Hi, I am trying to build Hail 0.2 on red hat linux system from source. Here is what I am doing:
git clone --branch seqr_hail "https://github.com/macarthur-lab/hail.git" && cd hail
./gradlew -Dspark.version=2.4.4 shadowJar archiveZip
And the second command fails. Here is the full stack trace that I get:
(cd libsimdpp-2.0-rc2 && cmake .)
-- Configuring done
-- Generating done
-- Build files have been written to: /nethome/vlasenkona/test_hail_build/hail/src/main/c/libsimdpp-2.0-rc2
mkdir -p lib/linux-x86-64/libhail
g++ -fvisibility=hidden -rdynamic -shared -O3 -march=native -g -std=c++11 -Ilibsimdpp-2.0-rc2 -Wall -Werror -fPIC -ggdb ibs.o -o lib/linux-x86-64/libhail.so
:compileScala
/nethome/vlasenkona/test_hail_build/hail/src/main/scala/is/hail/package.scala:3: object tools is not a member of package scala
import scala.tools.nsc.interpreter.InputStream
^
/nethome/vlasenkona/test_hail_build/hail/src/main/scala/is/hail/package.scala:22: not found: type InputStream
(is: InputStream) =>
^
/nethome/vlasenkona/test_hail_build/hail/src/main/scala/is/hail/utils/richUtils/RichRDD.scala:74: inferred existential type org.apache.spark.rdd.RDD[_3104] forSome { type _3104 >: String with _3103; type _3103 >: T }, which cannot be expressed by wildcards, should be enabled
by making the implicit value scala.language.existentials visible.
This can be achieved by adding the import clause 'import scala.language.existentials'
or by setting the compiler option -language:existentials.
See the Scaladoc for value scala.language.existentials for a discussion
why the feature should be explicitly enabled.
}.getOrElse(r)
^
one warning found
two errors found
:compileScala FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':compileScala'.
> Compilation failed
* Try:
Run with --info or --debug option to get more log output.
* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':compileScala'.
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:69)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:46)
at org.gradle.api.internal.tasks.execution.PostExecutionAnalysisTaskExecuter.execute(PostExecutionAnalysisTaskExecuter.java:35)
at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:66)
at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:52)
at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:53)
at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:203)
at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:185)
at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.processTask(AbstractTaskPlanExecutor.java:66)
at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.run(AbstractTaskPlanExecutor.java:50)
at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:25)
at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:110)
at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:32)
at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
at org.gradle.initialization.DefaultGradleLauncher$4.run(DefaultGradleLauncher.java:153)
at org.gradle.internal.Factories$1.create(Factories.java:22)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:53)
at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:150)
at org.gradle.initialization.DefaultGradleLauncher.access$200(DefaultGradleLauncher.java:32)
at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:98)
at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:92)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91)
at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:63)
at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:92)
at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:83)
at org.gradle.launcher.exec.InProcessBuildActionExecuter$DefaultBuildController.run(InProcessBuildActionExecuter.java:99)
at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:48)
at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:30)
at org.gradle.launcher.exec.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:81)
at org.gradle.launcher.exec.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:46)
at org.gradle.launcher.exec.DaemonUsageSuggestingBuildActionExecuter.execute(DaemonUsageSuggestingBuildActionExecuter.java:51)
at org.gradle.launcher.exec.DaemonUsageSuggestingBuildActionExecuter.execute(DaemonUsageSuggestingBuildActionExecuter.java:28)
at org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:43)
at org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:239)
at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:212)
at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:35)
at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:205)
at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:169)
at org.gradle.launcher.Main.doAction(Main.java:33)
at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:55)
at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:36)
at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
at org.gradle.wrapper.BootstrapMainStarter.start(BootstrapMainStarter.java:30)
at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:129)
at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
Caused by: org.gradle.api.internal.tasks.compile.CompilationFailedException: Compilation failed
at org.gradle.api.internal.tasks.scala.ZincScalaCompiler$Compiler.execute(ZincScalaCompiler.java:94)
at org.gradle.api.internal.tasks.scala.ZincScalaCompiler.execute(ZincScalaCompiler.java:66)
at org.gradle.api.internal.tasks.scala.ZincScalaCompiler.execute(ZincScalaCompiler.java:48)
at org.gradle.api.internal.tasks.compile.daemon.CompilerDaemonServer.execute(CompilerDaemonServer.java:31)
at org.gradle.process.internal.worker.request.WorkerAction.run(WorkerAction.java:87)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:377)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
Caused by: Compilation failed
at sbt.compiler.AnalyzingCompiler.call(AnalyzingCompiler.scala:105)
at sbt.compiler.AnalyzingCompiler.compile(AnalyzingCompiler.scala:47)
at sbt.compiler.AnalyzingCompiler.compile(AnalyzingCompiler.scala:41)
at sbt.compiler.AggressiveCompile$$anonfun$3$$anonfun$compileScala$1$1.apply$mcV$sp(AggressiveCompile.scala:97)
at sbt.compiler.AggressiveCompile$$anonfun$3$$anonfun$compileScala$1$1.apply(AggressiveCompile.scala:97)
at sbt.compiler.AggressiveCompile$$anonfun$3$$anonfun$compileScala$1$1.apply(AggressiveCompile.scala:97)
at sbt.compiler.AggressiveCompile.sbt$compiler$AggressiveCompile$$timed(AggressiveCompile.scala:162)
at sbt.compiler.AggressiveCompile$$anonfun$3.compileScala$1(AggressiveCompile.scala:96)
at sbt.compiler.AggressiveCompile$$anonfun$3.apply(AggressiveCompile.scala:139)
at sbt.compiler.AggressiveCompile$$anonfun$3.apply(AggressiveCompile.scala:86)
at sbt.inc.IncrementalCompile$$anonfun$doCompile$1.apply(Compile.scala:38)
at sbt.inc.IncrementalCompile$$anonfun$doCompile$1.apply(Compile.scala:36)
at sbt.inc.IncrementalCommon.cycle(IncrementalCommon.scala:31)
at sbt.inc.Incremental$$anonfun$1.apply(Incremental.scala:39)
at sbt.inc.Incremental$$anonfun$1.apply(Incremental.scala:38)
at sbt.inc.Incremental$.manageClassfiles(Incremental.scala:66)
at sbt.inc.Incremental$.compile(Incremental.scala:38)
at sbt.inc.IncrementalCompile$.apply(Compile.scala:26)
at sbt.compiler.AggressiveCompile.compile2(AggressiveCompile.scala:153)
at sbt.compiler.AggressiveCompile.compile1(AggressiveCompile.scala:70)
at com.typesafe.zinc.Compiler.compile(Compiler.scala:201)
at com.typesafe.zinc.Compiler.compile(Compiler.scala:183)
at com.typesafe.zinc.Compiler.compile(Compiler.scala:174)
at com.typesafe.zinc.Compiler.compile(Compiler.scala:165)
at org.gradle.api.internal.tasks.scala.ZincScalaCompiler$Compiler.execute(ZincScalaCompiler.java:92)
... 9 more
BUILD FAILED
Do you know what could be the problem?