[package - main-amd64-default][biology/jalview] Failed for jalview-2.11.1.4 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Thu, 02 Dec 2021 04:42:31 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://beefy18.nyi.freebsd.org/data/main-amd64-default/pb8c4bfe660b3_s610d908f8a/logs/jalview-2.11.1.4.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=pb8c4bfe660b3_s610d908f8a
Log:
=>> Building biology/jalview
build started at Thu Dec 2 04:41:18 UTC 2021
port directory: /usr/ports/biology/jalview
package name: jalview-2.11.1.4
building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400043 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400042
Jail OSVERSION: 1400043
Job Id: 10
!!! Jail is newer than host. (Jail: 1400043, Host: 1400042) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400043
UNAME_v=FreeBSD 14.0-CURRENT 1400043
UNAME_r=14.0-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
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
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/jalview/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jalview/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/jalview/work/.cache HOME=/wrkdirs/usr/ports/biology/jalview/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/jalview/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jalview/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jalview/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/jalview/work/.cache HOME=/wrkdirs/usr/ports/biology/jalview/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/jalview/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 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/jalview" EXAMPLESDIR="share/examples/jalview" DATADIR="share/java/jalview" WWWDIR="www/jalview" ETCDIR="etc/jalview"
--End PLIST_SUB--
--SUB_LIST--
JAVA=/usr/local/openjdk11/bin/java 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/java/jalview DOCSDIR=/usr/local/share/doc/jalview EXAMPLESDIR=/usr/local/share/examples/jalview WWWDIR=/usr/local/www/jalview ETCDIR=/usr/local/etc/jalview
--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 ####
_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
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 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400043
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
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) 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) 1024
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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> jalview-2.11.1.4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[main-amd64-default-job-10] Installing pkg-1.17.5...
[main-amd64-default-job-10] Extracting pkg-1.17.5: .......... done
===> jalview-2.11.1.4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of jalview-2.11.1.4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by jalview-2.11.1.4 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by jalview-2.11.1.4 for building
=> SHA256 Checksum OK for jalview_2_11_1_4.tar.gz.
=> SHA256 Checksum OK for jalview-2.11.1.4-deps.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by jalview-2.11.1.4 for building
===> Extracting for jalview-2.11.1.4
=> SHA256 Checksum OK for jalview_2_11_1_4.tar.gz.
=> SHA256 Checksum OK for jalview-2.11.1.4-deps.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for jalview-2.11.1.4
===========================================================================
=======================<phase: build-depends >============================
===> jalview-2.11.1.4 depends on executable: gradle - not found
===> Installing existing package /packages/All/gradle6-6.9.pkg
[main-amd64-default-job-10] Installing gradle6-6.9...
[main-amd64-default-job-10] `-- Installing openjdk8-8.312.07.1...
[main-amd64-default-job-10] | `-- Installing alsa-lib-1.2.2_1...
[main-amd64-default-job-10] | `-- Extracting alsa-lib-1.2.2_1: .......... done
[main-amd64-default-job-10] | `-- Installing dejavu-2.37_1...
<snip>
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-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 openjdk8-8.312.07.1:
--
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
===> jalview-2.11.1.4 depends on executable: gradle - found
===> Returning to build of jalview-2.11.1.4
===> jalview-2.11.1.4 depends on file: /usr/local/openjdk11/bin/java - not found
===> Installing existing package /packages/All/openjdk11-11.0.13+8.1.pkg
[main-amd64-default-job-10] Installing openjdk11-11.0.13+8.1...
[main-amd64-default-job-10] `-- Installing jpeg-turbo-2.1.1_1...
[main-amd64-default-job-10] `-- Extracting jpeg-turbo-2.1.1_1: .......... done
[main-amd64-default-job-10] `-- Installing lcms2-2.12...
[main-amd64-default-job-10] | `-- Installing tiff-4.3.0...
[main-amd64-default-job-10] | | `-- Installing jbigkit-2.1_1...
[main-amd64-default-job-10] | | `-- Extracting jbigkit-2.1_1: .......... done
[main-amd64-default-job-10] | `-- Extracting tiff-4.3.0: .......... done
[main-amd64-default-job-10] `-- Extracting lcms2-2.12: .......... done
[main-amd64-default-job-10] `-- Installing libXrandr-1.5.2...
[main-amd64-default-job-10] `-- Extracting libXrandr-1.5.2: .......... done
[main-amd64-default-job-10] `-- Installing xorg-fonts-truetype-7.7_1...
[main-amd64-default-job-10] | `-- Installing encodings-1.0.5,1...
[main-amd64-default-job-10] | `-- Extracting encodings-1.0.5,1: .......... done
[main-amd64-default-job-10] | `-- Installing font-bh-ttf-1.0.3_4...
