Your message dated Mon, 30 Dec 2024 11:06:48 +0000
with message-id <[email protected]>
and subject line Bug#1091589: fixed in htsjdk 4.1.3+dfsg-2
has caused the Debian Bug report #1091589,
regarding igv: 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 [email protected]
immediately.)
--
1091589: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1091589
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: igv
Version: 2.18.5+dfsg-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
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>>'
> cp debian/log4j.xml src/main/resources/
> # Converting my home-made svg icons into png ones
> cd debian/icons && \
> inkscape -o Home24.png Home24.svg && \
> inkscape -o Refresh24.png Refresh24.svg && \
> inkscape -o Stop16.png Stop16.svg && \
> inkscape -o ZoomIn24.png ZoomIn24.svg && \
> inkscape -o ZoomOut24.png ZoomOut24.svg && \
> mkdir ../../src/main/resources-icons && \
> mv *.png ../../src/main/resources-icons/
>
> ** (process:942754): WARNING **: 10:11:40.965: Unable to create profile
> directory (Permission denied) (13)
> ** Message: 10:11:40.974: Cannot create profile directory
> /sbuild-nonexistent/.config/inkscape.
> ** Message: 10:11:40.974: Inkscape will run with default settings, and new
> settings will not be saved.
> Fontconfig error: No writable cache directories
> Fontconfig error: No writable cache directories
>
> ** (inkscape:942754): WARNING **: 10:11:41.107: Could not create directory
> '/sbuild-nonexistent/.config/inkscape'
>
> ** (inkscape:942754): WARNING **: 10:11:41.107: Could not create extension
> error log file '/sbuild-nonexistent/.config/inkscape/extension-errors.log'
>
> (inkscape:942754): Gtk-CRITICAL **: 10:11:41.141: Unable to create user data
> directory '/sbuild-nonexistent/.local/share' for storing the recently used
> files list: Permission denied
>
> ** (inkscape:942754): WARNING **: 10:11:41.141: Failed to wrap object of type
> 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a
> library init() function.
>
> ** (process:942761): WARNING **: 10:11:41.225: Unable to create profile
> directory (Permission denied) (13)
> ** Message: 10:11:41.234: Cannot create profile directory
> /sbuild-nonexistent/.config/inkscape.
> ** Message: 10:11:41.234: Inkscape will run with default settings, and new
> settings will not be saved.
> Fontconfig error: No writable cache directories
> Fontconfig error: No writable cache directories
>
> ** (inkscape:942761): WARNING **: 10:11:41.366: Could not create directory
> '/sbuild-nonexistent/.config/inkscape'
>
> ** (inkscape:942761): WARNING **: 10:11:41.366: Could not create extension
> error log file '/sbuild-nonexistent/.config/inkscape/extension-errors.log'
>
> (inkscape:942761): Gtk-CRITICAL **: 10:11:41.400: Unable to create user data
> directory '/sbuild-nonexistent/.local/share' for storing the recently used
> files list: Permission denied
>
> ** (inkscape:942761): WARNING **: 10:11:41.400: Failed to wrap object of type
> 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a
> library init() function.
>
> ** (process:942768): WARNING **: 10:11:41.486: Unable to create profile
> directory (Permission denied) (13)
> ** Message: 10:11:41.494: Cannot create profile directory
> /sbuild-nonexistent/.config/inkscape.
> ** Message: 10:11:41.494: Inkscape will run with default settings, and new
> settings will not be saved.
> Fontconfig error: No writable cache directories
> Fontconfig error: No writable cache directories
>
> ** (inkscape:942768): WARNING **: 10:11:41.624: Could not create directory
> '/sbuild-nonexistent/.config/inkscape'
>
> ** (inkscape:942768): WARNING **: 10:11:41.624: Could not create extension
> error log file '/sbuild-nonexistent/.config/inkscape/extension-errors.log'
>
> (inkscape:942768): Gtk-CRITICAL **: 10:11:41.657: Unable to create user data
> directory '/sbuild-nonexistent/.local/share' for storing the recently used
> files list: Permission denied
>
> ** (inkscape:942768): WARNING **: 10:11:41.657: Failed to wrap object of type
> 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a
> library init() function.
