Bug 239392 - biology/gatk: fails to build with Gradle 4.10.3
Summary: biology/gatk: fails to build with Gradle 4.10.3
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Some People
Assignee: Tobias Kortkamp
URL:
Keywords:
Depends on:
Blocks: 237443
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Reported: 2019-07-23 04:32 UTC by Tobias Kortkamp
Modified: 2019-07-23 06:33 UTC (History)
1 user (show)

See Also:
koobs: maintainer-feedback+


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Description Tobias Kortkamp freebsd_committer freebsd_triage 2019-07-23 04:32:46 UTC
I want to update java/openjfx8-devel and for that I also need to
update devel/gradle4 to at least 4.8.  While updating it to 4.10.3
seems to be fine for biology/igv and openjfx8-devel, it break gatk:

FAILURE: Build failed with an exception.

* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.0.11.0/build.gradle' line: 17

* What went wrong:
Plugin [id: 'de.undercouch.download', version: '2.1.0'] was not found in any of the following sources:

- Gradle Core Plugins (plugin is not in 'org.gradle' namespace)
- Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:2.1.0')
  Searched in the following repositories:
    Gradle Central Plugin Repository

* 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.

* Get more help at https://help.gradle.org

BUILD FAILED in 4s
*** Error code 1

Any ideas how to fix this other than creating a devel/gradle46 for gatk?

The devel/gradle4 update is part of the patch attached to bug #237443.
Comment 1 Yuri Victorovich freebsd_committer freebsd_triage 2019-07-23 05:11:37 UTC
They said that gradle higher than 3.1 is not supported: https://github.com/broadinstitute/gatk/issues/5483

I have no idea how to fix this. Just create a devel/gradle46 for gatk, like you suggested.


Yuri
Comment 2 commit-hook freebsd_committer freebsd_triage 2019-07-23 05:29:12 UTC
A commit references this bug:

Author: tobik
Date: Tue Jul 23 05:28:47 UTC 2019
New revision: 507197
URL: https://svnweb.freebsd.org/changeset/ports/507197

Log:
  Prepare for devel/gradle4 and java/openjfx8-devel updates

  openjfx8-devel now requires at least Gradle 4.8.  biology/gatk
  however does not build with Gradle 4.10.3.  Preserve Gradle 4.6 for
  now.

  PR:		239392

Changes:
  head/biology/gatk/Makefile
  head/devel/Makefile
  head/devel/gradle46/
  head/devel/gradle46/Makefile
Comment 3 Tobias Kortkamp freebsd_committer freebsd_triage 2019-07-23 05:36:13 UTC
That's unfortunate but thanks for the prompt reply.
Comment 4 Kubilay Kocak freebsd_committer freebsd_triage 2019-07-23 06:33:27 UTC
Assign to committer that resolved