars
-    compileOnly(javadocJDKFiles)
-    testCompile(javadocJDKFiles)
+    //compileOnly(javadocJDKFiles)
+    //testCompile(javadocJDKFiles)
 
     compile 'org.broadinstitute:barclay:' + barclayVersion
     // Library for configuration:
@@ -646,7 +646,7 @@ task gatkDoc(type: Javadoc, dependsOn: classes) {
 
     // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
     // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
-    classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
+    //classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
     options.docletpath = classpath.asType(List)
     options.doclet = "org.broadinstitute.hellbender.utils.help.GATKHelpDoclet"
 
@@ -682,7 +682,7 @@ task gatkTabComplete(type: Javadoc, dependsOn: classes) {
 
     // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
     // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives, and Picard.
-    classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
+    //classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
 
     options.docletpath = classpath.asType(List)
     options.doclet = "org.broadinstitute.barclay.help.BashTabCompletionDoclet"