############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data netDx ### ############################################################################## ############################################################################## * checking for file ‘netDx/DESCRIPTION’ ... OK * preparing ‘netDx’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘RawDataConversion.Rmd’ using rmarkdown Exception in thread "main" java.lang.ExceptionInInitializerError at net.sf.cglib.core.KeyFactory$Generator.generateClass(KeyFactory.java:166) at net.sf.cglib.core.DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:25) at net.sf.cglib.core.AbstractClassGenerator.create(AbstractClassGenerator.java:216) at net.sf.cglib.core.KeyFactory$Generator.create(KeyFactory.java:144) at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:116) at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:108) at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:104) at net.sf.cglib.proxy.Enhancer.(Enhancer.java:69) at org.genemania.mediator.lucene.LuceneMediator.createOrganism(LuceneMediator.java:447) at org.genemania.mediator.lucene.LuceneOrganismMediator$2.handleHit(LuceneOrganismMediator.java:75) at org.genemania.mediator.lucene.AbstractCollector.collect(AbstractCollector.java:52) at org.apache.lucene.search.MultiSearcher$1.collect(MultiSearcher.java:258) at org.apache.lucene.search.TermScorer.score(TermScorer.java:78) at org.apache.lucene.search.TermScorer.score(TermScorer.java:70) at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:212) at org.apache.lucene.search.MultiSearcher.search(MultiSearcher.java:270) at org.apache.lucene.search.Searcher.search(Searcher.java:67) at org.genemania.mediator.lucene.LuceneMediator.search(LuceneMediator.java:201) at org.genemania.mediator.lucene.LuceneOrganismMediator.createOrganisms(LuceneOrganismMediator.java:70) at org.genemania.mediator.lucene.LuceneOrganismMediator.getAllOrganisms(LuceneOrganismMediator.java:65) at org.genemania.engine.apps.CacheBuilder.processAllOrganisms(CacheBuilder.java:87) at org.genemania.engine.apps.CacheBuilder.process(CacheBuilder.java:237) at org.genemania.engine.apps.CacheBuilder.main(CacheBuilder.java:260) Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @48f63233 at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:200) at java.base/java.lang.reflect.Method.setAccessible(Method.java:194) at net.sf.cglib.core.ReflectUtils$2.run(ReflectUtils.java:56) at java.base/java.security.AccessController.doPrivileged(AccessController.java:318) at net.sf.cglib.core.ReflectUtils.(ReflectUtils.java:46) ... 23 more Quitting from lines 189-208 (RawDataConversion.Rmd) Error: processing vignette 'RawDataConversion.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘RawDataConversion.Rmd’ --- re-building ‘ThreeWayClassifier.Rmd’ using rmarkdown Exception in thread "main" java.lang.ExceptionInInitializerError at net.sf.cglib.core.KeyFactory$Generator.generateClass(KeyFactory.java:166) at net.sf.cglib.core.DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:25) at net.sf.cglib.core.AbstractClassGenerator.create(AbstractClassGenerator.java:216) at net.sf.cglib.core.KeyFactory$Generator.create(KeyFactory.java:144) at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:116) at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:108) at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:104) at net.sf.cglib.proxy.Enhancer.(Enhancer.java:69) at org.genemania.mediator.lucene.LuceneMediator.createOrganism(LuceneMediator.java:447) at org.genemania.mediator.lucene.LuceneOrganismMediator$2.handleHit(LuceneOrganismMediator.java:75) at org.genemania.mediator.lucene.AbstractCollector.collect(AbstractCollector.java:52) at org.apache.lucene.search.MultiSearcher$1.collect(MultiSearcher.java:258) at org.apache.lucene.search.TermScorer.score(TermScorer.java:78) at org.apache.lucene.search.TermScorer.score(TermScorer.java:70) at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:212) at org.apache.lucene.search.MultiSearcher.search(MultiSearcher.java:270) at org.apache.lucene.search.Searcher.search(Searcher.java:67) at org.genemania.mediator.lucene.LuceneMediator.search(LuceneMediator.java:201) at org.genemania.mediator.lucene.LuceneOrganismMediator.createOrganisms(LuceneOrganismMediator.java:70) at org.genemania.mediator.lucene.LuceneOrganismMediator.getAllOrganisms(LuceneOrganismMediator.java:65) at org.genemania.engine.apps.CacheBuilder.processAllOrganisms(CacheBuilder.java:87) at org.genemania.engine.apps.CacheBuilder.process(CacheBuilder.java:237) at org.genemania.engine.apps.CacheBuilder.main(CacheBuilder.java:260) Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @48f63233 at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:200) at java.base/java.lang.reflect.Method.setAccessible(Method.java:194) at net.sf.cglib.core.ReflectUtils$2.run(ReflectUtils.java:56) at java.base/java.security.AccessController.doPrivileged(AccessController.java:318) at net.sf.cglib.core.ReflectUtils.(ReflectUtils.java:46) ... 23 more Quitting from lines 302-322 (ThreeWayClassifier.Rmd) Error: processing vignette 'ThreeWayClassifier.Rmd' failed with diagnostics: cannot open the connection --- failed re-building 'ThreeWayClassifier.Rmd' SUMMARY: processing the following files failed: 'RawDataConversion.Rmd' 'ThreeWayClassifier.Rmd' Error: Vignette re-building failed. Execution halted