[package - 124amd64-default][biology/gatk] Failed for gatk-4.3.0.0 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sun, 28 May 2023 16:17:59 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/beefy6/data/124amd64-default/89b75dd0eed4/logs/gatk-4.3.0.0.log
Build URL:      https://pkg-status.freebsd.org/beefy6/build.html?mastername=124amd64-default&build=89b75dd0eed4
Log:

=>> Building biology/gatk
build started at Sun May 28 16:16:47 UTC 2023
port directory: /usr/ports/biology/gatk
package name: gatk-4.3.0.0
building for: FreeBSD 124amd64-default-job-03 12.4-RELEASE-p2 FreeBSD 12.4-RELEASE-p2 amd64
maintained by: yuri@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-23-ga7f8d188
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Jail OSVERSION: 1204000
Job Id: 03

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---Begin OPTIONS List---
===> The following configuration options are available for gatk-4.3.0.0:
     WITH_LARGE_FILES=off: Download large LFS files needed for build and tests
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

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--End PLIST_SUB--

--SUB_LIST--
PORTVERSION=4.3.0.0 JAVA=/usr/local/openjdk17/bin/java JAVASHAREDIR="/usr/local/share/java"  JAVAJARDIR="/usr/local/share/java/classes"  JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17" PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/gatk DOCSDIR=/usr/local/share/doc/gatk EXAMPLESDIR=/usr/local/share/examples/gatk  WWWDIR=/usr/local/www/gatk ETCDIR=/usr/local/etc/gatk
--End SUB_LIST--

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=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gatk-4.3.0.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.19.1_1.pkg
[124amd64-default-job-03] Installing pkg-1.19.1_1...
[124amd64-default-job-03] Extracting pkg-1.19.1_1: .......... done
===>   gatk-4.3.0.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gatk-4.3.0.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.3.0.0 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.3.0.0 for building
=> SHA256 Checksum OK for gatk-4.3.0.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.3.0.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.3.0.0 for building
===>  Extracting for gatk-4.3.0.0
=> SHA256 Checksum OK for gatk-4.3.0.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.3.0.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for gatk-4.3.0.0
===>  Applying FreeBSD patches for gatk-4.3.0.0 from /usr/ports/biology/gatk/files
===========================================================================
=======================<phase: build-depends  >============================
===>   gatk-4.3.0.0 depends on executable: gradle - not found
===>   Installing existing package /packages/All/gradle-8.0.1.pkg
[124amd64-default-job-03] Installing gradle-8.0.1...
[124amd64-default-job-03] `-- Installing openjdk8-8.372.07.1_1...
[124amd64-default-job-03] |   `-- Installing alsa-lib-1.2.2_1...
[124amd64-default-job-03] |   `-- Extracting alsa-lib-1.2.2_1: .......... done
[124amd64-default-job-03] |   `-- Installing dejavu-2.37_1...
[124amd64-default-job-03] |   | `-- Installing fontconfig-2.14.2,1...
[124amd64-default-job-03] |   |   `-- Installing expat-2.5.0...
[124amd64-default-job-03] |   |   `-- Extracting expat-2.5.0: .......... done
<snip>
leads to different rendering results, and you might change port's options to
adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment
variable).

The environment variable "FREETYPE_PROPERTIES" can be used to control the
driver properties. Example:

FREETYPE_PROPERTIES=truetype:interpreter-version=35 \
	cff:no-stem-darkening=1 \
	autofitter:warping=1

This allows to select, say, the subpixel hinting mode at runtime for a given
application.

