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Date:      Sat, 19 Jan 2019 03:35:25 GMT
From:      pkg-fallout@FreeBSD.org
To:        yuri@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - 120i386-default][biology/gatk] Failed for gatk-4.0.11.0 in build
Message-ID:  <201901190335.x0J3ZP6q065166@beefy5.nyi.freebsd.org>

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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
Last committer: yuri@FreeBSD.org
Ident:          $FreeBSD: head/biology/gatk/Makefile 486619 2018-12-04 17:53:46Z yuri $
Log URL:        http://beefy5.nyi.freebsd.org/data/120i386-default/490694/logs/gatk-4.0.11.0.log
Build URL:      http://beefy5.nyi.freebsd.org/build.html?mastername=120i386-default&build=490694
Log:

=>> Building biology/gatk
build started at Sat Jan 19 03:33:34 UTC 2019
port directory: /usr/ports/biology/gatk
package name: gatk-4.0.11.0
building for: FreeBSD 120i386-default-job-08 12.0-RELEASE-p2 FreeBSD 12.0-RELEASE-p2 i386
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/gatk/Makefile 486619 2018-12-04 17:53:46Z yuri $
Poudriere version: 3.2.8
Host OSVERSION: 1300002
Jail OSVERSION: 1200086
Job Id: 08

---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1200086
UNAME_v=FreeBSD 12.0-RELEASE-p2
UNAME_r=12.0-RELEASE-p2
BLOCKSIZE=K
MAIL=/var/mail/root
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
MASTERMNT=/usr/local/poudriere/data/.m/120i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/120i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=120i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/120i386-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/gatk/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work  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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work  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 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 -fno-strict-aliasing "  CPP="cpp" CPPFLAGS=""  LDFLAGS=" -fstack-protector " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -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=12.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gatk"  EXAMPLESDIR="share/examples/gatk"  DATADIR="share/gatk"  WWWDIR="www/gatk"  ETCDIR="etc/gatk"
--End PLIST_SUB--

--SUB_LIST--
PORTVERSION=4.0.11.0 JAVA=/usr/local/openjdk8/bin/java JAVASHAREDIR="/usr/local/share/java"  JAVAJARDIR="/usr/local/share/java/classes"  JAVALIBDIR="/usr/local/share/java/classes" 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
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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

# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT=	true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: i386-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: i386-unknown-freebsd12.0 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" "-m" "elf_i386_fbsd" "-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 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: i386-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=12.0-RELEASE-p2
OSREL=12.0
OSVERSION=1200086
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  524288
stack size              (kbytes, -s)  65536
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 BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gatk-4.0.11.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[120i386-default-job-08] Installing pkg-1.10.5_5...
[120i386-default-job-08] Extracting pkg-1.10.5_5: .......... done
===>   gatk-4.0.11.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gatk-4.0.11.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.0.11.0 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.0.11.0 for building
=> SHA256 Checksum OK for gatk-4.0.11.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.0.11.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.0.11.0 for building
===>  Extracting for gatk-4.0.11.0
=> SHA256 Checksum OK for gatk-4.0.11.0-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.0.11.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for gatk-4.0.11.0
===>  Applying FreeBSD patches for gatk-4.0.11.0
===========================================================================
=======================<phase: build-depends  >============================
===>   gatk-4.0.11.0 depends on executable: gradle4 - not found
===>   Installing existing package /packages/All/gradle4-4.6.txz
[120i386-default-job-08] Installing gradle4-4.6...
[120i386-default-job-08] `-- Installing openjdk8-8.192.26_4...
[120i386-default-job-08] |   `-- Installing alsa-lib-1.1.2_2...
[120i386-default-job-08] |   `-- Extracting alsa-lib-1.1.2_2: .......... done
[120i386-default-job-08] |   `-- Installing dejavu-2.37...
<snip>
=============================================================================
Message from openjdk8-8.192.26_4:

