[package - 141amd64-default][biology/gatk] Failed for gatk-4.6.1.0_1 in build
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Date: Sun, 02 Feb 2025 01:08:33 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/beefy22/data/141amd64-default/2388692a094c/logs/gatk-4.6.1.0_1.log
Build URL: https://pkg-status.freebsd.org/beefy22/build.html?mastername=141amd64-default&build=2388692a094c
Log:
=>> Building biology/gatk
build started at Sun Feb 2 01:06:40 UTC 2025
port directory: /usr/ports/biology/gatk
package name: gatk-4.6.1.0_1
building for: FreeBSD 141amd64-default-job-18 14.1-RELEASE-p7 FreeBSD 14.1-RELEASE-p7 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 5047 Jan 2 01:01 /usr/ports/biology/gatk/Makefile
Ports top last git commit: 2388692a09
Ports top unclean checkout: no
Port dir last git commit: 0835676e36
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500028
Jail OSVERSION: 1401000
Job Id: 18
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1401000
UNAME_v=FreeBSD 14.1-RELEASE-p7
UNAME_r=14.1-RELEASE-p7
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/141amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/141amd64-default/18/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=141amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/141amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for gatk-4.6.1.0_1:
WITH_LARGE_FILES=on: 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--
PYTHON="/usr/local/bin/python3.11" 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 " 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="i
nstall -m 444"
--End MAKE_ENV--
--PLIST_SUB--
JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.1 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=4.6.1.0 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" PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
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 >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gatk-4.6.1.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.0.5.pkg
[141amd64-default-job-18] Installing pkg-2.0.5...
[141amd64-default-job-18] Extracting pkg-2.0.5: .......... done
===> gatk-4.6.1.0_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gatk-4.6.1.0_1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gatk-4.6.1.0_1 depends on executable: git - not found
===> Installing existing package /packages/All/git-2.48.1.pkg
[141amd64-default-job-18] Installing git-2.48.1...
[141amd64-default-job-18] `-- Installing curl-8.11.1_1...
[141amd64-default-job-18] | `-- Installing brotli-1.1.0,1...
[141amd64-default-job-18] | `-- Extracting brotli-1.1.0,1: .......... done
[141amd64-default-job-18] | `-- Installing libidn2-2.3.7...
[141amd64-default-job-18] | | `-- Installing indexinfo-0.3.1...
[141amd64-default-job-18] | | `-- Extracting indexinfo-0.3.1: .... done
[141amd64-default-job-18] | | `-- Installing libunistring-1.3...
[141amd64-default-job-18] | | `-- Extracting libunistring-1.3: .......... done
[141amd64-default-job-18] | `-- Extracting libidn2-2.3.7: .......... done
[141amd64-default-job-18] | `-- Installing libnghttp2-1.64.0...
[141amd64-default-job-18] | `-- Extracting libnghttp2-1.64.0: .......... done
[141amd64-default-job-18] | `-- Installing libpsl-0.21.5_1...
[141amd64-default-job-18] | `-- Extracting libpsl-0.21.5_1: .......... done
[141amd64-default-job-18] | `-- Installing libssh2-1.11.1,3...
[141amd64-default-job-18] | `-- Extracting libssh2-1.11.1,3: .......... done
[141amd64-default-job-18] | `-- Installing zstd-1.5.6...
[141amd64-default-job-18] | | `-- Installing liblz4-1.10.0,1...
[141amd64-default-job-18] | | `-- Extracting liblz4-1.10.0,1: .......... done
[141amd64-default-job-18] | `-- Extracting zstd-1.5.6: .......... done
[141amd64-default-job-18] `-- Extracting curl-8.11.1_1: .......... done
[141amd64-default-job-18] `-- Installing expat-2.6.4...
[141amd64-default-job-18] `-- Extracting expat-2.6.4: .......... done
[141amd64-default-job-18] `-- Installing gettext-runtime-0.23.1...
