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java.lang.IncompatibleClassChangeError: Implementing class #1544

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jokerbea opened this Issue May 22, 2017 · 8 comments

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@jokerbea

jokerbea commented May 22, 2017

Hi
I am using the function vcf2adam and get the following error:Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using SPARK_SUBMIT=/usr/bin/spark-submit
17/05/22 02:12:58 INFO ADAMMain: ADAM invoked with args: "vcf2adam" "/myvcf.vcf" "/home/G/_adam"
Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing class
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.bdgenomics.adam.cli.Vcf2ADAM.(Vcf2ADAM.scala:57)
at org.bdgenomics.adam.cli.Vcf2ADAM$.apply(Vcf2ADAM.scala:32)
at org.bdgenomics.adam.cli.Vcf2ADAM$.apply(Vcf2ADAM.scala:27)
at org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:127)
at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:66)
at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
I got the latest version in the repository.
Any help please?

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heuermh May 22, 2017

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This is often a mismatch in Scala versions. Which versions of Spark and Scala did you build for? Which versions of Spark and Scala are you running on?

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heuermh commented May 22, 2017

This is often a mismatch in Scala versions. Which versions of Spark and Scala did you build for? Which versions of Spark and Scala are you running on?

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jokerbea May 22, 2017

jokerbea commented May 22, 2017

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fnothaft May 22, 2017

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Hi @jokerbea! You'll need to build specifically for Spark 2. You can do this by running the ./scripts/move_to_spark_2.sh script before doing mvn package. We don't currently support Scala 2.12, as most of our upstream dependencies don't provide releases for Scala 2.12. Are you doing a custom build of Spark for Scala 2.12?

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fnothaft commented May 22, 2017

Hi @jokerbea! You'll need to build specifically for Spark 2. You can do this by running the ./scripts/move_to_spark_2.sh script before doing mvn package. We don't currently support Scala 2.12, as most of our upstream dependencies don't provide releases for Scala 2.12. Are you doing a custom build of Spark for Scala 2.12?

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jokerbea commented May 22, 2017

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Hi @jokerbea! As far as I understand, Spark doesn't currently support Scala 2.12. We don't plan to support building ADAM against Scala 2.12 until Spark adds support for Scala 2.12, which is currently slated for Spark 2.3.0.

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fnothaft commented May 22, 2017

Hi @jokerbea! As far as I understand, Spark doesn't currently support Scala 2.12. We don't plan to support building ADAM against Scala 2.12 until Spark adds support for Scala 2.12, which is currently slated for Spark 2.3.0.

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jokerbea commented May 22, 2017

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We support both Scala 2.10 and 2.11.

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fnothaft commented May 22, 2017

We support both Scala 2.10 and 2.11.

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I'm going to close this as resolved. Please reopen if you're still seeing issues @jokerbea!

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fnothaft commented Jun 22, 2017

I'm going to close this as resolved. Please reopen if you're still seeing issues @jokerbea!

@fnothaft fnothaft closed this Jun 22, 2017

@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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