Your message dated Thu, 26 May 2022 14:34:11 +0000
with message-id <[email protected]>
and subject line Bug#1011731: fixed in capsule-maven-nextflow 1.0.3.1+dfsg-4
has caused the Debian Bug report #1011731,
regarding capsule-maven-nextflow: FTBFS: UserSettings.java:183: error:
exception PlexusCipherException is never thrown in body of corresponding try
statement
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1011731: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1011731
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: capsule-maven-nextflow
Version: 1.0.3.1+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: [email protected]
Usertags: ftbfs-20220525 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --buildsystem=gradle --with maven_repo_helper --with javahelper
> dh_update_autotools_config -O--buildsystem=gradle
> dh_autoreconf -O--buildsystem=gradle
> dh_auto_configure -O--buildsystem=gradle
> jh_linkjars -O--buildsystem=gradle
> dh_auto_build -O--buildsystem=gradle
> mkdir -p .gradle/init.d
> cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
> gradle --info --console plain --offline --stacktrace --no-daemon
> --refresh-dependencies --gradle-user-home .gradle -Duser.home=.
> -Duser.name=debian -Ddebian.package=capsule-maven-nextflow
> -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar
> Initialized native services in: /<<PKGBUILDDIR>>/.gradle/native
> To honour the JVM settings for this build a new JVM will be forked. Please
> consider using the daemon:
> https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html.
> Starting process 'Gradle build daemon'. Working directory:
> /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1 Command:
> /usr/lib/jvm/java-11-openjdk-amd64/bin/java
> -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar
> --add-opens java.base/java.lang=ALL-UNNAMED -Dfile.encoding=UTF-8
> -Duser.country -Duser.language=en -Duser.variant -cp
> /usr/share/gradle/lib/gradle-launcher-4.4.1.jar
> org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1
> Successfully started process 'Gradle build daemon'
> An attempt to start the daemon took 0.875 secs.
> The client will now receive all logging from the daemon (pid: 1150806). The
> daemon log file: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1/daemon-1150806.out.log
> Daemon will be stopped at the end of the build stopping after processing
> Closing daemon's stdin at end of input.
> The daemon will no longer process any standard input.
> Using 8 worker leases.
> Creating new cache for fileHashes, path
> /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@3740947f
> Creating new cache for resourceHashesCache, path
> /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin,
> access org.gradle.cache.internal.DefaultCacheAccess@3740947f
> Creating new cache for fileHashes, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@ed388aa
> Starting Build
> Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle'
> using SubsetScriptTransformer.
> Creating new cache for metadata-1.1/results, path
> /<<PKGBUILDDIR>>/.gradle/caches/transforms-1/metadata-1.1/results.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@b555180
> Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle'
> using BuildScriptTransformer.
> Compiling settings file '/<<PKGBUILDDIR>>/settings.gradle' using
> SubsetScriptTransformer.
> Compiling settings file '/<<PKGBUILDDIR>>/settings.gradle' using
> BuildScriptTransformer.
> Settings evaluated using settings file '/<<PKGBUILDDIR>>/settings.gradle'.
> Projects loaded. Root project using build file
> '/<<PKGBUILDDIR>>/build.gradle'.
> Included projects: [root project 'capsule-maven']
> Keep-alive timer started
> Adding Debian repository to project 'capsule-maven'
> Parallel execution is an incubating feature.
> Evaluating root project 'capsule-maven' using build file
> '/<<PKGBUILDDIR>>/build.gradle'.
> Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using
> SubsetScriptTransformer.
> Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using
> BuildScriptTransformer.
> Adding Maven pom generation to project 'capsule-maven'
> Linking the generated javadoc to the system JDK API documentation
> All projects evaluated.