>
> ** (process:942775): WARNING **: 10:11:41.741: Unable to create profile
> directory (Permission denied) (13)
> ** Message: 10:11:41.749: Cannot create profile directory
> /sbuild-nonexistent/.config/inkscape.
> ** Message: 10:11:41.749: Inkscape will run with default settings, and new
> settings will not be saved.
> Fontconfig error: No writable cache directories
> Fontconfig error: No writable cache directories
>
> ** (inkscape:942775): WARNING **: 10:11:41.887: Could not create directory
> '/sbuild-nonexistent/.config/inkscape'
>
> ** (inkscape:942775): WARNING **: 10:11:41.887: Could not create extension
> error log file '/sbuild-nonexistent/.config/inkscape/extension-errors.log'
>
> (inkscape:942775): Gtk-CRITICAL **: 10:11:41.921: Unable to create user data
> directory '/sbuild-nonexistent/.local/share' for storing the recently used
> files list: Permission denied
>
> ** (inkscape:942775): WARNING **: 10:11:41.922: Failed to wrap object of type
> 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a
> library init() function.
>
> ** (process:942782): WARNING **: 10:11:42.007: Unable to create profile
> directory (Permission denied) (13)
> ** Message: 10:11:42.015: Cannot create profile directory
> /sbuild-nonexistent/.config/inkscape.
> ** Message: 10:11:42.015: Inkscape will run with default settings, and new
> settings will not be saved.
> Fontconfig error: No writable cache directories
> Fontconfig error: No writable cache directories
>
> ** (inkscape:942782): WARNING **: 10:11:42.148: Could not create directory
> '/sbuild-nonexistent/.config/inkscape'
>
> ** (inkscape:942782): WARNING **: 10:11:42.148: Could not create extension
> error log file '/sbuild-nonexistent/.config/inkscape/extension-errors.log'
>
> (inkscape:942782): Gtk-CRITICAL **: 10:11:42.181: Unable to create user data
> directory '/sbuild-nonexistent/.local/share' for storing the recently used
> files list: Permission denied
>
> ** (inkscape:942782): WARNING **: 10:11:42.181: Failed to wrap object of type
> 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a
> library init() function.
> 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=igv -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 0.971 secs.
> The client will now receive all logging from the daemon (pid: 942897). The
> daemon log file: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1/daemon-942897.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@609b8c73
> Creating new cache for resourceHashesCache, path
> /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin,
> access org.gradle.cache.internal.DefaultCacheAccess@609b8c73
> Creating new cache for fileHashes, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@156a3fce
> 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@526e68bf
> 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 'igv']
> Keep-alive timer started
> Adding Debian repository to project 'igv'
> Parallel execution is an incubating feature.
> Evaluating root project 'igv' 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 'igv'
> 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@254af9f6
> 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@156a3fce
> Creating new cache for taskHistory, path
> /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@1db85863
> Creating new cache for outputFiles, path
> /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access
> org.gradle.cache.internal.DefaultCacheAccess@1fd28a8e
> :compileJava (Thread[#49,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@1902d242
> Loading the Maven rules...
