Your message dated Mon, 30 Dec 2024 11:06:48 +0000
with message-id <e1tsdbk-0015ur...@fasolo.debian.org>
and subject line Bug#1091589: fixed in htsjdk 4.1.3+dfsg-2
has caused the Debian Bug report #1091589,
regarding gkl: FTBFS: Could not resolve org.sharegov:mjson:debian.
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 ow...@bugs.debian.org
immediately.)
--
1091589: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1091589
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: gkl
Version: 0.8.11+dfsg-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20241228 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # As we provide a Debian-made POM file, we have to update the version number
> # that is inside each time the upstream version changes. This is done
> # automatically with this tiny hack.
> sed 's/@VERSION@/0.8.11+dfsg/ ; s/\+dfsg[[:digit:]]*//' debian/pom-gkl.xml.in
> > debian/pom-gkl.xml
> dh_auto_configure
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> jh_linkjars -O--buildsystem=gradle
> Duplicate specification "unlink|u" for option "u"
> Duplicate specification "unlink|u" for option "u"
> 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=gkl -Dfile.encoding=UTF-8 --parallel
> --max-workers=8 jar
> openjdk version "21.0.6-ea" 2025-01-21
> OpenJDK Runtime Environment (build 21.0.6-ea+6-Debian-1)
> OpenJDK 64-Bit Server VM (build 21.0.6-ea+6-Debian-1, mixed mode, sharing)
> 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-21-openjdk-amd64/bin/java --add-opens
> java.base/java.lang=ALL-UNNAMED
> -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar
> -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 0.722 secs.
> The client will now receive all logging from the daemon (pid: 723481). The
> daemon log file: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1/daemon-723481.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@504de8ed
> Creating new cache for resourceHashesCache, path
> /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin,
> access org.gradle.cache.internal.DefaultCacheAccess@504de8ed
> Creating new cache for fileHashes, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@36d2d932
> 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@3fc0abfd
> Compiling initialization script '/<<PKGBUILDDIR>>/.gradle/init.d/init.gradle'
> using BuildScriptTransformer.
> Settings evaluated using settings file '/<<PKGBUILDDIR>>/settings.gradle'.
> Settings file not found (/<<PKGBUILDDIR>>/settings.gradle)
> Root project name not defined in settings.gradle, defaulting to 'gkl'
> instead of the name of the root directory 'gkl-0.8.11+dfsg'
> Projects loaded. Root project using build file
> '/<<PKGBUILDDIR>>/build.gradle'.
> Included projects: [root project 'gkl']
> Keep-alive timer started
> Adding Debian repository to project 'gkl'
> Parallel execution is an incubating feature.
> Evaluating root project 'gkl' using build file
> '/<<PKGBUILDDIR>>/build.gradle'.
> Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using
> SubsetScriptTransformer.
> Compiling build file '/<<PKGBUILDDIR>>/build.gradle' using
> BuildScriptTransformer.
> Starting process 'command 'dpkg-parsechangelog''. Working directory:
> /<<PKGBUILDDIR>> Command: dpkg-parsechangelog -S Version
> Successfully started process 'command 'dpkg-parsechangelog''
> Adding Maven pom generation to project 'gkl'
> 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@7087cc4
> Tasks to be executed: [task ':compileJava', task ':cmakeConfig', task
> ':cmakeBuild', task ':copyNativeLib', task ':processResources', task
> ':classes', task ':buildOnMac', task ':debianMavenPom', task ':jar']
> Creating new cache for resourceHashesCache, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@36d2d932
> Creating new cache for taskHistory, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@18f5fdd
> Creating new cache for outputFiles, path
> /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@5b57f45c
> :compileJava (Thread[#54,Task worker for ':' Thread 3,5,main]) started.
> :compileJava
> Putting task artifact state for task ':compileJava' into context took 0.004
> 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@1d553392
> Loading the Maven rules...
