[package - 114amd64-default][biology/igv] Failed for igv-2.9.4 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 29 Jun 2021 19:49:19 GMT
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
Log URL:        http://beefy9.nyi.freebsd.org/data/114amd64-default/1ac2d7ea8e41/logs/igv-2.9.4.log
Build URL:      http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=1ac2d7ea8e41
Log:

=>> Building biology/igv
build started at Tue Jun 29 19:48:04 UTC 2021
port directory: /usr/ports/biology/igv
package name: igv-2.9.4
building for: FreeBSD 114amd64-default-job-01 11.4-RELEASE-p11 FreeBSD 11.4-RELEASE-p11 amd64
maintained by: yuri_at_FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1400008
Jail OSVERSION: 1104001
Job Id: 01

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--MAINTAINER--
yuri_at_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  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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--PLIST_SUB--
JAVASHAREDIR="share/java"  JAVAJARDIR="share/java/classes" OSREL=11.4 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--

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--End resource limits--
=======================<phase: check-sanity   >============================
===>  License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   igv-2.9.4 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.16.3.txz
[114amd64-default-job-01] Installing pkg-1.16.3...
[114amd64-default-job-01] Extracting pkg-1.16.3: .......... done
===>   igv-2.9.4 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of igv-2.9.4
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by igv-2.9.4 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by igv-2.9.4 for building
=> SHA256 Checksum OK for igv-2.9.4/tools.png.
=> SHA256 Checksum OK for igv-2.9.4/igv-2.9.4-deps.tar.gz.
=> SHA256 Checksum OK for igv-2.9.4/igvteam-igv-v2.9.4_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by igv-2.9.4 for building
===>  Extracting for igv-2.9.4
=> SHA256 Checksum OK for igv-2.9.4/tools.png.
=> SHA256 Checksum OK for igv-2.9.4/igv-2.9.4-deps.tar.gz.
=> SHA256 Checksum OK for igv-2.9.4/igvteam-igv-v2.9.4_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for igv-2.9.4
===========================================================================
=======================<phase: build-depends  >============================
===>   igv-2.9.4 depends on package: openjfx14>0 - not found
===>   Installing existing package /packages/All/openjfx14-14.0.2.1+1_3.txz
[114amd64-default-job-01] Installing openjfx14-14.0.2.1+1_3...
[114amd64-default-job-01] `-- Installing alsa-lib-1.2.2...
[114amd64-default-job-01] `-- Extracting alsa-lib-1.2.2: .......... done
[114amd64-default-job-01] `-- Installing atk-2.36.0...
[114amd64-default-job-01] |   `-- Installing gettext-runtime-0.21...
[114amd64-default-job-01] |   | `-- Installing indexinfo-0.3.1...
[114amd64-default-job-01] |   | `-- Extracting indexinfo-0.3.1: .... done
[114amd64-default-job-01] |   `-- Extracting gettext-runtime-0.21: .......... done
[114amd64-default-job-01] |   `-- Installing glib-2.66.8,2...
[114amd64-default-job-01] |   | `-- Installing libffi-3.3_1...
[114amd64-default-job-01] |   | `-- Extracting libffi-3.3_1: .......... done
[114amd64-default-job-01] |   | `-- Installing libiconv-1.16...
[114amd64-default-job-01] |   | `-- Extracting libiconv-1.16: .......... done
[114amd64-default-job-01] |   | `-- Installing libxml2-2.9.12...
<snip>
	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 libxkbcommon-1.3.0:

--
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 openjdk11-11.0.11+9.1:

--
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-2.9.4 depends on package: openjfx14>0 - found
===>   Returning to build of igv-2.9.4
===>   igv-2.9.4 depends on executable: gradle - not found
===>   Installing existing package /packages/All/gradle6-6.9.txz
[114amd64-default-job-01] Installing gradle6-6.9...
[114amd64-default-job-01] `-- Installing openjdk8-8.292.10.1...
[114amd64-default-job-01] |   `-- Installing java-zoneinfo-2021.a...
[114amd64-default-job-01] |   `-- Extracting java-zoneinfo-2021.a: .......... done
[114amd64-default-job-01] |   `-- Installing libinotify-20180201_2...
[114amd64-default-job-01] |   `-- Extracting libinotify-20180201_2: .......... done
[114amd64-default-job-01] `-- Extracting openjdk8-8.292.10.1: .......... done
[114amd64-default-job-01] Extracting gradle6-6.9: .......... done
=====
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 openjdk8-8.292.10.1:

--
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-2.9.4 depends on executable: gradle - found
===>   Returning to build of igv-2.9.4
===>   igv-2.9.4 depends on file: /usr/local/openjdk11/bin/java - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   igv-2.9.4 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for igv-2.9.4
===========================================================================
=======================<phase: build          >============================
===>  Building for igv-2.9.4
cd /wrkdirs/usr/ports/biology/igv/work/igv-2.9.4 && /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  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 NO_PIE=yes 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  "  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" gradle  --gradle-u
 ser-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!

