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Build of picard Gradle project fails with error

SimpsonSimpson Member
edited April 2018 in Ask the GATK team

I have an error when tried to build a picard.jar using ./gradlew shadowJar with Java 9.
I am running Ubuntu 16.0.4 (64bit) system. Could you please let me know what should I do?
Thank you.

$ java -version
java version "9.0.4"
Java(TM) SE Runtime Environment (build 9.0.4+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.4+11, mixed mode)

$ ./gradlew --version
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass (file:/home/usser/.gradle/wrapper/dists/gradle-4.3-all/2c1rgv6vofd95kl0ugolfeu5r/gradle-4.3/lib/groovy-all-2.4.12.jar) to method java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

------------------------------------------------------------
Gradle 4.3
------------------------------------------------------------

Build time: 2017-10-30 15:43:29 UTC
Revision: c684c202534c4138b51033b52d871939b8d38d72

Groovy: 2.4.12
Ant: Apache Ant(TM) version 1.9.6 compiled on June 29 2015
JVM: 10.0.1 ("Oracle Corporation" 10.0.1+10)
OS: Linux 4.13.0-39-generic amd64

$ git --version
git version 2.7.4

$ ll
total 124
drwxr-xr-x 14 usser usser 4096 Apr 27 15:12 ./
drwxrwxr-x 4 usser usser 4096 Apr 27 15:15 ../
drwxr-xr-x 7 usser usser 4096 Mar 13 00:28 build/
-rw-rw-r-- 1 usser usser 13031 Apr 27 15:12 build.gradle
-rw-r--r-- 1 usser usser 1098 Feb 26 22:07 build.xml
-rw-r--r-- 1 usser usser 358 Feb 26 22:07 .classpath
-rw-r--r-- 1 usser usser 869 Mar 21 19:51 Dockerfile
-rw-r--r-- 1 usser usser 179 Feb 26 22:07 .dockerignore
drwxr-xr-x 3 usser usser 4096 Feb 26 22:07 etc/
drwxr-xr-x 8 usser usser 4096 Apr 4 19:52 .git/
drwxr-xr-x 2 usser usser 4096 Feb 26 22:07 .github/
-rw-r--r-- 1 usser usser 190 Feb 26 22:07 .gitignore
drwxr-xr-x 3 usser usser 4096 Feb 26 22:07 gradle/
drwxr-xr-x 3 usser usser 4096 Apr 27 15:15 .gradle/
-rwxr-xr-x 1 usser usser 5046 Mar 21 19:51 gradlew*
drwxr-xr-x 2 usser usser 4096 Apr 4 20:27 lib/
-rw-r--r-- 1 usser usser 1072 Feb 26 22:07 LICENSE.txt
drwxrwxr-x 4 usser usser 4096 Feb 26 22:22 out/
drwxr-xr-x 2 usser usser 4096 Feb 26 22:07 project/
-rw-r--r-- 1 usser usser 356 Feb 26 22:07 .project
-rw-r--r-- 1 usser usser 6045 Feb 26 22:07 README.md
-rw-r--r-- 1 usser usser 56 Feb 26 22:07 settings.gradle
drwxr-xr-x 4 usser usser 4096 Feb 26 22:07 src/
drwxr-xr-x 3 usser usser 4096 Feb 26 22:07 testdata/
-rw-r--r-- 1 usser usser 601 Feb 26 22:07 .travis.yml

$ ./gradlew shadowJar

FAILURE: Build failed with an exception.

  • What went wrong:
    Could not create an instance of type org.gradle.invocation.DefaultGradle_Decorated.
    >Could not configure services using GradleScopeCompileServices.configure().

  • Try:
    Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

I looked for advices on the Internet but none of them was helpful.

Post edited by Simpson on
Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Simpson
    Hi,

    Is it not possible for you to use a precompiled version of Picard?

    Have you tried:
    Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.? What does the stacktrace say? Can you post it?

    Thanks,
    Sheila

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