[package - main-arm64-default][biology/igv] Failed for igv-2.16.0_1 in stage
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Date: Mon, 26 Feb 2024 02:06:26 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/ampere2/data/main-arm64-default/p43e3af5f5763_sf5f08e41aa5/logs/igv-2.16.0_1.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p43e3af5f5763_sf5f08e41aa5
Log:
=>> Building biology/igv
build started at Mon Feb 26 02:04:10 UTC 2024
port directory: /usr/ports/biology/igv
package name: igv-2.16.0_1
building for: FreeBSD main-arm64-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500014 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2403 May 6 2023 /usr/ports/biology/igv/Makefile
Ports top last git commit: 43e3af5f576
Ports top unclean checkout: no
Port dir last git commit: feb1fa34f58
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6
Host OSVERSION: 1500006
Jail OSVERSION: 1500014
Job Id: 01
!!! Jail is newer than host. (Jail: 1500014, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500014
UNAME_v=FreeBSD 15.0-CURRENT 1500014
UNAME_r=15.0-CURRENT
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=3.4.1-1-g1e9f97d6
MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-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/main-arm64-default/01/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-1-g1e9f97d6
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---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/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--
GRADLE_USER_HOME=/wrkdirs/usr/ports/biology/igv/work JAVA_HOME=/usr/local/openjdk11 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/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_SCR
IPT="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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/igv" EXAMPLESDIR="share/examples/igv" DATADIR="share/igv" WWWDIR="www/igv" ETCDIR="etc/igv"
--End PLIST_SUB--
--SUB_LIST--
JAVA_HOME=/usr/local/openjdk11 JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="11" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/igv DOCSDIR=/usr/local/share/doc/igv EXAMPLESDIR=/usr/local/share/examples/igv WWWDIR=/usr/local/www/igv ETCDIR=/usr/local/etc/igv
--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
---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) 8192
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
igv-2.16.0_1: Makefile warning: in desktop entry #1 (igv): category Biology is not a valid desktop category
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> igv-2.16.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9_1.pkg
[main-arm64-default-job-01] Installing pkg-1.20.9_1...
[main-arm64-default-job-01] Extracting pkg-1.20.9_1: .......... done
===> igv-2.16.0_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of igv-2.16.0_1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by igv-2.16.0_1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
igv-2.16.0_1: Makefile warning: in desktop entry #1 (igv): category Biology is not a valid desktop category
===> License MIT accepted by the user
===> Fetching all distfiles required by igv-2.16.0_1 for building
=> SHA256 Checksum OK for igv-2.16.0/tools.png.
=> SHA256 Checksum OK for igv-2.16.0/igv-2.16.0-deps.tar.gz.
=> SHA256 Checksum OK for igv-2.16.0/igvteam-igv-v2.16.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
igv-2.16.0_1: Makefile warning: in desktop entry #1 (igv): category Biology is not a valid desktop category
===> License MIT accepted by the user
===> Fetching all distfiles required by igv-2.16.0_1 for building
===> Extracting for igv-2.16.0_1
=> SHA256 Checksum OK for igv-2.16.0/tools.png.
=> SHA256 Checksum OK for igv-2.16.0/igv-2.16.0-deps.tar.gz.
=> SHA256 Checksum OK for igv-2.16.0/igvteam-igv-v2.16.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for igv-2.16.0_1
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> igv-2.16.0_1 depends on package: openjfx14>0 - not found
===> Installing existing package /packages/All/openjfx14-14.0.2.1+1_15.pkg
[main-arm64-default-job-01] Installing openjfx14-14.0.2.1+1_15...
[main-arm64-default-job-01] `-- Installing alsa-lib-1.2.10_1...
[main-arm64-default-job-01] `-- Extracting alsa-lib-1.2.10_1: .......... done
[main-arm64-default-job-01] `-- Installing at-spi2-core-2.50.1...
[main-arm64-default-job-01] | `-- Installing dbus-1.14.10_4,1...
[main-arm64-default-job-01] | | `-- Installing expat-2.6.0...
[main-arm64-default-job-01] | | `-- Extracting expat-2.6.0: .......... done
[main-arm64-default-job-01] | | `-- Installing libICE-1.1.0_2,1...
<snip>
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 wayland-1.22.0:
--
Wayland requires XDG_RUNTIME_DIR to be defined to a path that will
contain "wayland-%d" unix(4) sockets. This is usually handled by
consolekit2 (via ck-launch-session) or pam_xdg (via login).
