[package - 130amd64-default][biology/gatk] Failed for gatk-4.2.6.1_1 in build
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Date: Tue, 09 Aug 2022 22:54:29 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://beefy16.nyi.freebsd.org/data/130amd64-default/240569d0a2e9/logs/gatk-4.2.6.1_1.log
Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=130amd64-default&build=240569d0a2e9
Log:
=>> Building biology/gatk
build started at Tue Aug 9 22:53:19 UTC 2022
port directory: /usr/ports/biology/gatk
package name: gatk-4.2.6.1_1
building for: FreeBSD 130amd64-default-job-05 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400063
Jail OSVERSION: 1300139
Job Id: 05
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---Begin OPTIONS List---
===> The following configuration options are available for gatk-4.2.6.1_1:
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 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
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--End PLIST_SUB--
--SUB_LIST--
PORTVERSION=4.2.6.1 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--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
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# XXX: We really need this but cannot use it while 'make checksum' does not
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#### /usr/ports/Mk/Scripts/ports_env.sh ####
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> gatk-4.2.6.1_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[130amd64-default-job-05] Installing pkg-1.18.4...
[130amd64-default-job-05] Extracting pkg-1.18.4: .......... done
===> gatk-4.2.6.1_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gatk-4.2.6.1_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.2.6.1_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.2.6.1_1 for building
=> SHA256 Checksum OK for gatk-4.2.6.1-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.2.6.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.2.6.1_1 for building
===> Extracting for gatk-4.2.6.1_1
=> SHA256 Checksum OK for gatk-4.2.6.1-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.2.6.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for gatk-4.2.6.1_1
===> Applying FreeBSD patches for gatk-4.2.6.1_1 from /usr/ports/biology/gatk/files
===========================================================================
=======================<phase: build-depends >============================
===> gatk-4.2.6.1_1 depends on executable: gradle - not found
===> Installing existing package /packages/All/gradle-7.5.1.pkg
[130amd64-default-job-05] Installing gradle-7.5.1...
[130amd64-default-job-05] `-- Installing openjdk8-8.342.07.1...
[130amd64-default-job-05] | `-- Installing alsa-lib-1.2.2_1...
[130amd64-default-job-05] | `-- Extracting alsa-lib-1.2.2_1: .......... done
[130amd64-default-job-05] | `-- Installing dejavu-2.37_1...
[130amd64-default-job-05] | | `-- Installing fontconfig-2.13.94_2,1...
[130amd64-default-job-05] | | `-- Installing expat-2.4.8...
[130amd64-default-job-05] | | `-- Extracting expat-2.4.8: .......... done
[130amd64-default-job-05] | | `-- Installing freetype2-2.12.1_2...
[130amd64-default-job-05] | | | `-- Installing brotli-1.0.9,1...
[130amd64-default-job-05] | | | `-- Extracting brotli-1.0.9,1: .......... done
<snip>
=====
Message from freetype2-2.12.1_2:
--
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 openjdk8-8.342.07.1:
--
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-4.2.6.1_1 depends on executable: gradle - found
===> Returning to build of gatk-4.2.6.1_1
===> gatk-4.2.6.1_1 depends on file: /usr/local/openjdk17/bin/java - not found
===> Installing existing package /packages/All/openjdk17-17.0.4+8.1.pkg
[130amd64-default-job-05] Installing openjdk17-17.0.4+8.1...
[130amd64-default-job-05] `-- Installing harfbuzz-5.1.0...
[130amd64-default-job-05] | `-- Installing gettext-runtime-0.21...
[130amd64-default-job-05] | | `-- Installing indexinfo-0.3.1...
[130amd64-default-job-05] | | `-- Extracting indexinfo-0.3.1: .... done
[130amd64-default-job-05] | `-- Extracting gettext-runtime-0.21: .......... done
[130amd64-default-job-05] | `-- Installing glib-2.72.3,2...
[130amd64-default-job-05] | | `-- Installing libffi-3.4.2...
[130amd64-default-job-05] | | `-- Extracting libffi-3.4.2: .......... done
[130amd64-default-job-05] | | `-- Installing libiconv-1.17...
