[Solved] Hail compilation error

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1

HI there,

I am trying to install Hail on our server and I get the following error:

== Expanded type of tree ==

TypeRef(
pre = TypeRef(TypeSymbol(class SampleQC extends Command))
TypeSymbol(class Options extends SampleQC.BaseOptions)
)

uncaught exception during compilation: scala.reflect.internal.Types$TypeError
:compileScala FAILED
:compileScala (Thread[main,5,main]) completed. Took 1 mins 3.16 secs.

FAILURE: Build failed with an exception.

  • What went wrong:
    Execution failed for task ‘:compileScala’.

bad symbolic reference. A signature in ResponseOps.class refers to term time
in package java which is not available.
It may be completely missing from the current classpath, or the version on
the classpath might be incompatible with the version used when compiling ResponseOps.class.

  • Try:
    Run with --stacktrace option to get the stack trace. Run with --debug option to get more log output.

BUILD FAILED

Total time: 1 mins 10.724 secs
Stopped 1 compiler daemon(s).

Any clue on solving this? Thanks in advance

S. Foisy
Project manager - Bioinformatics
Genomic Medecine of Inflammation
Montreal Heart Institute Research Center

2

Hello! I hope we can get this fixed quickly.

A few questions:

  1. What version of gradle are you running? Using the gradle wrapper in the hail directory (./gradlew) uses the appropriate version automatically
  2. What version of java do you have installed? Hail requires Java 8.
3

In particular, the missing “time” term occurs when using Java 7, as this API is new in Java 8:
http://docs.oracle.com/javase/8/docs/api/java/time/package-summary.html

4

Hi,

That would explain the problem… My Java is Java 7; I’ll work on updating everything and check again…

5

Hi,

Upgrading everything did the trick :wink: Thanks for the inputs.

S