=====
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 duktape-lib-2.7.0:
--
===> NOTICE:
The duktape-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 libxkbcommon-1.6.0_2:
--
If arrow keys don't work under X11 switch to legacy rules e.g.,
For sh/bash/ksh/zsh run and (optionally) add into ~/.profile:
export XKB_DEFAULT_RULES=xorg
For csh/tcsh run and (optionally) add into ~/.login:
setenv XKB_DEFAULT_RULES xorg
=====
Message from openjdk11-11.0.22+7.1_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
=====
Message from openjfx14-14.0.2.1+1_15:
--
===> NOTICE:
The openjfx14 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
===> igv-2.16.0_1 depends on package: openjfx14>0 - found
===> Returning to build of igv-2.16.0_1
===> igv-2.16.0_1 depends on executable: gradle - not found
===> Installing existing package /packages/All/gradle6-6.9.4.pkg
[main-arm64-default-job-01] Installing gradle6-6.9.4...
[main-arm64-default-job-01] `-- Installing openjdk8-8.402.06.1_1...
[main-arm64-default-job-01] | `-- Installing java-zoneinfo-2021.e...
[main-arm64-default-job-01] | `-- Extracting java-zoneinfo-2021.e: .......... done
[main-arm64-default-job-01] | `-- Installing libinotify-20211018_1...
[main-arm64-default-job-01] | `-- Extracting libinotify-20211018_1: .......... done
[main-arm64-default-job-01] `-- Extracting openjdk8-8.402.06.1_1: .......... done
[main-arm64-default-job-01] Extracting gradle6-6.9.4: .......... done
=====
Message from libinotify-20211018_1:
--
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 openjdk8-8.402.06.1_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
===> igv-2.16.0_1 depends on executable: gradle - found
===> Returning to build of igv-2.16.0_1
===> igv-2.16.0_1 depends on file: /usr/local/openjdk11/bin/java - found
===> igv-2.16.0_1 depends on package: gettext-runtime>=0.22_1 - found
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> igv-2.16.0_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 igv-2.16.0_1
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for igv-2.16.0_1
cd /wrkdirs/usr/ports/biology/igv/work/igv-2.16.0 && /usr/bin/env GRADLE_USER_HOME=/wrkdirs/usr/ports/biology/igv/work JAVA_HOME=/usr/local/openjdk11 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/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="install -m 444" gradle --gradle-user-home /wrkdirs/usr/ports/biology/igv/work/gradle-igv --project-cache-dir /wrkdirs/usr/ports/biology/igv/work/gradle-igv --offline --build-cache --stacktrace createDist
Welcome to Gradle 6.9.4!
Here are the highlights of this release:
- This is a small backport release.
- Java 16 can be used to compile when used with Java toolchains
- Dynamic versions can be used within plugin declarations
- Native support for Apple Silicon processors
For more details see https://docs.gradle.org/6.9.4/release-notes.html
Starting a Gradle Daemon (subsequent builds will be faster)
> Task :compileJava
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
> Task :processResources
> Task :classes
> Task :jar
> Task :createDist
Deprecated Gradle features were used in this build, making it incompatible with Gradle 7.0.
Use '--warning-mode all' to show the individual deprecation warnings.
See https://docs.gradle.org/6.9.4/userguide/command_line_interface.html#sec:command_line_warnings
BUILD SUCCESSFUL in 1m 30s
4 actionable tasks: 4 executed
===========================================================================
=======================<phase: run-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> igv-2.16.0_1 depends on package: openjfx14>0 - found
===> igv-2.16.0_1 depends on file: /usr/local/openjdk11/bin/java - found
===========================================================================
=======================<phase: stage >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Staging for igv-2.16.0_1
===> Generating temporary packing list
install -m 555 /wrkdirs/usr/ports/biology/igv/work/igv.sh /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/bin/igv
cd /wrkdirs/usr/ports/biology/igv/work/igv-2.16.0/build/IGV-dist/lib && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE ./ /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/share/java/classes/igv
install -m 0644 /portdistfiles/igv-2.16.0/tools.png /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/share/pixmaps/igv.png
install: /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/share/pixmaps/igv.png: No such file or directory
*** Error code 71
Stop.
make: stopped in /usr/ports/biology/igv