[package - 131releng-armv7-quarterly][biology/jalview] Failed for jalview-2.11.2.5 in build
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Date: Mon, 20 Feb 2023 23:13:21 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere1/data/131releng-armv7-quarterly/604744931878/logs/jalview-2.11.2.5.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=131releng-armv7-quarterly&build=604744931878
Log:
=>> Building biology/jalview
build started at Mon Feb 20 23:09:51 UTC 2023
port directory: /usr/ports/biology/jalview
package name: jalview-2.11.2.5
building for: FreeBSD 131releng-armv7-quarterly-job-06 13.1-RELEASE-p6 FreeBSD 13.1-RELEASE-p6 1301000 arm
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> jalview-2.11.2.5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.0.pkg
[131releng-armv7-quarterly-job-06] Installing pkg-1.19.0...
[131releng-armv7-quarterly-job-06] Extracting pkg-1.19.0: .......... done
===> jalview-2.11.2.5 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of jalview-2.11.2.5
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by jalview-2.11.2.5 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by jalview-2.11.2.5 for building
=> SHA256 Checksum OK for jalview_2_11_2_5.tar.gz.
=> SHA256 Checksum OK for jalview-2.11.2.5-deps.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by jalview-2.11.2.5 for building
===> Extracting for jalview-2.11.2.5
=> SHA256 Checksum OK for jalview_2_11_2_5.tar.gz.
=> SHA256 Checksum OK for jalview-2.11.2.5-deps.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for jalview-2.11.2.5
===========================================================================
=======================<phase: build-depends >============================
===> jalview-2.11.2.5 depends on executable: gradle - not found
===> Installing existing package /packages/All/gradle-7.6.pkg
[131releng-armv7-quarterly-job-06] Installing gradle-7.6...
[131releng-armv7-quarterly-job-06] `-- Installing openjdk8-8.352.08.1_1...
[131releng-armv7-quarterly-job-06] | `-- Installing alsa-lib-1.2.2_1...
[131releng-armv7-quarterly-job-06] | `-- Extracting alsa-lib-1.2.2_1: .......... done
[131releng-armv7-quarterly-job-06] | `-- Installing dejavu-2.37_1...
[131releng-armv7-quarterly-job-06] | | `-- Installing fontconfig-2.14.0,1...
[131releng-armv7-quarterly-job-06] | | `-- Installing expat-2.5.0...
[131releng-armv7-quarterly-job-06] | | `-- Extracting expat-2.5.0: .......... done
[131releng-armv7-quarterly-job-06] | | `-- Installing freetype2-2.12.1_2...
[131releng-armv7-quarterly-job-06] | | | `-- Installing brotli-1.0.9,1...
[131releng-armv7-quarterly-job-06] | | | `-- Extracting brotli-1.0.9,1: .......... done
[131releng-armv7-quarterly-job-06] | | | `-- Installing png-1.6.39...
<snip>
Welcome to Gradle 7.6!
Here are the highlights of this release:
- Added support for Java 19.
- Introduced `--rerun` flag for individual task rerun.
- Improved dependency block for test suites to be strongly typed.
- Added a pluggable system for Java toolchains provisioning.
For more details see https://docs.gradle.org/7.6/release-notes.html
Starting a Gradle Daemon (subsequent builds will be faster)
> Configure project :
Using properties from file './utils/channels/default/channel_gradle.properties'
JALVIEW_VERSION is set to '2.11.2.5'
HEADLESS BUILD
J2S ENABLED
Not in a git repository. Using git values from RELEASE properties file.
Using a LOCAL profile.
> Task :copyHelp
> Task :buildIndices
> Task :copyResources
> Task :copyChannelResources
> Task :createBuildProperties
Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
> Task :buildResources
> Task :copyDocs
> Task :convertMdFiles
Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/README-DMG_creation.html
Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/README-DMG_background_image_creation.html
Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/building.html
Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/releaseprocess.html
> Task :releasesTemplates
Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
> Task :prepare
> Task :compileJava
Setting target compatibility to 11
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
> Task :processResources
Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
> Task :classes
> Task :cleanPackageDir UP-TO-DATE
> Task :compileLinkCheck
Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
- Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem.