[130amd64-default-job-05] | | `-- Extracting libiconv-1.17: .......... done
[130amd64-default-job-05] | | `-- Installing libxml2-2.9.14...
[130amd64-default-job-05] | | `-- Installing readline-8.1.2...
[130amd64-default-job-05] | | `-- Extracting readline-8.1.2: .......... done
[130amd64-default-job-05] | | `-- Extracting libxml2-2.9.14: .......... done
[130amd64-default-job-05] | | `-- Installing pcre-8.45_1...
[130amd64-default-job-05] | | `-- Extracting pcre-8.45_1: .......... done
[130amd64-default-job-05] | | `-- Installing python39-3.9.13...
[130amd64-default-job-05] | | `-- Installing mpdecimal-2.5.1...
[130amd64-default-job-05] | | `-- Extracting mpdecimal-2.5.1: .......... done
[130amd64-default-job-05] | | `-- Extracting python39-3.9.13: .......... done
[130amd64-default-job-05] | `-- Extracting glib-2.72.3,2: .......... done
[130amd64-default-job-05] | `-- Installing graphite2-1.3.14...
[130amd64-default-job-05] | `-- Extracting graphite2-1.3.14: .......... done
[130amd64-default-job-05] `-- Extracting harfbuzz-5.1.0: .......... done
[130amd64-default-job-05] `-- Installing jpeg-turbo-2.1.3...
[130amd64-default-job-05] `-- Extracting jpeg-turbo-2.1.3: .......... done
[130amd64-default-job-05] `-- Installing lcms2-2.13.1...
[130amd64-default-job-05] | `-- Installing tiff-4.3.0...
[130amd64-default-job-05] | | `-- Installing jbigkit-2.1_1...
[130amd64-default-job-05] | | `-- Extracting jbigkit-2.1_1: .......... done
[130amd64-default-job-05] | `-- Extracting tiff-4.3.0: .......... done
[130amd64-default-job-05] `-- Extracting lcms2-2.13.1: .......... done
[130amd64-default-job-05] `-- Installing libXrandr-1.5.2...
[130amd64-default-job-05] `-- Extracting libXrandr-1.5.2: .......... done
[130amd64-default-job-05] `-- Installing xorg-fonts-truetype-7.7_1...
[130amd64-default-job-05] | `-- Installing encodings-1.0.5,1...
[130amd64-default-job-05] | `-- Extracting encodings-1.0.5,1: .......... done
[130amd64-default-job-05] | `-- Installing font-bh-ttf-1.0.3_4...
[130amd64-default-job-05] | `-- Extracting font-bh-ttf-1.0.3_4: .......... done
[130amd64-default-job-05] | `-- Installing font-misc-ethiopic-1.0.4...
[130amd64-default-job-05] | `-- Extracting font-misc-ethiopic-1.0.4: ...... done
[130amd64-default-job-05] | `-- Installing font-misc-meltho-1.0.3_4...
[130amd64-default-job-05] | `-- Extracting font-misc-meltho-1.0.3_4: .......... done
[130amd64-default-job-05] Extracting openjdk17-17.0.4+8.1: .......... done
Running fc-cache to build fontconfig cache...
Generating GIO modules cache
Compiling glib schemas
No schema files found: doing nothing.
=====
Message from python39-3.9.13:
--
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 openjdk17-17.0.4+8.1:
--
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-4.2.6.1_1 depends on file: /usr/local/openjdk17/bin/java - found
===> Returning to build of gatk-4.2.6.1_1
===========================================================================
=======================<phase: lib-depends >============================
===> gatk-4.2.6.1_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for gatk-4.2.6.1_1
===========================================================================
=======================<phase: build >============================
===> Building for gatk-4.2.6.1_1
Welcome to Gradle 7.5.1!
Here are the highlights of this release:
- Support for Java 18
- Support for building with Groovy 4
- Much more responsive continuous builds
- Improved diagnostics for dependency resolution
For more details see https://docs.gradle.org/7.5.1/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-4.2.6.1/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