If LONG_PCF_NAMES port's option was enabled, the PCF family names may include
the foundry and information whether they contain wide characters. For example,
"Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at
run time with using pcf:no-long-family-names property, if needed. Example:

FREETYPE_PROPERTIES=pcf:no-long-family-names=1

How to recreate fontconfig cache with using such environment variable,
if needed:
# env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv

The controllable properties are listed in the section "Controlling FreeType
Modules" in the reference's table of contents
(/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed).
=====
Message from dejavu-2.37_1:

--
Make sure that the freetype module is loaded.  If it is not, add the following
line to the "Modules" section of your X Windows configuration file:

	Load "freetype"

Add the following line to the "Files" section of X Windows configuration file:

	FontPath "/usr/local/share/fonts/dejavu/"

Note: your X Windows configuration file is typically /etc/X11/XF86Config
if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org.
=====
Message from libinotify-20211018:

--
You might want to consider increasing the kern.maxfiles tunable if you plan
to use this library for applications that need to monitor activity of a lot
of files.
=====
Message from openjdk8-8.372.07.1_1:

--
This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and
procfs(5) mounted on /proc.

If you have not done it yet, please do the following:

	mount -t fdescfs fdesc /dev/fd
	mount -t procfs proc /proc

To make it permanent, you need the following lines in /etc/fstab:

	fdesc	/dev/fd		fdescfs		rw	0	0
	proc	/proc		procfs		rw	0	0
===>   gatk-4.3.0.0 depends on executable: gradle - found
===>   Returning to build of gatk-4.3.0.0
===>   gatk-4.3.0.0 depends on file: /usr/local/openjdk17/bin/java - not found
===>   Installing existing package /packages/All/openjdk17-17.0.7+7.1.pkg
[124amd64-default-job-03] Installing openjdk17-17.0.7+7.1...
[124amd64-default-job-03] `-- Installing harfbuzz-7.3.0...
[124amd64-default-job-03] |   `-- Installing gettext-runtime-0.21.1...
[124amd64-default-job-03] |   | `-- Installing indexinfo-0.3.1...
[124amd64-default-job-03] |   | `-- Extracting indexinfo-0.3.1: .... done
[124amd64-default-job-03] |   `-- Extracting gettext-runtime-0.21.1: .......... done
[124amd64-default-job-03] |   `-- Installing glib-2.76.3,2...
[124amd64-default-job-03] |   | `-- Installing libffi-3.4.4...
[124amd64-default-job-03] |   | `-- Extracting libffi-3.4.4: .......... done
[124amd64-default-job-03] |   | `-- Installing libiconv-1.17...
[124amd64-default-job-03] |   | `-- Extracting libiconv-1.17: .......... done
[124amd64-default-job-03] |   | `-- Installing libxml2-2.10.4...
[124amd64-default-job-03] |   |   `-- Installing readline-8.2.1...
[124amd64-default-job-03] |   |   `-- Extracting readline-8.2.1: .......... done
[124amd64-default-job-03] |   | `-- Extracting libxml2-2.10.4: .......... done
[124amd64-default-job-03] |   | `-- Installing pcre2-10.42...
[124amd64-default-job-03] |   | `-- Extracting pcre2-10.42: .......... done
[124amd64-default-job-03] |   | `-- Installing python39-3.9.16_2...
[124amd64-default-job-03] |   |   `-- Installing mpdecimal-2.5.1...
[124amd64-default-job-03] |   |   `-- Extracting mpdecimal-2.5.1: .......... done
[124amd64-default-job-03] |   | `-- Extracting python39-3.9.16_2: .......... done
[124amd64-default-job-03] |   `-- Extracting glib-2.76.3,2: .......... done
[124amd64-default-job-03] |   `-- Installing graphite2-1.3.14...
[124amd64-default-job-03] |   `-- Extracting graphite2-1.3.14: .......... done
[124amd64-default-job-03] `-- Extracting harfbuzz-7.3.0: .......... done
[124amd64-default-job-03] `-- Installing jpeg-turbo-2.1.5.1...
[124amd64-default-job-03] `-- Extracting jpeg-turbo-2.1.5.1: .......... done
[124amd64-default-job-03] `-- Installing lcms2-2.15_1...
[124amd64-default-job-03] |   `-- Installing tiff-4.4.0_1...
[124amd64-default-job-03] |   | `-- Installing jbigkit-2.1_1...
[124amd64-default-job-03] |   | `-- Extracting jbigkit-2.1_1: .......... done
[124amd64-default-job-03] |   | `-- Installing libdeflate-1.18...
[124amd64-default-job-03] |   | `-- Extracting libdeflate-1.18: .......... done
[124amd64-default-job-03] |   | `-- Installing zstd-1.5.4_2...
[124amd64-default-job-03] |   |   `-- Installing liblz4-1.9.4,1...
[124amd64-default-job-03] |   |   `-- Extracting liblz4-1.9.4,1: .......... done
[124amd64-default-job-03] |   | `-- Extracting zstd-1.5.4_2: .......... done
[124amd64-default-job-03] |   `-- Extracting tiff-4.4.0_1: .......... done
[124amd64-default-job-03] `-- Extracting lcms2-2.15_1: .......... done
[124amd64-default-job-03] `-- Installing libXrandr-1.5.2...
[124amd64-default-job-03] `-- Extracting libXrandr-1.5.2: .......... done
[124amd64-default-job-03] `-- Installing xorg-fonts-truetype-7.7_1...
[124amd64-default-job-03] |   `-- Installing encodings-1.0.5,1...
[124amd64-default-job-03] |   `-- Extracting encodings-1.0.5,1: .......... done
[124amd64-default-job-03] |   `-- Installing font-bh-ttf-1.0.3_4...
[124amd64-default-job-03] |   `-- Extracting font-bh-ttf-1.0.3_4: .......... done
[124amd64-default-job-03] |   `-- Installing font-misc-ethiopic-1.0.4...
[124amd64-default-job-03] |   `-- Extracting font-misc-ethiopic-1.0.4: ...... done
[124amd64-default-job-03] |   `-- Installing font-misc-meltho-1.0.3_4...
[124amd64-default-job-03] |   `-- Extracting font-misc-meltho-1.0.3_4: .......... done
[124amd64-default-job-03] `-- Extracting xorg-fonts-truetype-7.7_1: ... done
[124amd64-default-job-03] Extracting openjdk17-17.0.7+7.1: .......... done
Running fc-cache to build fontconfig cache...
Generating GIO modules cache
Compiling glib schemas
No schema files found: doing nothing.
=====
Message from python39-3.9.16_2:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py39-gdbm       databases/py-gdbm@py39
py39-sqlite3    databases/py-sqlite3@py39
py39-tkinter    x11-toolkits/py-tkinter@py39
=====
Message from openjdk17-17.0.7+7.1:

