[package - 130arm64-quarterly][biology/gatk] Failed for gatk-4.2.0.0 in build/runaway
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Date: Sat, 04 Sep 2021 01:57:42 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://ampere1.nyi.freebsd.org/data/130arm64-quarterly/3b76cdf297ea/logs/gatk-4.2.0.0.log
Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=130arm64-quarterly&build=3b76cdf297ea
Log:
=>> Building biology/gatk
build started at Fri Sep 3 23:33:07 UTC 2021
port directory: /usr/ports/biology/gatk
package name: gatk-4.2.0.0
building for: FreeBSD 130arm64-quarterly-job-10 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 arm64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1300139
Job Id: 10
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PWD=/usr/local/poudriere/data/.m/130arm64-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
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POUDRIEREPATH=/usr/local/bin/poudriere
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PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for gatk-4.2.0.0:
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--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work 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
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work 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 NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gatk" EXAMPLESDIR="share/examples/gatk" DATADIR="share/gatk" WWWDIR="www/gatk" ETCDIR="etc/gatk"
--End PLIST_SUB--
--SUB_LIST--
PORTVERSION=4.2.0.0 JAVA=/usr/local/openjdk8/bin/java JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" 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--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
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CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
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ARCH=aarch64
OPSYS=FreeBSD
_OSRELEASE=13.0-RELEASE-p4
OSREL=13.0
OSVERSION=1300139
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 1048576
stack size (kbytes, -s) 1048576
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 2048
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<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-1.16.3.txz
[130arm64-quarterly-job-10] Installing pkg-1.16.3...
[130arm64-quarterly-job-10] Extracting pkg-1.16.3: .......... 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.txz
[130arm64-quarterly-job-10] Installing gradle62-6.2.2_1...
[130arm64-quarterly-job-10] `-- Installing openjdk8-8.292.10.1...
[130arm64-quarterly-job-10] | `-- Installing alsa-lib-1.2.2...
[130arm64-quarterly-job-10] | `-- Extracting alsa-lib-1.2.2: .......... done
[130arm64-quarterly-job-10] | `-- Installing dejavu-2.37_1...
[130arm64-quarterly-job-10] | | `-- Installing fontconfig-2.13.93_1,1...
[130arm64-quarterly-job-10] | | `-- Installing expat-2.4.1...
[130arm64-quarterly-job-10] | | `-- Extracting expat-2.4.1: .......... done
[130arm64-quarterly-job-10] | | `-- Installing freetype2-2.10.4...
[130arm64-quarterly-job-10] | | | `-- Installing png-1.6.37_1...
[130arm64-quarterly-job-10] | | | `-- Extracting png-1.6.37_1: .......... done
[130arm64-quarterly-job-10] | | `-- Extracting freetype2-2.10.4: .......... done
[130arm64-quarterly-job-10] | | `-- Extracting fontconfig-2.13.93_1,1: .......... done
[130arm64-quarterly-job-10] | | `-- Installing mkfontscale-1.2.1...
[130arm64-quarterly-job-10] | | `-- Installing libfontenc-1.1.4...
[130arm64-quarterly-job-10] | | `-- Extracting libfontenc-1.1.4: ......... done
[130arm64-quarterly-job-10] | | `-- Extracting mkfontscale-1.2.1: ....... done
[130arm64-quarterly-job-10] | `-- Extracting dejavu-2.37_1: .......... done
[130arm64-quarterly-job-10] | `-- Installing giflib-5.2.1...
[130arm64-quarterly-job-10] | `-- Extracting giflib-5.2.1: .......... done
[130arm64-quarterly-job-10] | `-- Installing java-zoneinfo-2021.a...
[130arm64-quarterly-job-10] | `-- Extracting java-zoneinfo-2021.a: .......... done
[130arm64-quarterly-job-10] | `-- Installing javavmwrapper-2.7.7...
[130arm64-quarterly-job-10] | `-- Extracting javavmwrapper-2.7.7: .......... done
[130arm64-quarterly-job-10] | `-- Installing libX11-1.7.2,1...
[130arm64-quarterly-job-10] | | `-- Installing libxcb-1.14_1...
[130arm64-quarterly-job-10] | | `-- Installing libXau-1.0.9...
