[package - 121armv7-quarterly][biology/gatk] Failed for gatk-4.1.5.0 in build/runaway
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Apr 9 23:34:22 UTC 2020
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 at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: branches/2020Q2/biology/gatk/Makefile 527743 2020-03-04 08:47:55Z yuri $
Log URL: http://beefy13.nyi.freebsd.org/data/121armv7-quarterly/531165/logs/gatk-4.1.5.0.log
Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=121armv7-quarterly&build=531165
Log:
=>> Building biology/gatk
build started at Thu Apr 9 14:33:25 UTC 2020
port directory: /usr/ports/biology/gatk
package name: gatk-4.1.5.0
building for: FreeBSD 121armv7-quarterly-job-05 12.1-RELEASE-p3 FreeBSD 12.1-RELEASE-p3 1201000 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q2/biology/gatk/Makefile 527743 2020-03-04 08:47:55Z yuri $
Poudriere version: 3.2.8-5-gc81843e5
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Jail OSVERSION: 1201000
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---End OPTIONS List---
--MAINTAINER--
yuri at 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--
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--End PLIST_SUB--
--SUB_LIST--
PORTVERSION=4.1.5.0 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--
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#### /usr/local/etc/poudriere.d/make.conf ####
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#### /usr/ports/Mk/Scripts/ports_env.sh ####
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max memory size (kbytes, -m) unlimited
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max user processes (-u) 89999
open files (-n) 2048
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swap limit (kbytes, -w) unlimited
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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-4.1.5.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.13.2.txz
[121armv7-quarterly-job-05] Installing pkg-1.13.2...
[121armv7-quarterly-job-05] Extracting pkg-1.13.2: .......... done
===> gatk-4.1.5.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gatk-4.1.5.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.1.5.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.1.5.0 for building
=> SHA256 Checksum OK for gatk-4.1.5.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.1.5.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.1.5.0 for building
===> Extracting for gatk-4.1.5.0
=> SHA256 Checksum OK for gatk-4.1.5.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.1.5.0_GH0.tar.gz.
<snip>
[121armv7-quarterly-job-05] | `-- Installing alsa-lib-1.1.2_2...
[121armv7-quarterly-job-05] | `-- Extracting alsa-lib-1.1.2_2: .......... done
[121armv7-quarterly-job-05] | `-- Installing dejavu-2.37_1...
[121armv7-quarterly-job-05] | | `-- Installing fontconfig-2.13.92_1,1...
[121armv7-quarterly-job-05] | | `-- Installing expat-2.2.8...
[121armv7-quarterly-job-05] | | `-- Extracting expat-2.2.8: .......... done
[121armv7-quarterly-job-05] | | `-- Installing freetype2-2.10.1...
[121armv7-quarterly-job-05] | | `-- Extracting freetype2-2.10.1: .......... done
[121armv7-quarterly-job-05] | | `-- Installing gettext-runtime-0.20.1...
[121armv7-quarterly-job-05] | | | `-- Installing indexinfo-0.3.1...
[121armv7-quarterly-job-05] | | | `-- Extracting indexinfo-0.3.1: .... done
[121armv7-quarterly-job-05] | | `-- Extracting gettext-runtime-0.20.1: .......... done
[121armv7-quarterly-job-05] | | `-- Extracting fontconfig-2.13.92_1,1: .......... done
Running fc-cache to build fontconfig cache...
Font directories:
/usr/local/share/fonts
/usr/local/lib/X11/fonts
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: skipping, no such directory
/var/db/fontconfig: cleaning cache directory
fc-cache: succeeded
[121armv7-quarterly-job-05] | | `-- Installing mkfontscale-1.2.1...
[121armv7-quarterly-job-05] | | `-- Installing libfontenc-1.1.4...
[121armv7-quarterly-job-05] | | `-- Extracting libfontenc-1.1.4: ......... done
[121armv7-quarterly-job-05] | | `-- Extracting mkfontscale-1.2.1: ....... done
[121armv7-quarterly-job-05] | `-- Extracting dejavu-2.37_1: .......... done
[121armv7-quarterly-job-05] | `-- Installing giflib-5.2.1...
[121armv7-quarterly-job-05] | `-- Extracting giflib-5.2.1: .......... done
[121armv7-quarterly-job-05] | `-- Installing java-zoneinfo-2019.b...
[121armv7-quarterly-job-05] | `-- Extracting java-zoneinfo-2019.b: .......... done
[121armv7-quarterly-job-05] | `-- Installing javavmwrapper-2.7.5...
