Date: Mon, 24 Dec 2018 02:34:44 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: <201812240234.wBO2YijT075872@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/488160/logs/gatk-4.0.11.0.log Build URL: http://beefy5.nyi.freebsd.org/build.html?mastername=120i386-default&build=488160 Log: =>> Building biology/gatk build started at Mon Dec 24 02:33:07 UTC 2018 port directory: /usr/ports/biology/gatk package name: gatk-4.0.11.0 building for: FreeBSD 120i386-default-job-19 12.0-RELEASE-p1 FreeBSD 12.0-RELEASE-p1 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: 19 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p1 UNAME_r=12.0-RELEASE-p1 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-p1 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-19] Installing pkg-1.10.5_5... [120i386-default-job-19] 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-19] Installing gradle4-4.6... [120i386-default-job-19] `-- Installing openjdk8-8.192.26_1... [120i386-default-job-19] | `-- Installing alsa-lib-1.1.2_2... [120i386-default-job-19] | `-- Extracting alsa-lib-1.1.2_2: .......... done [120i386-default-job-19] | `-- Installing dejavu-2.37... <snip> if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from openjdk8-8.192.26_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 ====================================================================== ===> 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-19] Installing gettext-runtime-0.19.8.1_2... [120i386-default-job-19] `-- Installing indexinfo-0.3.1... [120i386-default-job-19] `-- Extracting indexinfo-0.3.1: .... done [120i386-default-job-19] 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.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.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.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 57s 3 actionable tasks: 3 executed *** Error code 1 Stop. make: stopped in /usr/ports/biology/gatk
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