> Selected primary task 'jar' from project :
> Creating new cache for annotation-processors, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/fileContent/annotation-processors.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@6f83f3b4
> Tasks to be executed: [task ':compileJava', task ':processResources', task
> ':classes', task ':debianMavenPom', task ':jar']
> Creating new cache for resourceHashesCache, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@ed388aa
> Creating new cache for taskHistory, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@641d275f
> Creating new cache for outputFiles, path
> /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@63a30ae1
> :compileJava (Thread[Task worker for ':' Thread 5,5,main]) started.
> :compileJava
> Putting task artifact state for task ':compileJava' into context took 0.005
> secs.
> Creating new cache for metadata-2.36/module-metadata, path
> /<<PKGBUILDDIR>>/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin,
> access org.gradle.cache.internal.DefaultCacheAccess@448d0d4a
> Loading the Maven rules...
> Replacing io.nextflow:capsule:jar:1.0.3.1 ->
> io.nextflow:capsule:jar:debian
> Ignoring org.eclipse.aether:aether-api:jar:1.1.0
> Ignoring org.eclipse.aether:aether-util:jar:1.1.0
> Ignoring org.eclipse.aether:aether-impl:jar:1.1.0
> Replacing org.eclipse.aether:aether-connector-basic:jar:1.1.0 ->
> org.apache.maven.resolver:maven-resolver-connector-basic:jar:debian
> Passing through org.apache.maven.resolver:maven-resolver:jar:debian
> Replacing org.eclipse.aether:aether-transport-file:jar:1.1.0 ->
> org.apache.maven.resolver:maven-resolver-transport-file:jar:debian
> Replacing org.eclipse.aether:aether-transport-http:jar:1.1.0 ->
> org.apache.maven.resolver:maven-resolver-transport-http:jar:debian
> Replacing org.apache.maven:maven-aether-provider:jar:3.3.9 ->
> org.apache.maven:maven-aether-provider:jar:3.x
> org.apache.maven:maven-aether-provider:3.x is relocated to
> org.apache.maven:maven-resolver-provider:3.x. Please update your dependencies.
> Replacing org.apache.maven:maven-model:jar:3.3.9 ->
> org.apache.maven:maven-model:jar:3.x
> Passing through org.apache.maven:maven:jar:3.x
> Passing through org.apache.maven:maven-parent:jar:debian
> Passing through org.apache:apache:jar:debian
> Replacing org.apache.maven:maven-settings-builder:jar:3.3.9 ->
> org.apache.maven:maven-settings-builder:jar:3.x
> Replacing org.codehaus.plexus:plexus-container-default:jar:1.6 ->
> org.codehaus.plexus:plexus-container-default:jar:debian
> Passing through org.codehaus.plexus:plexus-containers:jar:debian
> Ignoring io.takari.aether:takari-local-repository:jar:0.11.2
> Ignoring io.takari:takari-filemanager:jar:0.8.3
> Passing through org.apache.maven.resolver:maven-resolver-api:jar:debian
> Passing through org.apache.maven.resolver:maven-resolver-spi:jar:debian
> Passing through org.apache.maven.resolver:maven-resolver-util:jar:debian
> Passing through org.slf4j:slf4j-api:jar:debian
> Passing through org.slf4j:slf4j-parent:jar:debian
> Passing through org.apache.httpcomponents:httpclient:jar:debian
> Passing through
> org.apache.httpcomponents:httpcomponents-client:jar:debian
> Passing through org.apache.httpcomponents:httpcore:jar:debian
> Passing through org.apache.httpcomponents:httpcomponents-core:jar:debian
> Passing through org.slf4j:jcl-over-slf4j:jar:debian
> Passing through org.apache.maven:maven-resolver-provider:jar:3.x
> Passing through org.codehaus.plexus:plexus-utils:jar:2.x
> Passing through org.apache.maven:maven-builder-support:jar:3.x
> Passing through javax.inject:javax.inject:jar:debian
> Passing through org.codehaus.plexus:plexus-interpolation:jar:debian
> Passing through org.apache.maven:maven-settings:jar:3.x
> Passing through org.sonatype.plexus:plexus-sec-dispatcher:jar:debian
> org.sonatype.plexus:plexus-sec-dispatcher:debian is relocated to
> org.codehaus.plexus:plexus-sec-dispatcher:debian. Please update your
> dependencies.
