Bug 239901 - biology/gatk: Fails to build with Gradle 5.6
Summary: biology/gatk: Fails to build with Gradle 5.6
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: Tobias Kortkamp
URL: https://people.freebsd.org/~pi/logs/g...
Depends on:
Blocks: 239875
  Show dependency treegraph
Reported: 2019-08-16 10:06 UTC by Tobias Kortkamp
Modified: 2019-11-20 09:52 UTC (History)
0 users

See Also:
bugzilla: maintainer-feedback? (yuri)


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Description Tobias Kortkamp freebsd_committer 2019-08-16 10:06:25 UTC
FAILURE: Build failed with an exception.

* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-' line: 16

* 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

*** Error code 1

Comment 1 Yuri Victorovich freebsd_committer 2019-08-16 22:43:59 UTC
The upstream bug report: https://github.com/broadinstitute/gatk/issues/6097
Comment 2 Yuri Victorovich freebsd_committer 2019-08-16 22:46:06 UTC
I don't think I can do anything beyond creating the upstream bug report.

Please feel free to branch the gradle-5 ports off if they wouldn't be able to resolve it quick.
Comment 3 Tobias Kortkamp freebsd_committer 2019-08-17 20:37:52 UTC
(In reply to Yuri Victorovich from comment #2)
> I don't think I can do anything beyond creating the upstream bug report.

Thanks, but are you sure that the dependency tarball you provide
does not need to be regenerated?  The error says that it cannot
find the de.undercouch.download/2.1.0 artifact anywhere suggesting
it is not available in the tarball

However it is available in there, so maybe the project cache dir
layout has changed slightly between Gradle 5.0 and 5.6.  Can you
please take a look?

> Please feel free to branch the gradle-5 ports off if they wouldn't be able to resolve it quick.

I do not think that any of this is very urgent.

Branching devel/gradle everytime we run into some build problem is
suboptimal and should only happen as a last resort.  I'd think that
going from Gradle 5.x to 5.y should not be as difficult as going
from Gradle 4 to 5 but maybe this is wishful thinking.
Comment 4 Yuri Victorovich freebsd_committer 2019-08-20 21:58:26 UTC
(In reply to Tobias Kortkamp from comment #3)

It might be that the deps archive simply needs to be regenerated for it to work with gradle-5.6.
Comment 5 commit-hook freebsd_committer 2019-11-20 09:51:56 UTC
A commit references this bug:

Author: tobik
Date: Wed Nov 20 09:51:45 UTC 2019
New revision: 517997
URL: https://svnweb.freebsd.org/changeset/ports/517997

  Create devel/gradle5 in preparation of devel/gradle update

  Many consumers fail to build with newer Gradle versions.

  PR:		239875, 239900, 239901, 239902