compiler message file broken: key=compiler.misc.msg.bug arguments=11.0.17, {1}, {2}, {3}, {4}, {5}, {6}, {7}
java.lang.NullPointerException
at jdk.compiler/com.sun.tools.javac.util.UnsharedNameTable.fromUtf(UnsharedNameTable.java:107)
at jdk.compiler/com.sun.tools.javac.util.Names.fromUtf(Names.java:398)
at jdk.compiler/com.sun.tools.javac.jvm.ClassReader.readPool(ClassReader.java:469)
at jdk.compiler/com.sun.tools.javac.jvm.ClassReader.readName(ClassReader.java:592)
at jdk.compiler/com.sun.tools.javac.jvm.ClassReader.readMethod(ClassReader.java:2416)
at jdk.compiler/com.sun.tools.javac.jvm.ClassReader.readClass(ClassReader.java:2739)
at jdk.compiler/com.sun.tools.javac.jvm.ClassReader.readClassBuffer(ClassReader.java:2811)
at jdk.compiler/com.sun.tools.javac.jvm.ClassReader.readClassFile(ClassReader.java:2824)
at jdk.compiler/com.sun.tools.javac.code.ClassFinder.fillIn(ClassFinder.java:359)
at jdk.compiler/com.sun.tools.javac.code.ClassFinder.complete(ClassFinder.java:291)
at jdk.compiler/com.sun.tools.javac.code.Symtab$1.complete(Symtab.java:305)
at jdk.compiler/com.sun.tools.javac.code.Symbol.complete(Symbol.java:642)
at jdk.compiler/com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:1326)
at jdk.compiler/com.sun.tools.javac.code.Symbol$ClassSymbol.members(Symbol.java:1264)
at jdk.compiler/com.sun.tools.javac.comp.Resolve.findMethod(Resolve.java:1803)
at jdk.compiler/com.sun.tools.javac.comp.Resolve.findMethod(Resolve.java:1776)
at jdk.compiler/com.sun.tools.javac.comp.Resolve$10.doLookup(Resolve.java:2654)
at jdk.compiler/com.sun.tools.javac.comp.Resolve$BasicLookupHelper.lookup(Resolve.java:3293)
at jdk.compiler/com.sun.tools.javac.comp.Resolve.lookupMethod(Resolve.java:3543)
at jdk.compiler/com.sun.tools.javac.comp.Resolve.resolveQualifiedMethod(Resolve.java:2651)
at jdk.compiler/com.sun.tools.javac.comp.Resolve.resolveInternalMethod(Resolve.java:2733)
at jdk.compiler/com.sun.tools.javac.jvm.StringConcat$IndyConstants.doCall(StringConcat.java:489)
at jdk.compiler/com.sun.tools.javac.jvm.StringConcat$IndyConstants.emit(StringConcat.java:449)
at jdk.compiler/com.sun.tools.javac.jvm.StringConcat$Indy.makeConcat(StringConcat.java:273)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitBinary(Gen.java:1935)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCBinary.accept(JCTree.java:2009)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genExpr(Gen.java:819)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genArgs(Gen.java:838)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitApply(Gen.java:1663)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCMethodInvocation.accept(JCTree.java:1650)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genExpr(Gen.java:819)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitExec(Gen.java:1594)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCExpressionStatement.accept(JCTree.java:1468)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genDef(Gen.java:597)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:632)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:618)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStats(Gen.java:669)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitBlock(Gen.java:1031)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCBlock.accept(JCTree.java:1036)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genDef(Gen.java:597)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:632)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:618)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitIf(Gen.java:1568)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCIf.accept(JCTree.java:1437)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genDef(Gen.java:597)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:632)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:618)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStats(Gen.java:669)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitBlock(Gen.java:1031)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCBlock.accept(JCTree.java:1036)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genDef(Gen.java:597)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genStat(Gen.java:632)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genMethod(Gen.java:903)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.visitMethodDef(Gen.java:866)
at jdk.compiler/com.sun.tools.javac.tree.JCTree$JCMethodDecl.accept(JCTree.java:866)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genDef(Gen.java:597)
at jdk.compiler/com.sun.tools.javac.jvm.Gen.genClass(Gen.java:2202)
at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.genCode(JavaCompiler.java:756)
at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.generate(JavaCompiler.java:1631)
at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.generate(JavaCompiler.java:1599)
at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:973)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.lambda$doCall$0(JavacTaskImpl.java:104)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.handleExceptions(JavacTaskImpl.java:147)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.doCall(JavacTaskImpl.java:100)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.call(JavacTaskImpl.java:94)
at org.gradle.internal.compiler.java.IncrementalCompileTask.call(IncrementalCompileTask.java:89)
at org.gradle.api.internal.tasks.compile.AnnotationProcessingCompileTask.call(AnnotationProcessingCompileTask.java:94)
at org.gradle.api.internal.tasks.compile.ResourceCleaningCompilationTask.call(ResourceCleaningCompilationTask.java:57)
at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:54)
at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:39)
at org.gradle.api.internal.tasks.compile.daemon.AbstractDaemonCompiler$CompilerWorkAction.execute(AbstractDaemonCompiler.java:135)
at org.gradle.workers.internal.DefaultWorkerServer.execute(DefaultWorkerServer.java:63)
at org.gradle.workers.internal.AbstractClassLoaderWorker$1.create(AbstractClassLoaderWorker.java:49)
at org.gradle.workers.internal.AbstractClassLoaderWorker$1.create(AbstractClassLoaderWorker.java:43)
at org.gradle.internal.classloader.ClassLoaderUtils.executeInClassloader(ClassLoaderUtils.java:100)
at org.gradle.workers.internal.AbstractClassLoaderWorker.executeInClassLoader(AbstractClassLoaderWorker.java:43)
at org.gradle.workers.internal.FlatClassLoaderWorker.run(FlatClassLoaderWorker.java:32)
at org.gradle.workers.internal.FlatClassLoaderWorker.run(FlatClassLoaderWorker.java:22)
at org.gradle.workers.internal.WorkerDaemonServer.run(WorkerDaemonServer.java:87)
at org.gradle.workers.internal.WorkerDaemonServer.run(WorkerDaemonServer.java:56)
at org.gradle.process.internal.worker.request.WorkerAction$1.call(WorkerAction.java:138)
at org.gradle.process.internal.worker.child.WorkerLogEventListener.withWorkerLoggingProtocol(WorkerLogEventListener.java:41)
at org.gradle.process.internal.worker.request.WorkerAction.run(WorkerAction.java:135)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:182)
at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:164)
at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:414)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:49)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
> Task :compileLinkCheck FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':compileLinkCheck'.
> Compilation failed; see the compiler error output for details.
* 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 8.0.
You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
See https://docs.gradle.org/7.6/userguide/command_line_interface.html#sec:command_line_warnings
Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
Please consult deprecation warnings for more details.
BUILD FAILED in 2m 34s
12 actionable tasks: 11 executed, 1 up-to-date
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/jalview