> Passing through org.codehaus.plexus:plexus-classworlds:jar:debian
> Passing through org.apache.xbean:xbean-reflect:jar:debian
> Passing through commons-codec:commons-codec:jar:debian
> Passing through org.apache.commons:commons-parent:jar:debian
> Passing through org.apache.maven:maven-model-builder:jar:3.x
> Passing through org.apache.maven:maven-repository-metadata:jar:3.x
> Passing through org.apache.maven.resolver:maven-resolver-impl:jar:debian
> Passing through org.codehaus.plexus:plexus-sec-dispatcher:jar:debian
> Passing through org.apache.maven:maven-artifact:jar:3.x
> Passing through org.apache.commons:commons-lang3:jar:debian
> Passing through org.codehaus.plexus:plexus-cipher:jar:debian
> Up-to-date check for task ':compileJava' took 1.15 secs. It is not up-to-date
> because:
> No history is available.
> All input files are considered out-of-date for incremental task
> ':compileJava'.
> Compiling with JDK Java compiler API.
> /<<PKGBUILDDIR>>/src/main/java/capsule/UserSettings.java:183: error:
> exception PlexusCipherException is never thrown in body of corresponding try
> statement
> } catch (PlexusCipherException e) {
> ^
> 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.
> 1 error
> :compileJava FAILED
> :compileJava (Thread[Task worker for ':' Thread 5,5,main]) completed. Took
> 2.121 secs.
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Execution failed for task ':compileJava'.
> > Compilation failed; see the compiler error output for details.
>
> * Try:
> Run with --debug option to get more log output. Run with --scan to get full
> insights.
>
> * Exception is:
> org.gradle.api.tasks.TaskExecutionException: Execution failed for task
> ':compileJava'.
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
> at
> org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51)
> at
> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:62)
> at
> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
> at
> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
> at
> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
> at
> org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
> at
> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
> at
> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
> 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$1.run(DefaultTaskGraphExecuter.java:248)
> at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$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:241)
> at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
> at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$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$1.execute(DefaultTaskPlanExecutor.java:98)
> at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
> at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
> at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
> at
> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
> at
> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
> at
> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
> Caused by: org.gradle.api.internal.tasks.compile.CompilationFailedException:
> Compilation failed; see the compiler error output for details.
> at
> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:50)
> at
> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:35)
> at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:98)
> at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:51)
> at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37)
> at
> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
> at
> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
> at
> org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:207)
> at
> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:192)
> at
> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:124)
> 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 org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
> at
> org.gradle.api.internal.project.taskfactory.IncrementalTaskAction.doExecute(IncrementalTaskAction.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.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121)
> at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$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:110)
> at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
> ... 29 more
>
>
> * Get more help at https://help.gradle.org
>
> BUILD FAILED in 6s
> 1 actionable task: 1 executed
> dh_auto_build: error: gradle --info --console plain --offline --stacktrace
> --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=.
> -Duser.name=debian -Ddebian.package=capsule-maven-nextflow
> -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar returned exit code 1
> make: *** [debian/rules:4: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2022/05/25/capsule-maven-nextflow_1.0.3.1+dfsg-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220525;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220525&[email protected]&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: capsule-maven-nextflow
Source-Version: 1.0.3.1+dfsg-4
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
capsule-maven-nextflow, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated capsule-maven-nextflow
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 26 May 2022 15:20:05 +0200
Source: capsule-maven-nextflow
Architecture: source
Version: 1.0.3.1+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1011731
Changes:
capsule-maven-nextflow (1.0.3.1+dfsg-4) unstable; urgency=medium
.
* Fixing FTBFS due to trying to catch an Exception that is not thrown
anymore (Closes: #1011731)
* Raising Standards version to 4.6.1 (no change)
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