> Replacing commons-io:commons-io:jar:2.7 ->
> commons-io:commons-io:jar:debian
> Passing through org.apache.commons:commons-parent:jar:debian
> Passing through org.apache:apache:jar:debian
> Replacing org.broadinstitute:gatk-native-bindings:jar:1.0.0 ->
> org.broadinstitute:gatk-native-bindings:jar:debian
> Replacing commons-logging:commons-logging:jar:1.2 ->
> commons-logging:commons-logging:jar:debian
> Replacing com.github.samtools:htsjdk:jar:3.0.5 ->
> com.github.samtools:htsjdk:jar:debian
> Passing through org.apache.commons:commons-jexl:jar:debian
> Passing through org.xerial.snappy:snappy-java:jar:debian
> Passing through org.apache.commons:commons-compress:jar:debian
> Passing through org.tukaani:xz:jar:debian
> Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian
> Passing through org.sharegov:mjson:jar:debian
> Passing through commons-codec:commons-codec:jar:debian
> :compileJava FAILED
> :compileJava (Thread[#54,Task worker for ':' Thread 3,5,main]) completed.
> Took 0.273 secs.
> :cmakeConfig (Thread[#54,Task worker for ':' Thread 3,5,main]) started.
> :cmakeConfig
> Putting task artifact state for task ':cmakeConfig' into context took 0.0
> secs.
> Up-to-date check for task ':cmakeConfig' took 0.009 secs. It is not
> up-to-date because:
> No history is available.
> Starting process 'command 'cmake''. Working directory:
> /<<PKGBUILDDIR>>/build/native Command: cmake -Wno-dev /<<PKGBUILDDIR>>
> Successfully started process 'command 'cmake''
> :cmakeConfig (Thread[#54,Task worker for ':' Thread 3,5,main]) completed.
> Took 1.664 secs.
> :cmakeBuild (Thread[#54,Task worker for ':' Thread 3,5,main]) started.
> :cmakeBuild
> Putting task artifact state for task ':cmakeBuild' into context took 0.0 secs.
> Up-to-date check for task ':cmakeBuild' took 0.0 secs. It is not up-to-date
> because:
> Task has not declared any outputs.
> Starting process 'command 'make''. Working directory:
> /<<PKGBUILDDIR>>/build/native Command: make install
> Successfully started process 'command 'make''
> /<<PKGBUILDDIR>>/build/native/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/match.c:121:27:
> warning: ‘always_inline’ function might not be inlinable unless also
> declared ‘inline’ [-Wattributes]
> 121 | local zalways_inline uInt std2_longest_match(deflate_state *z_const
> s, IPos cur_match)
> | ^~~~~~~~~~~~~~~~~~
> configure.ac:53: warning: The macro 'AC_PROG_CC_STDC' is obsolete.
> configure.ac:53: You should run autoupdate.
> ./lib/autoconf/c.m4:1669: AC_PROG_CC_STDC is expanded from...
> configure.ac:53: the top level
> configure.ac:54: warning: The macro 'AC_PROG_LD' is obsolete.
> configure.ac:54: You should run autoupdate.
> aclocal.m4:3375: AC_PROG_LD is expanded from...
> configure.ac:54: the top level
> configure.ac:73: warning: The macro 'AC_TRY_COMPILE' is obsolete.
> configure.ac:73: You should run autoupdate.
> ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from...
> configure.ac:73: the top level
> configure.ac:23: installing 'build-aux/compile'
> configure.ac:25: installing 'build-aux/config.guess'
> configure.ac:25: installing 'build-aux/config.sub'
> configure.ac:12: installing 'build-aux/install-sh'
> configure.ac:12: installing 'build-aux/missing'
> Makefile.am: installing 'build-aux/depcomp'
> parallel-tests: installing 'build-aux/test-driver'
> configure.ac:53: warning: The macro 'AC_PROG_CC_STDC' is obsolete.
> configure.ac:53: You should run autoupdate.
> ./lib/autoconf/c.m4:1669: AC_PROG_CC_STDC is expanded from...
> configure.ac:53: the top level
> configure.ac:54: warning: The macro 'AC_PROG_LD' is obsolete.