[121armv7-quarterly-job-05] | `-- Extracting javavmwrapper-2.7.5: .......... done
[121armv7-quarterly-job-05] | `-- Installing libX11-1.6.9,1...
[121armv7-quarterly-job-05] | | `-- Installing libXau-1.0.9...
[121armv7-quarterly-job-05] | | `-- Extracting libXau-1.0.9: .......... done
[121armv7-quarterly-job-05] | | `-- Installing libXdmcp-1.1.3...
[121armv7-quarterly-job-05] | | `-- Installing xorgproto-2019.2...
[121armv7-quarterly-job-05] | | `-- Extracting xorgproto-2019.2: .......... done
[121armv7-quarterly-job-05] | | `-- Extracting libXdmcp-1.1.3: ......... done
[121armv7-quarterly-job-05] | | `-- Installing libxcb-1.13.1...
[121armv7-quarterly-job-05] | | `-- Installing libpthread-stubs-0.4...
[121armv7-quarterly-job-05] | | `-- Extracting libpthread-stubs-0.4: .... done
[121armv7-quarterly-job-05] | | `-- Installing libxml2-2.9.10...
[121armv7-quarterly-job-05] | | `-- Extracting libxml2-2.9.10: .......... done
[121armv7-quarterly-job-05] | | `-- Extracting libxcb-1.13.1: .......... done
[121armv7-quarterly-job-05] | `-- Extracting libX11-1.6.9,1: .......... done
[121armv7-quarterly-job-05] | `-- Installing libXext-1.3.4,1...
[121armv7-quarterly-job-05] | `-- Extracting libXext-1.3.4,1: .......... done
[121armv7-quarterly-job-05] | `-- Installing libXi-1.7.10,1...
[121armv7-quarterly-job-05] | | `-- Installing libXfixes-5.0.3_2...
[121armv7-quarterly-job-05] | | `-- Extracting libXfixes-5.0.3_2: .......... done
[121armv7-quarterly-job-05] | `-- Extracting libXi-1.7.10,1: .......... done
[121armv7-quarterly-job-05] | `-- Installing libXrender-0.9.10_2...
[121armv7-quarterly-job-05] | `-- Extracting libXrender-0.9.10_2: .......... done
[121armv7-quarterly-job-05] | `-- Installing libXt-1.2.0,1...
[121armv7-quarterly-job-05] | | `-- Installing libICE-1.0.10,1...
[121armv7-quarterly-job-05] | | `-- Extracting libICE-1.0.10,1: .......... done
[121armv7-quarterly-job-05] | | `-- Installing libSM-1.2.3,1...
[121armv7-quarterly-job-05] | | `-- Extracting libSM-1.2.3,1: .......... done
[121armv7-quarterly-job-05] | `-- Extracting libXt-1.2.0,1: .......... done
[121armv7-quarterly-job-05] | `-- Installing libXtst-1.2.3_2...
[121armv7-quarterly-job-05] | `-- Extracting libXtst-1.2.3_2: .......... done
[121armv7-quarterly-job-05] | `-- Installing libffi-3.2.1_3...
[121armv7-quarterly-job-05] | `-- Extracting libffi-3.2.1_3: .......... done
[121armv7-quarterly-job-05] | `-- Installing libinotify-20180201_1...
[121armv7-quarterly-job-05] | `-- Extracting libinotify-20180201_1: .......... done
[121armv7-quarterly-job-05] `-- Extracting openjdk8-8.242.07.1: .......... done
[121armv7-quarterly-job-05] Extracting gradle-6.2.2: .......... done
=====
Message from freetype2-2.10.1:
--
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/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_1:
--
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 openjdk8-8.242.07.1:
--
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-4.1.5.0 depends on executable: gradle - found
===> Returning to build of gatk-4.1.5.0
===> gatk-4.1.5.0 depends on file: /usr/local/openjdk8/bin/java - found
===========================================================================
=======================<phase: lib-depends >============================
===> gatk-4.1.5.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for gatk-4.1.5.0
===========================================================================
=======================<phase: build >============================
===> Building for gatk-4.1.5.0
Welcome to Gradle 6.2.2!
Here are the highlights of this release:
- Dependency checksum and signature verification
- Shareable read-only dependency cache
- Documentation links in deprecation messages
For more details see https://docs.gradle.org/6.2.2/release-notes.html
Starting a Gradle Daemon (subsequent builds will be faster)
> Task :compileJava
> Task :processResources
> Task :classes
> Task :shadowJar
=>> Killing runaway build after 21600 seconds with no output
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