> Replacing com.google.code.gson:gson:jar:2.8.9 ->
> com.google.code.gson:gson:jar:debian
> Passing through com.google.code.gson:gson-parent:jar:debian
> Replacing org.apache.commons:commons-math3:jar:3.6.1 ->
> org.apache.commons:commons-math3:jar:debian
> 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.apache.commons:commons-compress:jar:1.26.0 ->
> org.apache.commons:commons-compress:jar:debian
> Replacing org.apache.commons:commons-jexl:jar:2.1.1 ->
> org.apache.commons:commons-jexl:jar:debian
> Replacing org.apache.commons:commons-lang3:jar:3.9 ->
> org.apache.commons:commons-lang3:jar:debian
> Replacing com.github.samtools:htsjdk:jar:4.1.2 ->
> com.github.samtools:htsjdk:jar:debian
> Replacing org.swinglabs:swing-layout:jar:1.0.3 ->
> org.swinglabs:swing-layout:jar:debian
> Replacing com.formdev:jide-oss:jar:3.7.12 ->
> com.jidesoft:jide-oss:jar:debian
> Replacing com.google.guava:guava:jar:32.1.3-jre ->
> com.google.guava:guava:jar:debian
> Passing through com.google.guava:guava-parent:jar:debian
> Replacing org.apache.xmlgraphics:batik-dom:jar:1.17 ->
> org.apache.xmlgraphics:batik-dom:jar:debian
> Passing through org.apache.xmlgraphics:batik:jar:debian
> Replacing org.apache.xmlgraphics:batik-svggen:jar:1.17 ->
> org.apache.xmlgraphics:batik-svggen:jar:debian
> Replacing org.apache.xmlgraphics:batik-codec:jar:1.17 ->
> org.apache.xmlgraphics:batik-codec:jar:debian
> Replacing org.netbeans.external:AbsoluteLayout:jar:RELEASE110 ->
> org.netbeans.external:AbsoluteLayout:jar:debian
> Ignoring software.amazon.awssdk:cognitoidentity:jar:2.27.4
> Ignoring software.amazon.awssdk:sts:jar:2.27.4
> Ignoring software.amazon.awssdk:s3:jar:2.27.4
> Ignoring software.amazon.awssdk:sso:jar:2.27.4
> Passing through commons-codec:commons-codec:jar:debian
> Passing through commons-logging:commons-logging:jar:debian
> Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian
> Passing through org.sharegov:mjson:jar:debian
> Passing through org.jsr-305:jsr305:jar:0.x
> Passing through org.apache.xmlgraphics:batik-ext:jar:debian
> Passing through org.apache.xmlgraphics:batik-shared-resources:jar:debian
> Passing through org.apache.xmlgraphics:batik-util:jar:debian
> Passing through org.apache.xmlgraphics:batik-xml:jar:debian
> Passing through org.apache.xmlgraphics:batik-awt-util:jar:debian
> Passing through org.apache.xmlgraphics:batik-transcoder:jar:debian
> Passing through org.apache.xmlgraphics:batik-constants:jar:debian
> Passing through org.apache.xmlgraphics:batik-i18n:jar:debian
> Passing through org.apache.xmlgraphics:xmlgraphics-commons:jar:debian
> :compileJava FAILED
> :compileJava (Thread[#49,Task worker for ':' Thread 3,5,main]) completed.
> Took 0.504 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.
>
> * 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 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=igv -Dfile.encoding=UTF-8 --parallel
> --max-workers=8 jar returned exit code 1
> make: *** [debian/rules:9: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2024/12/28/igv_2.18.5+dfsg-1_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20241228;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241228&[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 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 <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (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 [email protected])
-----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
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
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)
Checksums-Sha1:
3853e3d7529f8e3f3c7635aa1a9c30a3d5d2eaae 2648 htsjdk_4.1.3+dfsg-2.dsc
4218a8a24269cd52264460ecc62adee7cbe1603c 38280
htsjdk_4.1.3+dfsg-2.debian.tar.xz
079f21c24e878d3dd026987090ffcb70d261f29f 18859
htsjdk_4.1.3+dfsg-2_amd64.buildinfo
Checksums-Sha256:
a1c04709c8a2663d8d70b2be1c31840cc93e9e03929571f39d74e185d10f0304 2648
htsjdk_4.1.3+dfsg-2.dsc
0a6e889ee91d24b3e9d2a4b35d03b67f7cf667cd84cc25c08d6e1fa06b158b74 38280
htsjdk_4.1.3+dfsg-2.debian.tar.xz
7d2c2846c01e8cfeab20599f40ed182d4ef1c5553339df87bcebe3bc3e4b52af 18859
htsjdk_4.1.3+dfsg-2_amd64.buildinfo
Files:
7fe59a07a2258f31dfe864ff68584dca 2648 science optional htsjdk_4.1.3+dfsg-2.dsc
d4560ab16fc82bf09b30ad5dce1b565c 38280 science optional
htsjdk_4.1.3+dfsg-2.debian.tar.xz
5ad78d62bd1b966b2905e8cda8e5d294 18859 science optional
htsjdk_4.1.3+dfsg-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=IJED
-----END PGP SIGNATURE-----
pgp2zbS58tqHg.pgp
Description: PGP signature
--- End Message ---
