Bug 239392
| Summary: | biology/gatk: fails to build with Gradle 4.10.3 | ||
|---|---|---|---|
| Product: | Ports & Packages | Reporter: | Tobias Kortkamp <tobik> |
| Component: | Individual Port(s) | Assignee: | Tobias Kortkamp <tobik> |
| Status: | Closed FIXED | ||
| Severity: | Affects Some People | CC: | yuri |
| Priority: | --- | Flags: | koobs:
maintainer-feedback+
|
| Version: | Latest | ||
| Hardware: | Any | ||
| OS: | Any | ||
| See Also: |
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=237443 https://github.com/broadinstitute/gatk/issues/5483 |
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| Bug Depends on: | |||
| Bug Blocks: | 237443 | ||
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 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 That's unfortunate but thanks for the prompt reply. Assign to committer that resolved |
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.