[130arm64-quarterly-job-10] | | `-- Extracting libXau-1.0.9: .......... done
[130arm64-quarterly-job-10] | | `-- Installing libXdmcp-1.1.3...
[130arm64-quarterly-job-10] | | | `-- Installing xorgproto-2021.4...
[130arm64-quarterly-job-10] | | | `-- Extracting xorgproto-2021.4: .......... done
[130arm64-quarterly-job-10] | | `-- Extracting libXdmcp-1.1.3: ......... done
[130arm64-quarterly-job-10] | | `-- Installing libpthread-stubs-0.4...
[130arm64-quarterly-job-10] | | `-- Extracting libpthread-stubs-0.4: .... done
[130arm64-quarterly-job-10] | | `-- Extracting libxcb-1.14_1: .......... done
[130arm64-quarterly-job-10] | `-- Extracting libX11-1.7.2,1: .......... done
[130arm64-quarterly-job-10] | `-- Installing libXext-1.3.4,1...
[130arm64-quarterly-job-10] | `-- Extracting libXext-1.3.4,1: .......... done
[130arm64-quarterly-job-10] | `-- Installing libXi-1.7.10,1...
[130arm64-quarterly-job-10] | | `-- Installing libXfixes-5.0.3_2...
[130arm64-quarterly-job-10] | | `-- Extracting libXfixes-5.0.3_2: .......... done
[130arm64-quarterly-job-10] | `-- Extracting libXi-1.7.10,1: .......... done
[130arm64-quarterly-job-10] | `-- Installing libXrender-0.9.10_2...
[130arm64-quarterly-job-10] | `-- Extracting libXrender-0.9.10_2: .......... done
[130arm64-quarterly-job-10] | `-- Installing libXt-1.2.1,1...
[130arm64-quarterly-job-10] | | `-- Installing libICE-1.0.10,1...
[130arm64-quarterly-job-10] | | `-- Extracting libICE-1.0.10,1: .......... done
[130arm64-quarterly-job-10] | | `-- Installing libSM-1.2.3,1...
[130arm64-quarterly-job-10] | | `-- Extracting libSM-1.2.3,1: .......... done
[130arm64-quarterly-job-10] | `-- Extracting libXt-1.2.1,1: .......... done
[130arm64-quarterly-job-10] | `-- Installing libXtst-1.2.3_2...
[130arm64-quarterly-job-10] | `-- Extracting libXtst-1.2.3_2: .......... done
[130arm64-quarterly-job-10] | `-- Installing libffi-3.3_1...
[130arm64-quarterly-job-10] | | `-- Installing indexinfo-0.3.1...
[130arm64-quarterly-job-10] | | `-- Extracting indexinfo-0.3.1: .... done
[130arm64-quarterly-job-10] | `-- Extracting libffi-3.3_1: .......... done
[130arm64-quarterly-job-10] | `-- Installing libinotify-20180201_2...
[130arm64-quarterly-job-10] | `-- Extracting libinotify-20180201_2: .......... done
[130arm64-quarterly-job-10] `-- Extracting openjdk8-8.292.10.1: .......... done
[130arm64-quarterly-job-10] Extracting gradle62-6.2.2_1: .......... done
=====
Message from alsa-lib-1.2.2:
--
===> 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 freetype2-2.10.4:
--
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/site/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-20180201_2:
--
Libinotify functionality on FreeBSD is missing support for
- detecting a file being moved into or out of a directory within the
same filesystem
- certain modifications to a symbolic link (rather than the
file it points to.)
in addition to the known limitations on all platforms using kqueue(2)
where various open and close notifications are unimplemented.
This means the following regression tests will fail:
Directory notifications:
IN_MOVED_FROM
IN_MOVED_TO
Open/close notifications:
IN_OPEN
IN_CLOSE_NOWRITE
IN_CLOSE_WRITE
Symbolic Link notifications:
IN_DONT_FOLLOW
IN_ATTRIB
IN_MOVE_SELF
IN_DELETE_SELF
Kernel patches to address the missing directory and symbolic link
notifications are available from:
https://github.com/libinotify-kqueue/libinotify-kqueue/tree/master/patches
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 openjdk8-8.292.10.1:
--
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.txz
[130arm64-quarterly-job-10] Installing gettext-runtime-0.21...
[130arm64-quarterly-job-10] 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 7200 seconds with no output