java.lang.IncompatibleClassChangeError: Implementing class

[bkanzki]

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?

[heuermh]

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?

[bkanzki]

I run SparK 2.1.0 and Scala 2.12.2 ᐧ 2017-05-22 11:24 GMT-04:00 Michael L Heuer <notifications@github.com>:

…

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? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1544 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALxP28mVhIvSnyKqrFM9iTg9xOKB7l1Rks5r8aiRgaJpZM4Nhz8J> .

-- *Beatriz Kanzki* Bsc Bioinformatics

[fnothaft]

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?

[bkanzki]

Hi I did run the ./scripts/move_to_spark_2.sh script before the mvn command. But it didn't do it. I might create a move to Scala function and put it to your repository for Scala 2.12

…

Sent from my iPhone

On May 22, 2017, at 11:33 AM, Frank Austin Nothaft ***@***.***> wrote: 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? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[fnothaft]

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.

[bkanzki]

Which version of scala are you using? ᐧ 2017-05-22 11:55 GMT-04:00 Frank Austin Nothaft <notifications@github.com>:

…

Hi @jokerbea <https://github.com/jokerbea>! As far as I understand, Spark doesn't currently support Scala 2.12 <https://issues.apache.org/jira/browse/SPARK-14220>. 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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1544 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALxP2xQAi3VnhgneOv-jqtcBSziz8Pucks5r8bADgaJpZM4Nhz8J> .

-- *Beatriz Kanzki* Bsc Bioinformatics

[fnothaft]

We support both Scala 2.10 and 2.11.

[fnothaft]

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