--
This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and
procfs(5) mounted on /proc.

If you have not done it yet, please do the following:

	mount -t fdescfs fdesc /dev/fd
	mount -t procfs proc /proc

To make it permanent, you need the following lines in /etc/fstab:

	fdesc	/dev/fd		fdescfs		rw	0	0
	proc	/proc		procfs		rw	0	0
===>   gatk-4.3.0.0 depends on file: /usr/local/openjdk17/bin/java - found
===>   Returning to build of gatk-4.3.0.0
===========================================================================
=======================<phase: lib-depends    >============================
===>   gatk-4.3.0.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for gatk-4.3.0.0
===========================================================================
=======================<phase: build          >============================
===>  Building for gatk-4.3.0.0

Welcome to Gradle 8.0.1!

Here are the highlights of this release:
 - Improvements to the Kotlin DSL
 - Fine-grained parallelism from the first build with configuration cache
 - Configurable Gradle user home cache cleanup

For more details see https://docs.gradle.org/8.0.1/release-notes.html

Starting a Gradle Daemon (subsequent builds will be faster)

FAILURE: Build failed with an exception.

* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.3.0.0/build.gradle' line: 15

* What went wrong:
Plugin [id: 'de.undercouch.download', version: '4.1.2'] 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:4.1.2')
  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 8s
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/gatk