> configure.ac:54: You should run autoupdate.
> aclocal.m4:3375: AC_PROG_LD is expanded from...
> configure.ac:54: the top level
> configure.ac:73: warning: The macro 'AC_TRY_COMPILE' is obsolete.
> configure.ac:73: You should run autoupdate.
> ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from...
> configure.ac:73: the top level
> :cmakeBuild (Thread[#54,Task worker for ':' Thread 3,5,main]) completed. Took
> 1 mins 14.972 secs.
> :copyNativeLib (Thread[#54,Task worker for ':' Thread 3,5,main]) started.
> :copyNativeLib
> Putting task artifact state for task ':copyNativeLib' into context took 0.0
> secs.
> Up-to-date check for task ':copyNativeLib' took 0.015 secs. It is not
> up-to-date because:
> No history is available.
> :copyNativeLib (Thread[#54,Task worker for ':' Thread 3,5,main]) completed.
> Took 0.044 secs.
> :buildOnMac (Thread[#54,Task worker for ':' Thread 3,5,main]) started.
> :buildOnMac
> Skipping task ':buildOnMac' as task onlyIf is false.
> :buildOnMac SKIPPED
> :buildOnMac (Thread[#54,Task worker for ':' Thread 3,5,main]) completed. Took
> 0.005 secs.
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Could not resolve all files for configuration ':compileClasspath'.
> > Could not resolve org.sharegov:mjson:debian.
> Required by:
> project : > com.github.samtools:htsjdk:debian
> > No cached version of org.sharegov:mjson:debian available for offline
> mode.
> > No cached version of org.sharegov:mjson:debian available for offline
> mode.
>
> * Try:
> Run with --debug option to get more log output. Run with --scan to get full
> insights.
>
> * Exception is:
> org.gradle.api.internal.artifacts.ivyservice.DefaultLenientConfiguration$ArtifactResolveException:
> Could not resolve all files for configuration ':compileClasspath'.
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.rethrowFailure(DefaultConfiguration.java:918)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.access$1600(DefaultConfiguration.java:116)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$ConfigurationFileCollection.getFiles(DefaultConfiguration.java:892)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.getFiles(DefaultConfiguration.java:404)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration_Decorated.getFiles(Unknown
> Source)
> at
> org.gradle.api.internal.file.AbstractFileCollection.iterator(AbstractFileCollection.java:68)
> at
> org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:70)
> at
> org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234)
> at
> org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185)
> at
> org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53)
> at
> org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38)
> at
> org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331)
> at
> org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154)
> at
> org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61)
> at
> org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114)
> at
> org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201)
> at
> org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86)
> at
> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53)
> at
> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
> at
> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
> at
> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
> at
> org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
> at
> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
> at
> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
> at
> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
> at
> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
> at
> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
> at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$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.internal.resolve.ModuleVersionResolveException: Could
> not resolve org.sharegov:mjson:debian.
