Hi,
I am trying to produce a jar from the htsjdk using ant and the provided
command. I am getting a compile error of an uncaught exception.
Here is the error message.
compile-samtools:
[javac] /Users/mwads/KauweLab/htsjdk-1.118/build.xml:244: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds
[javac] Compiling 222 source files to
/Users/mwads/KauweLab/htsjdk-1.118/classes
[javac] warning: [options] bootstrap class path not set in conjunction
with -source 1.6
[javac]
[javac]
[javac] An annotation processor threw an uncaught exception.
[javac] Consult the following stack trace for details.
[javac] java.lang.NoClassDefFoundError:
com/sun/tools/javac/main/OptionName
[javac] at
com.google.java.contract.core.apt.AnnotationProcessor.setupPaths(Unknown
Source)
[javac] at
com.google.java.contract.core.apt.AnnotationProcessor.init(Unknown Source)
[javac] at
com.sun.tools.javac.processing.JavacProcessingEnvironment$ProcessorState.<init>(JavacProcessingEnvironment.java:500)
[javac] at
com.sun.tools.javac.processing.JavacProcessingEnvironment$DiscoveredProcessors$ProcessorStateIterator.next(JavacProcessingEnvironment.java:597)
[javac] at
com.sun.tools.javac.processing.JavacProcessingEnvironment.discoverAndRunProcs(JavacProcessingEnvironment.java:690)
[javac] at
com.sun.tools.javac.processing.JavacProcessingEnvironment.access$1800(JavacProcessingEnvironment.java:91)
[javac] at
com.sun.tools.javac.processing.JavacProcessingEnvironment$Round.run(JavacProcessingEnvironment.java:1035)
[javac] at
com.sun.tools.javac.processing.JavacProcessingEnvironment.doProcessing(JavacProcessingEnvironment.java:1176)
[javac] at
com.sun.tools.javac.main.JavaCompiler.processAnnotations(JavaCompiler.java:1173)
[javac] at
com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:859)
[javac] at com.sun.tools.javac.main.Main.compile(Main.java:523)
[javac] at com.sun.tools.javac.main.Main.compile(Main.java:381)
[javac] at com.sun.tools.javac.main.Main.compile(Main.java:370)
[javac] at com.sun.tools.javac.main.Main.compile(Main.java:361)
[javac] at com.sun.tools.javac.Main.compile(Main.java:56)
[javac] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[javac] at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[javac] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[javac] at java.lang.reflect.Method.invoke(Method.java:483)
[javac] at
org.apache.tools.ant.taskdefs.compilers.Javac13.execute(Javac13.java:56)
[javac] at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1159)
[javac] at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:935)
[javac] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
[javac] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
[javac] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[javac] at java.lang.reflect.Method.invoke(Method.java:483)
[javac] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
[javac] at org.apache.tools.ant.Task.perform(Task.java:348)
[javac] at
org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68)
[javac] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
[javac] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
[javac] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[javac] at java.lang.reflect.Method.invoke(Method.java:483)
[javac] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
[javac] at org.apache.tools.ant.Task.perform(Task.java:348)
[javac] at
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:396)
[javac] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
[javac] at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
[javac] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[javac] at java.lang.reflect.Method.invoke(Method.java:483)
[javac] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
[javac] at org.apache.tools.ant.Task.perform(Task.java:348)
[javac] at org.apache.tools.ant.Target.execute(Target.java:435)
[javac] at org.apache.tools.ant.Target.performTasks(Target.java:456)
[javac] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
[javac] at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
[javac] at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
[javac] at
org.apache.tools.ant.Project.executeTargets(Project.java:1248)
[javac] at org.apache.tools.ant.Main.runBuild(Main.java:851)
[javac] at org.apache.tools.ant.Main.startAnt(Main.java:235)
[javac] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
[javac] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
[javac] Caused by: java.lang.ClassNotFoundException:
com.sun.tools.javac.main.OptionName
[javac] at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
[javac] at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
[javac] at java.security.AccessController.doPrivileged(Native Method)
[javac] at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
[javac] at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
[javac] at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
[javac] ... 52 more
BUILD FAILED
/Users/mwads/KauweLab/htsjdk-1.118/build.xml:100: The following error
occurred while executing this line:
/Users/mwads/KauweLab/htsjdk-1.118/build.xml:244: Compile failed; see the
compiler error output for details.
Thanks,
Mark
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