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)
The message received from the daemon indicates that the daemon has disappeared.
Build request sent: Build{id=ad6871a3-b0f6-4a9b-a89a-e9cf85cbd90a, currentDir=/wrkdirs/usr/ports/biology/igv/work/igv-2.9.4}
Attempting to read last messages from the daemon log...
Daemon pid: 19655
  log file: /wrkdirs/usr/ports/biology/igv/work/gradle-igv/daemon/6.9/daemon-19655.out.log
----- Last  20 lines from daemon log file - daemon-19655.out.log -----
2021-06-29T19:49:14.929+0000 [ERROR] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] Command execution: started DaemonCommandExecution[command = Build{id=ad6871a3-b0f6-4a9b-a89a-e9cf85cbd90a, currentDir=/wrkdirs/usr/ports/biology/igv/work/igv-2.9.4}, connection = DefaultDaemonConnection: socket connection from /127.0.0.1:20945 to /127.0.0.1:43066] after 0.0 minutes of idle
2021-06-29T19:49:14.930+0000 [INFO] [org.gradle.launcher.daemon.server.DaemonRegistryUpdater] Marking the daemon as busy, address: [0de526e4-e5a8-4f74-bd3a-637f45761263 port:20945, addresses:[localhost/127.0.0.1]]
2021-06-29T19:49:14.930+0000 [DEBUG] [org.gradle.launcher.daemon.registry.PersistentDaemonRegistry] Marking busy by address: [0de526e4-e5a8-4f74-bd3a-637f45761263 port:20945, addresses:[localhost/127.0.0.1]]
2021-06-29T19:49:14.931+0000 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Waiting to acquire exclusive lock on daemon addresses registry.
2021-06-29T19:49:14.931+0000 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Lock acquired on daemon addresses registry.
2021-06-29T19:49:14.932+0000 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Releasing lock on daemon addresses registry.
2021-06-29T19:49:14.932+0000 [DEBUG] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] resetting idle timer
2021-06-29T19:49:14.933+0000 [DEBUG] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] daemon is running. Sleeping until state changes.
2021-06-29T19:49:14.934+0000 [INFO] [org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy] Daemon is about to start building Build{id=ad6871a3-b0f6-4a9b-a89a-e9cf85cbd90a, currentDir=/wrkdirs/usr/ports/biology/igv/work/igv-2.9.4}. Dispatching build started information...
2021-06-29T19:49:14.934+0000 [DEBUG] [org.gradle.launcher.daemon.server.SynchronizedDispatchConnection] thread 29: dispatching org.gradle.launcher.daemon.protocol.BuildStarted_at_618db6af
2021-06-29T19:49:14.936+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment] Configuring env variables: [P_PORTS_FEATURES, PATH, MASTERMNT, CXX, CPP, META_MODE, MASTERNAME, BSD_INSTALL_PROGRAM, SAVED_TERM, LDFLAGS, UNAME_r, NO_LINT, STATUS, SCRIPTPREFIX, UNAME_v, BSD_INSTALL_MAN, POUDRIERE_BUILD_TYPE, MAIL, OSREL, NO_DEPENDS, PWD, GID, SHELL, CPPFLAGS, _OSRELEASE, BSD_INSTALL_LIB, OLDPWD, LIBS, TMPDIR, UID, OSVERSION, LC_ALL, PREFIX, SCRIPTPATH, HAVE_COMPAT_IA32_KERN, MK_DEBUG_FILES, MANPREFIX, BLOCKSIZE, MAKEFLAGS, JAVA_HOME, ARCH, LANG, OPSYS, LOCALBASE, GRADLE_USER_HOME, CFLAGS, MK_KERNEL_SYMBOLS, .MAKE.LEVEL.ENV, BSD_INSTALL_SCRIPT, CC, XDG_DATA_HOME, POUDRIERE_VERSION, BSD_INSTALL_DATA, USER, XDG_CONFIG_HOME, NO_PIE, MAKELEVEL, LIBEXECPREFIX, POUDRIEREPATH, PACKAGE_BUILDING, HOME, CXXFLAGS]
2021-06-29T19:49:14.939+0000 [DEBUG] [org.gradle.launcher.daemon.server.SynchronizedDispatchConnection] thread 27: received class org.gradle.launcher.daemon.protocol.CloseInput
2021-06-29T19:49:14.940+0000 [DEBUG] [org.gradle.launcher.daemon.server.DefaultDaemonConnection] thread 27: Received IO message from client: org.gradle.launcher.daemon.protocol.CloseInput_at_119be773
2021-06-29T19:49:14.944+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.LogToClient] About to start relaying all logs to the client via the connection.
2021-06-29T19:49:14.944+0000 [INFO] [org.gradle.launcher.daemon.server.exec.LogToClient] The client will now receive all logging from the daemon (pid: 19655). The daemon log file: /wrkdirs/usr/ports/biology/igv/work/gradle-igv/daemon/6.9/daemon-19655.out.log
2021-06-29T19:49:14.946+0000 [INFO] [org.gradle.launcher.daemon.server.exec.LogAndCheckHealth] Starting build in new daemon [memory: 512 MiB]
2021-06-29T19:49:14.948+0000 [INFO] [org.gradle.launcher.daemon.server.exec.ForwardClientInput] Closing daemon's stdin at end of input.
2021-06-29T19:49:14.948+0000 [INFO] [org.gradle.launcher.daemon.server.exec.ForwardClientInput] The daemon will no longer process any standard input.
2021-06-29T19:49:14.953+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] The daemon has started executing the build.
2021-06-29T19:49:14.953+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] Executing build with daemon context: DefaultDaemonContext[uid=30479baa-a87d-45bf-be13-c445dba82eb7,javaHome=/usr/local/openjdk11,daemonRegistryDir=/wrkdirs/usr/ports/biology/igv/work/gradle-igv/daemon,pid=19655,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=US-ASCII,-Duser.country=US,-Duser.language=en,-Duser.variant]
----- End of the daemon 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 --info or --debug option to get more log output. Run with --scan to get full insights.

