[package - 130releng-armv6-quarterly][biology/gatk] Failed for gatk-4.2.0.0 in build/runaway

From: <pkg-fallout_at_FreeBSD.org>
Date: Fri, 10 Jun 2022 01:38:04 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:        http://beefy8.nyi.freebsd.org/data/130releng-armv6-quarterly/bb870272e22e/logs/gatk-4.2.0.0.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=130releng-armv6-quarterly&build=bb870272e22e
Log:

=>> Building biology/gatk
build started at Thu Jun  9 17:48:53 UTC 2022
port directory: /usr/ports/biology/gatk
package name: gatk-4.2.0.0
building for: FreeBSD 130releng-armv6-quarterly-job-04 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 1300139 arm
maintained by: yuri@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400050
Jail OSVERSION: 1300139
Job Id: 04

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===> Use 'make config' to modify these settings
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--MAINTAINER--
yuri@FreeBSD.org
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XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache  HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--SUB_LIST--
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=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gatk-4.2.0.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.17.5_1.pkg
[130releng-armv6-quarterly-job-04] Installing pkg-1.17.5_1...
[130releng-armv6-quarterly-job-04] Extracting pkg-1.17.5_1: .......... done
===>   gatk-4.2.0.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gatk-4.2.0.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.2.0.0 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.2.0.0 for building
=> SHA256 Checksum OK for gatk-4.2.0.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.2.0.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.2.0.0 for building
===>  Extracting for gatk-4.2.0.0
=> SHA256 Checksum OK for gatk-4.2.0.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.2.0.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for gatk-4.2.0.0
===>  Applying FreeBSD patches for gatk-4.2.0.0 from /usr/ports/biology/gatk/files
===========================================================================
=======================<phase: build-depends  >============================
===>   gatk-4.2.0.0 depends on executable: gradle62 - not found
===>   Installing existing package /packages/All/gradle62-6.2.2_1.pkg
[130releng-armv6-quarterly-job-04] Installing gradle62-6.2.2_1...
[130releng-armv6-quarterly-job-04] `-- Installing openjdk8-8.322.06.1...
[130releng-armv6-quarterly-job-04] |   `-- Installing alsa-lib-1.2.2_1...
[130releng-armv6-quarterly-job-04] |   `-- Extracting alsa-lib-1.2.2_1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing dejavu-2.37_1...
[130releng-armv6-quarterly-job-04] |   | `-- Installing fontconfig-2.13.94_2,1...
[130releng-armv6-quarterly-job-04] |   |   `-- Installing expat-2.4.8...
[130releng-armv6-quarterly-job-04] |   |   `-- Extracting expat-2.4.8: .......... done
[130releng-armv6-quarterly-job-04] |   |   `-- Installing freetype2-2.11.1...
[130releng-armv6-quarterly-job-04] |   |   | `-- Installing png-1.6.37_1...
[130releng-armv6-quarterly-job-04] |   |   | `-- Extracting png-1.6.37_1: .......... done
[130releng-armv6-quarterly-job-04] |   |   `-- Extracting freetype2-2.11.1: .......... done
[130releng-armv6-quarterly-job-04] |   | `-- Extracting fontconfig-2.13.94_2,1: .......... done
[130releng-armv6-quarterly-job-04] |   | `-- Installing mkfontscale-1.2.1...
[130releng-armv6-quarterly-job-04] |   |   `-- Installing libfontenc-1.1.4...
[130releng-armv6-quarterly-job-04] |   |   `-- Extracting libfontenc-1.1.4: ......... done
[130releng-armv6-quarterly-job-04] |   | `-- Extracting mkfontscale-1.2.1: ....... done
[130releng-armv6-quarterly-job-04] |   `-- Extracting dejavu-2.37_1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing giflib-5.2.1...
[130releng-armv6-quarterly-job-04] |   `-- Extracting giflib-5.2.1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing java-zoneinfo-2021.e...
[130releng-armv6-quarterly-job-04] |   `-- Extracting java-zoneinfo-2021.e: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing javavmwrapper-2.7.8...
[130releng-armv6-quarterly-job-04] |   `-- Extracting javavmwrapper-2.7.8: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libX11-1.7.2,1...