[141amd64-default-job-18] `-- Extracting gettext-runtime-0.23.1: .......... done
[141amd64-default-job-18] `-- Installing p5-Authen-SASL-2.17_1...
[141amd64-default-job-18] | `-- Installing p5-Digest-HMAC-1.05...
[141amd64-default-job-18] | | `-- Installing perl5-5.36.3_2...
[141amd64-default-job-18] | | `-- Extracting perl5-5.36.3_2: .......... done
[141amd64-default-job-18] | `-- Extracting p5-Digest-HMAC-1.05: .......... done
[141amd64-default-job-18] `-- Extracting p5-Authen-SASL-2.17_1: .......... done
[141amd64-default-job-18] `-- Installing p5-CGI-4.66...
[141amd64-default-job-18] | `-- Installing p5-HTML-Parser-3.83...
[141amd64-default-job-18] | | `-- Installing p5-HTML-Tagset-3.24...
[141amd64-default-job-18] | | `-- Extracting p5-HTML-Tagset-3.24: ....... done
[141amd64-default-job-18] | | `-- Installing p5-HTTP-Message-7.00...
[141amd64-default-job-18] | | `-- Installing p5-Clone-0.47...
[141amd64-default-job-18] | | `-- Extracting p5-Clone-0.47: ......... done
[141amd64-default-job-18] | | `-- Installing p5-Encode-Locale-1.05...
[141amd64-default-job-18] | | `-- Extracting p5-Encode-Locale-1.05: ....... done
[141amd64-default-job-18] | | `-- Installing p5-HTTP-Date-6.06...
[141amd64-default-job-18] | | | `-- Installing p5-TimeDate-2.33,1...
[141amd64-default-job-18] | | | `-- Extracting p5-TimeDate-2.33,1: .......... done
[141amd64-default-job-18] | | `-- Extracting p5-HTTP-Date-6.06: ....... done
[141amd64-default-job-18] | | `-- Installing p5-IO-HTML-1.004...
[141amd64-default-job-18] | | `-- Extracting p5-IO-HTML-1.004: ....... done
[141amd64-default-job-18] | | `-- Installing p5-LWP-MediaTypes-6.04...
[141amd64-default-job-18] | | `-- Extracting p5-LWP-MediaTypes-6.04: ........ done
[141amd64-default-job-18] | | `-- Installing p5-URI-5.31...
[141amd64-default-job-18] | | `-- Extracting p5-URI-5.31: .......... done
[141amd64-default-job-18] | | `-- Extracting p5-HTTP-Message-7.00: .......... done
[141amd64-default-job-18] | `-- Extracting p5-HTML-Parser-3.83: .......... done
<snip>
--
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_3:
--
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-20240724:
--
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 openjdk8-8.432.06.1:
--
This OpenJDK implementation may require fdescfs(5) mounted on /dev/fd
and procfs(5) mounted on /proc for some applications.
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
=====
Message from gradle-8.12.1:
--
===> NOTICE:
The gradle 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
===> gatk-4.6.1.0_1 depends on executable: gradle - found
===> Returning to build of gatk-4.6.1.0_1
===> gatk-4.6.1.0_1 depends on package: gettext-runtime>=0.22_1 - found
===> gatk-4.6.1.0_1 depends on file: /usr/local/openjdk17/bin/java - not found
===> Installing existing package /packages/All/openjdk17-17.0.13+11.1.pkg
[141amd64-default-job-18] Installing openjdk17-17.0.13+11.1...
[141amd64-default-job-18] `-- Installing harfbuzz-10.2.0...
[141amd64-default-job-18] | `-- Installing glib-2.80.5_1,2...
[141amd64-default-job-18] | | `-- Installing libiconv-1.17_1...
[141amd64-default-job-18] | | `-- Extracting libiconv-1.17_1: .......... done
[141amd64-default-job-18] | | `-- Installing py311-packaging-24.2...