[main-amd64-default-job-10] | `-- Extracting font-bh-ttf-1.0.3_4: .......... done
[main-amd64-default-job-10] | `-- Installing font-misc-ethiopic-1.0.4...
[main-amd64-default-job-10] | `-- Extracting font-misc-ethiopic-1.0.4: ...... done
[main-amd64-default-job-10] | `-- Installing font-misc-meltho-1.0.3_4...
[main-amd64-default-job-10] | `-- Extracting font-misc-meltho-1.0.3_4: .......... done
[main-amd64-default-job-10] Extracting openjdk11-11.0.13+8.1: .......... done
=====
Message from openjdk11-11.0.13+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
===> jalview-2.11.1.4 depends on file: /usr/local/openjdk11/bin/java - found
===> Returning to build of jalview-2.11.1.4
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for jalview-2.11.1.4
===========================================================================
=======================<phase: build >============================
===> Building for jalview-2.11.1.4
Welcome to Gradle 6.9!
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/release-notes.html
Starting a Gradle Daemon (subsequent builds will be faster)
> Configure project :
HEADLESS BUILD
Using a LOCAL profile.
> Task :compileJava
Setting target compatibility to 11
/wrkdirs/usr/ports/biology/jalview/work/jalview/src/jalview/ws/dbsources/EmblXmlSource.java:73: warning: [dep-ann] deprecated item is not annotated with @Deprecated
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
^
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.
1 warning
The message received from the daemon indicates that the daemon has disappeared.
Build request sent: Build{id=a0c042ec-94bb-46f2-8d17-8612ca86c716, currentDir=/wrkdirs/usr/ports/biology/jalview/work/jalview}
Attempting to read last messages from the daemon log...
Daemon pid: 51620
log file: /wrkdirs/usr/ports/biology/jalview/work/gradle-jalview/daemon/6.9/daemon-51620.out.log
----- Last 20 lines from daemon log file - daemon-51620.out.log -----
2021-12-02T04:42:06.300+0000 [DEBUG] [org.gradle.launcher.daemon.server.SynchronizedDispatchConnection] thread 30: received class org.gradle.launcher.daemon.protocol.CloseInput
2021-12-02T04:42:06.300+0000 [DEBUG] [org.gradle.launcher.daemon.server.DefaultDaemonConnection] thread 30: Received IO message from client: org.gradle.launcher.daemon.protocol.CloseInput@66c11c9
2021-12-02T04:42:06.304+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.LogToClient] About to start relaying all logs to the client via the connection.
2021-12-02T04:42:06.305+0000 [INFO] [org.gradle.launcher.daemon.server.exec.LogToClient] The client will now receive all logging from the daemon (pid: 51620). The daemon log file: /wrkdirs/usr/ports/biology/jalview/work/gradle-jalview/daemon/6.9/daemon-51620.out.log
2021-12-02T04:42:06.308+0000 [INFO] [org.gradle.launcher.daemon.server.exec.LogAndCheckHealth] Starting build in new daemon [memory: 512 MiB]
2021-12-02T04:42:06.310+0000 [INFO] [org.gradle.launcher.daemon.server.exec.ForwardClientInput] Closing daemon's stdin at end of input.
2021-12-02T04:42:06.311+0000 [INFO] [org.gradle.launcher.daemon.server.exec.ForwardClientInput] The daemon will no longer process any standard input.
2021-12-02T04:42:06.317+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] The daemon has started executing the build.
2021-12-02T04:42:06.318+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] Executing build with daemon context: DefaultDaemonContext[uid=752bd8b2-da36-4c6c-beae-66e7c7c12636,javaHome=/usr/local/openjdk11,daemonRegistryDir=/wrkdirs/usr/ports/biology/jalview/work/gradle-jalview/daemon,pid=51620,idleTimeout=10800000,priority=NORMAL,daemonOpts=--add-opens,java.base/java.util=ALL-UNNAMED,--add-opens,java.base/java.lang=ALL-UNNAMED,--add-opens,java.base/java.lang.invoke=ALL-UNNAMED,--add-opens,java.prefs/java.util.prefs=ALL-UNNAMED,-XX:MaxMetaspaceSize=256m,-XX:+HeapDumpOnOutOfMemoryError,-Xms256m,-Xmx512m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]
HEADLESS BUILD
Using a LOCAL profile.
Setting target compatibility to 11
/wrkdirs/usr/ports/biology/jalview/work/jalview/src/jalview/ws/dbsources/EmblXmlSource.java:73: warning: [dep-ann] deprecated item is not annotated with @Deprecated
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
^
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.
1 warning
----- End of the daemon log -----
JVM crash log found: file:///wrkdirs/usr/ports/biology/jalview/work/jalview/hs_err_pid51620.log
FAILURE: Build failed with an exception.
* What went wrong:
Gradle build daemon disappeared unexpectedly (it may have been killed or may have crashed)
* 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
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/jalview