* Exception is:
org.gradle.launcher.daemon.client.DaemonDisappearedException: Gradle build daemon disappeared unexpectedly (it may have been killed or may have crashed)
	at org.gradle.launcher.daemon.client.DaemonClient.handleDaemonDisappearance(DaemonClient.java:249)
	at org.gradle.launcher.daemon.client.DaemonClient.monitorBuild(DaemonClient.java:222)
	at org.gradle.launcher.daemon.client.DaemonClient.executeBuild(DaemonClient.java:184)
	at org.gradle.launcher.daemon.client.DaemonClient.execute(DaemonClient.java:147)
	at org.gradle.launcher.daemon.client.DaemonClient.execute(DaemonClient.java:98)
	at org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:57)
	at org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:212)
	at org.gradle.launcher.cli.DefaultCommandLineActionFactory$ParseAndBuildAction.execute(DefaultCommandLineActionFactory.java:275)
	at org.gradle.launcher.cli.DefaultCommandLineActionFactory$ParseAndBuildAction.execute(DefaultCommandLineActionFactory.java:247)
	at org.gradle.launcher.cli.DebugLoggerWarningAction.execute(DebugLoggerWarningAction.java:82)
	at org.gradle.launcher.cli.DebugLoggerWarningAction.execute(DebugLoggerWarningAction.java:30)
	at org.gradle.launcher.cli.WelcomeMessageAction.execute(WelcomeMessageAction.java:92)
	at org.gradle.launcher.cli.WelcomeMessageAction.execute(WelcomeMessageAction.java:38)
	at org.gradle.launcher.cli.NativeServicesInitializingAction.execute(NativeServicesInitializingAction.java:44)
	at org.gradle.launcher.cli.NativeServicesInitializingAction.execute(NativeServicesInitializingAction.java:26)
	at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:41)
	at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:26)
	at org.gradle.launcher.cli.DefaultCommandLineActionFactory$WithLogging.execute(DefaultCommandLineActionFactory.java:240)
	at org.gradle.launcher.Main.doAction(Main.java:35)
	at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:50)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)
	at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)
	at org.gradle.launcher.GradleMain.main(GradleMain.java:31)


* Get more help at https://help.gradle.org
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/igv
Received on Tue Jun 29 2021 - 19:49:19 UTC

Original text of this message