======================================================================

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-4.0.11.0 depends on executable: gradle4 - found
===>   Returning to build of gatk-4.0.11.0
===>   gatk-4.0.11.0 depends on file: /usr/local/openjdk8/bin/java - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   gatk-4.0.11.0 depends on shared library: libintl.so - not found
===>   Installing existing package /packages/All/gettext-runtime-0.19.8.1_2.txz
[120i386-default-job-08] Installing gettext-runtime-0.19.8.1_2...
[120i386-default-job-08] `-- Installing indexinfo-0.3.1...
[120i386-default-job-08] `-- Extracting indexinfo-0.3.1: .... done
[120i386-default-job-08] Extracting gettext-runtime-0.19.8.1_2: .......... done
===>   gatk-4.0.11.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===>   Returning to build of gatk-4.0.11.0
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for gatk-4.0.11.0
===========================================================================
=======================<phase: build          >============================
===>  Building for gatk-4.0.11.0
Starting a Gradle Daemon (subsequent builds will be faster)
:compileJava
:processResources
:classes
:shadowJarex
org.gradle.api.GradleException: Could not add file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.0.11.0/build/classes/java/main/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/AlignedAssembly$1.class' to ZIP '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.0.11.0/build/libs/gatk-package-1.0-SNAPSHOT-local.jar'.
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83)
	at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:255)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction$StreamAction.visitFile(ShadowCopyAction.groovy:185)
	at sun.reflect.GeneratedMethodAccessor36.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction$StreamAction.processFile(ShadowCopyAction.groovy:151)
	at org.gradle.api.internal.file.copy.NormalizingCopyActionDecorator$1$1.processFile(NormalizingCopyActionDecorator.java:66)
	at org.gradle.api.internal.file.copy.DuplicateHandlingCopyActionDecorator$1$1.processFile(DuplicateHandlingCopyActionDecorator.java:60)
	at org.gradle.api.internal.file.copy.CopyFileVisitorImpl.processFile(CopyFileVisitorImpl.java:62)
	at org.gradle.api.internal.file.copy.CopyFileVisitorImpl.visitFile(CopyFileVisitorImpl.java:46)
	at org.gradle.api.internal.file.collections.jdk7.Jdk7DirectoryWalker$1.visitFile(Jdk7DirectoryWalker.java:86)
	at org.gradle.api.internal.file.collections.jdk7.Jdk7DirectoryWalker$1.visitFile(Jdk7DirectoryWalker.java:59)
	at java.nio.file.Files.walkFileTree(Files.java:2670)
	at org.gradle.api.internal.file.collections.jdk7.Jdk7DirectoryWalker.walkDir(Jdk7DirectoryWalker.java:59)
	at org.gradle.api.internal.file.collections.DirectoryFileTree.walkDir(DirectoryFileTree.java:154)
	at org.gradle.api.internal.file.collections.DirectoryFileTree.visitFrom(DirectoryFileTree.java:132)
	at org.gradle.api.internal.file.collections.DirectoryFileTree.visit(DirectoryFileTree.java:117)
	at org.gradle.api.internal.file.collections.FileTreeAdapter.visit(FileTreeAdapter.java:116)
	at org.gradle.api.internal.file.CompositeFileTree.visit(CompositeFileTree.java:87)
	at org.gradle.api.internal.file.copy.CopySpecActionImpl.execute(CopySpecActionImpl.java:39)
	at org.gradle.api.internal.file.copy.CopySpecActionImpl.execute(CopySpecActionImpl.java:24)
	at org.gradle.api.internal.file.copy.DefaultCopySpec$DefaultCopySpecResolver.walk(DefaultCopySpec.java:648)
	at org.gradle.api.internal.file.copy.DefaultCopySpec$DefaultCopySpecResolver.walk(DefaultCopySpec.java:650)
	at org.gradle.api.internal.file.copy.DefaultCopySpec.walk(DefaultCopySpec.java:458)
	at org.gradle.api.internal.file.copy.CopySpecBackedCopyActionProcessingStream.process(CopySpecBackedCopyActionProcessingStream.java:38)
	at org.gradle.api.internal.file.copy.DuplicateHandlingCopyActionDecorator$1.process(DuplicateHandlingCopyActionDecorator.java:44)
	at org.gradle.api.internal.file.copy.NormalizingCopyActionDecorator$1.process(NormalizingCopyActionDecorator.java:57)
	at org.gradle.api.internal.file.copy.CopyActionProcessingStream$process.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction$1.execute(ShadowCopyAction.groovy:78)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction$1$execute.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction.withResource(ShadowCopyAction.groovy:109)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite$StaticMetaMethodSiteNoUnwrapNoCoerce.invoke(StaticMetaMethodSite.java:151)
	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:102)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:56)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:194)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:214)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction.execute(ShadowCopyAction.groovy:75)
	at org.gradle.api.internal.file.copy.NormalizingCopyActionDecorator.execute(NormalizingCopyActionDecorator.java:53)
	at org.gradle.api.internal.file.copy.DuplicateHandlingCopyActionDecorator.execute(DuplicateHandlingCopyActionDecorator.java:42)
	at org.gradle.api.internal.file.copy.CopyActionExecuter.execute(CopyActionExecuter.java:40)
	at org.gradle.api.tasks.AbstractCopyTask.copy(AbstractCopyTask.java:174)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar.copy(ShadowJar.java:70)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
	at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46)
	at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39)
	at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26)
	at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:788)
	at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:755)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:124)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:113)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:95)
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:73)
	at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51)
	at org.gradle.api.internal.tasks.execution.SkipCachedTaskExecuter.execute(SkipCachedTaskExecuter.java:103)
	at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:59)
	at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ResolveBuildCacheKeyExecuter.execute(ResolveBuildCacheKeyExecuter.java:66)
	at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:59)
	at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:101)
	at org.gradle.api.internal.tasks.execution.FinalizeInputFilePropertiesTaskExecuter.execute(FinalizeInputFilePropertiesTaskExecuter.java:44)
	at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:91)
	at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:62)
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:59)
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
	at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:256)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:249)
	at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:238)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:663)
	at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:597)
	at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.FileNotFoundException: /wrkdirs/usr/ports/biology/gatk/work/gatk-4.0.11.0/build/classes/java/main/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/AlignedAssembly$1.class (Too many open files)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at org.codehaus.groovy.runtime.ResourceGroovyMethods.newInputStream(ResourceGroovyMethods.java:1977)
	at org.codehaus.groovy.runtime.dgm$974.invoke(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
	at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction$StreamAction.remapClass(ShadowCopyAction.groovy:251)
	at sun.reflect.GeneratedMethodAccessor38.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at com.github.jengelman.gradle.plugins.shadow.tasks.ShadowCopyAction$StreamAction.visitFile(ShadowCopyAction.groovy:181)
	... 106 more
 FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':shadowJar'.
> Could not add file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.0.11.0/build/classes/java/main/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/AlignedAssembly$1.class' to ZIP '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.0.11.0/build/libs/gatk-package-1.0-SNAPSHOT-local.jar'.

* 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

Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0.
See https://docs.gradle.org/4.6/userguide/command_line_interface.html#sec:command_line_warnings

BUILD FAILED in 1m 3s
3 actionable tasks: 3 executed
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/gatk



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