[130releng-armv6-quarterly-job-04] |   | `-- Installing libxcb-1.14_1...
[130releng-armv6-quarterly-job-04] |   |   `-- Installing libXau-1.0.9...
[130releng-armv6-quarterly-job-04] |   |   `-- Extracting libXau-1.0.9: .......... done
[130releng-armv6-quarterly-job-04] |   |   `-- Installing libXdmcp-1.1.3...
[130releng-armv6-quarterly-job-04] |   |   | `-- Installing xorgproto-2021.5...
[130releng-armv6-quarterly-job-04] |   |   | `-- Extracting xorgproto-2021.5: .......... done
[130releng-armv6-quarterly-job-04] |   |   `-- Extracting libXdmcp-1.1.3: ......... done
[130releng-armv6-quarterly-job-04] |   |   `-- Installing libpthread-stubs-0.4...
[130releng-armv6-quarterly-job-04] |   |   `-- Extracting libpthread-stubs-0.4: .... done
[130releng-armv6-quarterly-job-04] |   | `-- Extracting libxcb-1.14_1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Extracting libX11-1.7.2,1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libXext-1.3.4,1...
[130releng-armv6-quarterly-job-04] |   `-- Extracting libXext-1.3.4,1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libXi-1.8,1...
[130releng-armv6-quarterly-job-04] |   | `-- Installing libXfixes-6.0.0...
[130releng-armv6-quarterly-job-04] |   | `-- Extracting libXfixes-6.0.0: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Extracting libXi-1.8,1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libXrender-0.9.10_2...
[130releng-armv6-quarterly-job-04] |   `-- Extracting libXrender-0.9.10_2: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libXt-1.2.1,1...
[130releng-armv6-quarterly-job-04] |   | `-- Installing libICE-1.0.10,1...
[130releng-armv6-quarterly-job-04] |   | `-- Extracting libICE-1.0.10,1: .......... done
[130releng-armv6-quarterly-job-04] |   | `-- Installing libSM-1.2.3,1...
[130releng-armv6-quarterly-job-04] |   | `-- Extracting libSM-1.2.3,1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Extracting libXt-1.2.1,1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libXtst-1.2.3_2...
[130releng-armv6-quarterly-job-04] |   `-- Extracting libXtst-1.2.3_2: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libffi-3.3_1...
[130releng-armv6-quarterly-job-04] |   | `-- Installing indexinfo-0.3.1...
[130releng-armv6-quarterly-job-04] |   | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv6-quarterly-job-04] |   `-- Extracting libffi-3.3_1: .......... done
[130releng-armv6-quarterly-job-04] |   `-- Installing libinotify-20211018...
[130releng-armv6-quarterly-job-04] |   `-- Extracting libinotify-20211018: .......... done
[130releng-armv6-quarterly-job-04] `-- Extracting openjdk8-8.322.06.1: .......... done
[130releng-armv6-quarterly-job-04] Extracting gradle62-6.2.2_1: .......... done
Running fc-cache to build fontconfig cache...
=====
Message from alsa-lib-1.2.2_1:

--
===>   NOTICE:

The alsa-lib port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing
=====
Message from freetype2-2.11.1:

--
The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as
the default, emulating a modern version of ClearType. This change inevitably
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 openjdk8-8.322.06.1:

--
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-4.2.0.0 depends on executable: gradle62 - found
===>   Returning to build of gatk-4.2.0.0
===>   gatk-4.2.0.0 depends on file: /usr/local/openjdk8/bin/java - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   gatk-4.2.0.0 depends on shared library: libintl.so - not found
===>   Installing existing package /packages/All/gettext-runtime-0.21.pkg
[130releng-armv6-quarterly-job-04] Installing gettext-runtime-0.21...
[130releng-armv6-quarterly-job-04] Extracting gettext-runtime-0.21: .......... done
===>   gatk-4.2.0.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===>   Returning to build of gatk-4.2.0.0
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for gatk-4.2.0.0
===========================================================================
=======================<phase: build          >============================
===>  Building for gatk-4.2.0.0
Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be reused, use --status for details
> Task :compileJava
> Task :processResources
> Task :classes
> Task :shadowJar
=>> Killing runaway build after 21600 seconds with no output