[141amd64-default-job-18] | | `-- Extracting py311-packaging-24.2: .......... done
[141amd64-default-job-18] | `-- Extracting glib-2.80.5_1,2: .......... done
[141amd64-default-job-18] | `-- Installing graphite2-1.3.14...
[141amd64-default-job-18] | `-- Extracting graphite2-1.3.14: .......... done
[141amd64-default-job-18] `-- Extracting harfbuzz-10.2.0: .......... done
[141amd64-default-job-18] `-- Installing jpeg-turbo-3.1.0...
[141amd64-default-job-18] `-- Extracting jpeg-turbo-3.1.0: .......... done
[141amd64-default-job-18] `-- Installing lcms2-2.16_2...
[141amd64-default-job-18] | `-- Installing tiff-4.7.0...
[141amd64-default-job-18] | | `-- Installing jbigkit-2.1_3...
[141amd64-default-job-18] | | `-- Extracting jbigkit-2.1_3: .......... done
[141amd64-default-job-18] | | `-- Installing lerc-4.0.0...
[141amd64-default-job-18] | | `-- Extracting lerc-4.0.0: ........ done
[141amd64-default-job-18] | | `-- Installing libdeflate-1.22...
[141amd64-default-job-18] | | `-- Extracting libdeflate-1.22: .......... done
[141amd64-default-job-18] | `-- Extracting tiff-4.7.0: .......... done
[141amd64-default-job-18] `-- Extracting lcms2-2.16_2: .......... done
[141amd64-default-job-18] `-- Installing libXrandr-1.5.4...
[141amd64-default-job-18] `-- Extracting libXrandr-1.5.4: .......... done
[141amd64-default-job-18] `-- Installing xorg-fonts-truetype-7.7_1...
[141amd64-default-job-18] | `-- Installing encodings-1.1.0,1...
[141amd64-default-job-18] | `-- Extracting encodings-1.1.0,1: .......... done
[141amd64-default-job-18] | `-- Installing font-bh-ttf-1.0.3_5...
[141amd64-default-job-18] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done
[141amd64-default-job-18] | `-- Installing font-misc-ethiopic-1.0.4...
[141amd64-default-job-18] | `-- Extracting font-misc-ethiopic-1.0.4: ...... done
[141amd64-default-job-18] | `-- Installing font-misc-meltho-1.0.3_5...
[141amd64-default-job-18] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done
[141amd64-default-job-18] `-- Extracting xorg-fonts-truetype-7.7_1: ... done
[141amd64-default-job-18] Extracting openjdk17-17.0.13+11.1: .......... done
==> Running trigger: fontconfig.ucl
Running fc-cache to build fontconfig cache...
==> Running trigger: gio-modules.ucl
Generating GIO modules cache
==> Running trigger: glib-schemas.ucl
Compiling glib schemas
No schema files found: doing nothing.
=====
Message from openjdk17-17.0.13+11.1:
--
This OpenJDK implementation may require fdescfs(5) mounted on /dev/fd
and procfs(5) mounted on /proc for some applications.
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-4.6.1.0_1 depends on file: /usr/local/openjdk17/bin/java - found
===> Returning to build of gatk-4.6.1.0_1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gatk-4.6.1.0_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for gatk-4.6.1.0_1
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for gatk-4.6.1.0_1
Welcome to Gradle 8.12.1!
Here are the highlights of this release:
- Enhanced error and warning reporting with the Problems API
- File-system watching support on Alpine Linux
- Build and test Swift 6 libraries and apps
For more details see https://docs.gradle.org/8.12.1/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-4.6.1.0/build.gradle' line: 15
* What went wrong:
Plugin [id: 'de.undercouch.download', version: '5.6.0'] was not found in any of the following sources:
- Gradle Core Plugins (plugin is not in 'org.gradle' namespace)
- Included Builds (No included builds contain this plugin)
- Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:5.6.0')
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.
BUILD FAILED in 15s
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/gatk