Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: Don't try to test Java
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
@@ -2659,32 +2659,6 @@
     unless ($java_prog) {
         die "Error, cannot find 'java'.  Please be sure it is available within your \${PATH} setting and then try again.";
     }
-    
-
-    my $cmd = "java -Xmx64m -XX:ParallelGCThreads=$bflyGCThreads $JAVA_OPTS -jar $UTILDIR/support_scripts/ExitTester.jar 0";
-    eval {
-        &process_cmd($cmd);
-    };
-    if ($@) {
-        print STDERR "Error encountered in testing for running of a simple java application. ";
-        print "$@\n\n";
-        print STDERR "Please check your java configuration.\n";
-        exit(1);
-        
-    }
-    
-    $cmd = "java -Xmx64m -XX:ParallelGCThreads=$bflyGCThreads $JAVA_OPTS -jar $UTILDIR/support_scripts/ExitTester.jar 1";
-    eval {
-        &process_cmd($cmd);
-    };
-
-    if ($@) {
-        print "-we properly captured the java failure status, as needed.  Looking good.\n" if $VERBOSE;
-    }
-    else {
-        print STDERR "-we are unable to properly capture java failure status.  Please be sure that java (or any wrapper around java that's being used) can properly capture and propagate failure status before proceeding.\n";
-        exit(1);
-    }
 
     print "Java tests succeeded.\n" if $VERBOSE;
     print "###################################\n\n" if $VERBOSE;
