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  1. Jalview
  2. JAL-3745

A problem with gradle 6.6.1 is preventing command line build of jalviewjs

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    Details

    • Type: Bug
    • Status: Ready for testing
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.11.1.0, 2.11.1.1, 2.11.1.2, 2.11.1.3, 2.11.1.4
    • Fix Version/s: 2.11.1_js, 2.11.1.5, 2.11.2
    • Component/s: gradle, jalview-j2s
    • Labels:
      None
    • Environment:
      Java 11.0.8 OpenJDK
      gradle 6.6.1 (binary distribution)
      Eclipse 2020-03 or 2020-06

      Description

      Using gradle 6.6.1, there is a NullPointerException caused when a task in out build.gradle uses org.apache.tools.ant.util.TeeOutputStream class to stream output to STDOUT as well as into a file. This can be seen in linkChecks task, although it is not fatal.
      When running the jalviewjsTranspile task, there is a NullPointerException caused by TeeOutputStream, but in this case the task does not seem to complete (although it does seem to start transpiling).

      > Task :jalviewjsTranspile
      Running task jalviewjsTranspile as IN_ECLIPSE=false
      Could not read standard output of command '/home/bsoares/buildtools/eclipse/jee-2020-03/eclipse/eclipse'.
      java.lang.NullPointerException
              at org.apache.tools.ant.util.TeeOutputStream.write(TeeOutputStream.java:86)
              at org.gradle.process.internal.streams.ExecOutputHandleRunner.forwardContent(ExecOutputHandleRunner.java:67)
              at org.gradle.process.internal.streams.ExecOutputHandleRunner.run(ExecOutputHandleRunner.java:53)
              at org.gradle.internal.operations.CurrentBuildOperationPreservingRunnable.run(CurrentBuildOperationPreservingRunnable.java:42)
              at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
              at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
              at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
              at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
              at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
              at java.base/java.lang.Thread.run(Thread.java:834)
      <=====--------> 38% EXECUTING [6m 5s]

      It is likely that finding and fixing the NullPointerException will fix this problem, although it's just possible that it is unrelated.

      The problem (including the NullPointerException) does not occur with gradle-6.5 so check with and focus on changes in 6.5.1, 6.6 and 6.6.1

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              Assignee:
              soares Ben Soares
              Reporter:
              soares Ben Soares
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                Dates

                Created:
                Updated: