[package - 114amd64-default][biology/igv] Failed for igv-2.8.13 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Dec 19 17:37:40 UTC 2020
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
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: head/biology/igv/Makefile 556663 2020-11-30 17:29:48Z yuri $
Log URL: http://beefy9.nyi.freebsd.org/data/114amd64-default/558421/logs/igv-2.8.13.log
Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=558421
Log:
=>> Building biology/igv
build started at Sat Dec 19 17:36:22 UTC 2020
port directory: /usr/ports/biology/igv
package name: igv-2.8.13
building for: FreeBSD 114amd64-default-job-09 11.4-RELEASE-p6 FreeBSD 11.4-RELEASE-p6 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/igv/Makefile 556663 2020-11-30 17:29:48Z yuri $
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1300121
Jail OSVERSION: 1104001
Job Id: 09
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---End OPTIONS List---
--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
--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 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"
--End MAKE_ENV--
--PLIST_SUB--
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--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---
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#### /usr/local/etc/poudriere.d/make.conf ####
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# try the next if the size is mismatched though.
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MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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GID=0
UID=0
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---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
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pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> igv-2.8.13 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.10.txz
[114amd64-default-job-09] Installing pkg-1.15.10...
[114amd64-default-job-09] Extracting pkg-1.15.10: .......... done
===> igv-2.8.13 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of igv-2.8.13
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by igv-2.8.13 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by igv-2.8.13 for building
=> SHA256 Checksum OK for igv-2.8.13/tools.png.
=> SHA256 Checksum OK for igv-2.8.13/igv-2.8.13-deps.tar.gz.
=> SHA256 Checksum OK for igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by igv-2.8.13 for building
===> Extracting for igv-2.8.13
=> SHA256 Checksum OK for igv-2.8.13/tools.png.
=> SHA256 Checksum OK for igv-2.8.13/igv-2.8.13-deps.tar.gz.
=> SHA256 Checksum OK for igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for igv-2.8.13
===========================================================================
=======================<phase: build-depends >============================
===> igv-2.8.13 depends on package: openjfx14>0 - not found
===> Installing existing package /packages/All/openjfx14-14.0.2.1+1_1.txz
[114amd64-default-job-09] Installing openjfx14-14.0.2.1+1_1...
[114amd64-default-job-09] `-- Installing alsa-lib-1.1.2_2...
[114amd64-default-job-09] `-- Extracting alsa-lib-1.1.2_2: .......... done
[114amd64-default-job-09] `-- Installing atk-2.36.0...
[114amd64-default-job-09] | `-- Installing gettext-runtime-0.21...
[114amd64-default-job-09] | | `-- Installing indexinfo-0.3.1...
[114amd64-default-job-09] | | `-- Extracting indexinfo-0.3.1: .... done
[114amd64-default-job-09] | `-- Extracting gettext-runtime-0.21: .......... done
[114amd64-default-job-09] | `-- Installing glib-2.66.3,1...
[114amd64-default-job-09] | | `-- Installing libffi-3.3_1...
[114amd64-default-job-09] | | `-- Extracting libffi-3.3_1: .......... done
[114amd64-default-job-09] | | `-- Installing libiconv-1.16...
[114amd64-default-job-09] | | `-- Extracting libiconv-1.16: .......... done
[114amd64-default-job-09] | | `-- Installing libxml2-2.9.10_2...
<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-1.0.1:
--
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 openjdk11-11.0.9+11.1_2:
--
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-2.8.13 depends on package: openjfx14>0 - found
===> Returning to build of igv-2.8.13
===> igv-2.8.13 depends on executable: gradle - not found
===> Installing existing package /packages/All/gradle-6.7.1.txz
[114amd64-default-job-09] Installing gradle-6.7.1...
[114amd64-default-job-09] `-- Installing openjdk8-8.275.01.1...
[114amd64-default-job-09] | `-- Installing java-zoneinfo-2020.d...
[114amd64-default-job-09] | `-- Extracting java-zoneinfo-2020.d: .......... done
[114amd64-default-job-09] | `-- Installing libinotify-20180201_2...
[114amd64-default-job-09] | `-- Extracting libinotify-20180201_2: .......... done
[114amd64-default-job-09] `-- Extracting openjdk8-8.275.01.1: .......... done
[114amd64-default-job-09] Extracting gradle-6.7.1: .......... 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 openjdk8-8.275.01.1:
--
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-2.8.13 depends on executable: gradle - found
===> Returning to build of igv-2.8.13
===> igv-2.8.13 depends on file: /usr/local/openjdk11/bin/java - found
===========================================================================
=======================<phase: lib-depends >============================
===> igv-2.8.13 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for igv-2.8.13
===========================================================================
=======================<phase: build >============================
===> Building for igv-2.8.13
cd /wrkdirs/usr/ports/biology/igv/work/igv-2.8.13 && /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-
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 6.7.1!
Here are the highlights of this release:
- File system watching is ready for production use
- Declare the version of Java your build requires
- Java 15 support
For more details see https://docs.gradle.org/6.7.1/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=b9b679a4-9987-4b8f-87b5-2469be3f1d47, currentDir=/wrkdirs/usr/ports/biology/igv/work/igv-2.8.13}
Attempting to read last messages from the daemon log...
Daemon pid: 86863
log file: /wrkdirs/usr/ports/biology/igv/work/gradle-igv/daemon/6.7.1/daemon-86863.out.log
----- Last 20 lines from daemon log file - daemon-86863.out.log -----
2020-12-19T17:37:37.703+0000 [ERROR] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] Command execution: started DaemonCommandExecution[command = Build{id=b9b679a4-9987-4b8f-87b5-2469be3f1d47, currentDir=/wrkdirs/usr/ports/biology/igv/work/igv-2.8.13}, connection = DefaultDaemonConnection: socket connection from /127.0.0.1:37338 to /127.0.0.1:37339] after 0.0 minutes of idle
2020-12-19T17:37:37.703+0000 [INFO] [org.gradle.launcher.daemon.server.DaemonRegistryUpdater] Marking the daemon as busy, address: [09599699-ae18-44ee-aad2-aedbb169d933 port:37338, addresses:[localhost/127.0.0.1]]
2020-12-19T17:37:37.704+0000 [DEBUG] [org.gradle.launcher.daemon.registry.PersistentDaemonRegistry] Marking busy by address: [09599699-ae18-44ee-aad2-aedbb169d933 port:37338, addresses:[localhost/127.0.0.1]]
2020-12-19T17:37:37.705+0000 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Waiting to acquire exclusive lock on daemon addresses registry.
2020-12-19T17:37:37.705+0000 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Lock acquired on daemon addresses registry.
2020-12-19T17:37:37.706+0000 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Releasing lock on daemon addresses registry.
2020-12-19T17:37:37.707+0000 [DEBUG] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] resetting idle timer
2020-12-19T17:37:37.707+0000 [DEBUG] [org.gradle.launcher.daemon.server.DaemonStateCoordinator] daemon is running. Sleeping until state changes.
2020-12-19T17:37:37.708+0000 [INFO] [org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy] Daemon is about to start building Build{id=b9b679a4-9987-4b8f-87b5-2469be3f1d47, currentDir=/wrkdirs/usr/ports/biology/igv/work/igv-2.8.13}. Dispatching build started information...
2020-12-19T17:37:37.709+0000 [DEBUG] [org.gradle.launcher.daemon.server.SynchronizedDispatchConnection] thread 29: dispatching org.gradle.launcher.daemon.protocol.BuildStarted at 3e51205b
2020-12-19T17:37:37.712+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]
2020-12-19T17:37:37.714+0000 [DEBUG] [org.gradle.launcher.daemon.server.SynchronizedDispatchConnection] thread 27: received class org.gradle.launcher.daemon.protocol.CloseInput
2020-12-19T17:37:37.714+0000 [DEBUG] [org.gradle.launcher.daemon.server.DefaultDaemonConnection] thread 27: Received IO message from client: org.gradle.launcher.daemon.protocol.CloseInput at 55f86f15
2020-12-19T17:37:37.722+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.LogToClient] About to start relaying all logs to the client via the connection.
2020-12-19T17:37:37.723+0000 [INFO] [org.gradle.launcher.daemon.server.exec.LogToClient] The client will now receive all logging from the daemon (pid: 86863). The daemon log file: /wrkdirs/usr/ports/biology/igv/work/gradle-igv/daemon/6.7.1/daemon-86863.out.log
2020-12-19T17:37:37.727+0000 [INFO] [org.gradle.launcher.daemon.server.exec.LogAndCheckHealth] Starting build in new daemon [memory: 536.9 MB]
2020-12-19T17:37:37.729+0000 [INFO] [org.gradle.launcher.daemon.server.exec.ForwardClientInput] Closing daemon's stdin at end of input.
2020-12-19T17:37:37.729+0000 [INFO] [org.gradle.launcher.daemon.server.exec.ForwardClientInput] The daemon will no longer process any standard input.
2020-12-19T17:37:37.735+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] The daemon has started executing the build.
2020-12-19T17:37:37.736+0000 [DEBUG] [org.gradle.launcher.daemon.server.exec.ExecuteBuild] Executing build with daemon context: DefaultDaemonContext[uid=26765103-99dd-4a46-9f89-88f3a231f45f,javaHome=/usr/local/openjdk11,daemonRegistryDir=/wrkdirs/usr/ports/biology/igv/work/gradle-igv/daemon,pid=86863,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
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