Comments (2)
Perhaps the problem isn't with adam-plugins
$ ADDL_JARS=adam-plugins_2.11-0.16.1-SNAPSHOT.jar bin/adam-submit \
> plugin com.github.heuermh.adam.plugins.CountAlignments \
> adam-core/src/test/resources/small.sam
Exception in thread "main" java.lang.NoSuchMethodError: scala.Predef$.$conforms()Lscala/Predef$$less$colon$less;
at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:104)
at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:569)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:166)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:189)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:110)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
$ bin/adam-submit transform adam-core/src/test/resources/small.sam /tmp/small.adam
Exception in thread "main" java.lang.NoSuchMethodError: scala.Predef$.$conforms()Lscala/Predef$$less$colon$less;
at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:104)
at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:569)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:166)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:189)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:110)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
$ which scala
/usr/local/bin/scala
$ ls -als `which scala`
8 lrwxr-xr-x 1 user admin 32 Mar 16 15:15 /usr/local/bin/scala -> ../Cellar/scala/2.11.6/bin/scala
from adam-plugins.
Fixed by commit 1274bff
from adam-plugins.
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from adam-plugins.