> Required by:
> project : > com.github.samtools:htsjdk:debian
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.resolveModule(RepositoryChainComponentMetaDataResolver.java:103)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.resolve(RepositoryChainComponentMetaDataResolver.java:63)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.ComponentResolversChain$ComponentMetaDataResolverChain.resolve(ComponentResolversChain.java:93)
> at
> org.gradle.api.internal.artifacts.ivyservice.clientmodule.ClientModuleResolver.resolve(ClientModuleResolver.java:48)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.ComponentState.resolve(ComponentState.java:157)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.ComponentState.getMetaData(ComponentState.java:168)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.EdgeState.calculateTargetConfigurations(EdgeState.java:134)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.EdgeState.attachToTargetConfigurations(EdgeState.java:105)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.DependencyGraphBuilder.attachToTargetRevisionsSerially(DependencyGraphBuilder.java:239)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.DependencyGraphBuilder.resolveEdges(DependencyGraphBuilder.java:229)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.DependencyGraphBuilder.traverseGraph(DependencyGraphBuilder.java:143)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.builder.DependencyGraphBuilder.resolve(DependencyGraphBuilder.java:109)
> at
> org.gradle.api.internal.artifacts.ivyservice.resolveengine.DefaultArtifactDependencyResolver.resolve(DefaultArtifactDependencyResolver.java:90)
> at
> org.gradle.api.internal.artifacts.ivyservice.DefaultConfigurationResolver.resolveGraph(DefaultConfigurationResolver.java:146)
> at
> org.gradle.api.internal.artifacts.ivyservice.ShortCircuitEmptyConfigurationResolver.resolveGraph(ShortCircuitEmptyConfigurationResolver.java:73)
> at
> org.gradle.api.internal.artifacts.ivyservice.ErrorHandlingConfigurationResolver.resolveGraph(ErrorHandlingConfigurationResolver.java:66)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$4.run(DefaultConfiguration.java:483)
> at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$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.artifacts.configurations.DefaultConfiguration.resolveGraphIfRequired(DefaultConfiguration.java:474)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.resolveToStateOrLater(DefaultConfiguration.java:459)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.access$1700(DefaultConfiguration.java:116)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$ConfigurationFileCollection.getSelectedArtifacts(DefaultConfiguration.java:901)
> at
> org.gradle.api.internal.artifacts.configurations.DefaultConfiguration$ConfigurationFileCollection.getFiles(DefaultConfiguration.java:889)
> ... 41 more
> Caused by: org.gradle.internal.resolve.ModuleVersionResolveException: No
> cached version of org.sharegov:mjson:debian available for offline mode.
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.StartParameterResolutionOverride$FailedRemoteAccess.resolveComponentMetaData(StartParameterResolutionOverride.java:129)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.CachingModuleComponentRepository$ResolveAndCacheRepositoryAccess.resolveComponentMetaData(CachingModuleComponentRepository.java:363)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.BaseModuleComponentRepositoryAccess.resolveComponentMetaData(BaseModuleComponentRepositoryAccess.java:50)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.memcache.InMemoryCachedModuleComponentRepository$CachedAccess.resolveComponentMetaData(InMemoryCachedModuleComponentRepository.java:95)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.ErrorHandlingModuleComponentRepository$ErrorHandlingModuleComponentRepositoryAccess.resolveComponentMetaData(ErrorHandlingModuleComponentRepository.java:126)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.ComponentMetaDataResolveState.process(ComponentMetaDataResolveState.java:66)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.ComponentMetaDataResolveState.resolve(ComponentMetaDataResolveState.java:58)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:138)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.findBestMatch(RepositoryChainComponentMetaDataResolver.java:119)
> at
> org.gradle.api.internal.artifacts.ivyservice.ivyresolve.RepositoryChainComponentMetaDataResolver.resolveModule(RepositoryChainComponentMetaDataResolver.java:92)
> ... 66 more
>
>
> * Get more help at https://help.gradle.org
>
> BUILD FAILED in 1m 21s
> 4 actionable tasks: 4 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=gkl -Dfile.encoding=UTF-8 --parallel
> --max-workers=8 jar returned exit code 1
> make: *** [debian/rules:11: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2024/12/28/gkl_0.8.11+dfsg-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20241228;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241228&fusertaguser=lu...@debian.org&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 mark 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: htsjdk
Source-Version: 4.1.3+dfsg-2
Done: Pierre Gruet <p...@debian.org>
We believe that the bug you reported is fixed in the latest version of
htsjdk, 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 1091...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <p...@debian.org> (supplier of updated htsjdk 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 30 Dec 2024 10:33:32 +0100
Source: htsjdk
Architecture: source
Version: 4.1.3+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <p...@debian.org>
Closes: 1091589
Changes:
htsjdk (4.1.3+dfsg-2) unstable; urgency=medium
.
* Updating the classpath of the built jar
* Updating the installed POM file (Closes: #1091589)
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htsjdk_4.1.3+dfsg-2.debian.tar.xz
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htsjdk_4.1.3+dfsg-2.debian.tar.xz
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htsjdk_4.1.3+dfsg-2_amd64.buildinfo
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