[Debian-med-packaging] Bug#1013577: picard-tools: FTBFS: PicardHelpDocWorkUnitHandler.java:6: error: cannot find symbol
Lucas Nussbaum
lucas at debian.org
Fri Jun 24 11:02:27 BST 2022
Source: picard-tools
Version: 2.27.1+dfsg-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220624 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> blhc: ignore-line-regexp: .*gradle.*ScriptTransformer.*
> dh_auto_build -- jar javadoc
> 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=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar javadoc
> 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 -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 0.8 secs.
> The client will now receive all logging from the daemon (pid: 2743140). The daemon log file: /<<PKGBUILDDIR>>/.gradle/daemon/4.4.1/daemon-2743140.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 at 5d50d694
> Creating new cache for resourceHashesCache, path /<<PKGBUILDDIR>>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at 5d50d694
> Creating new cache for fileHashes, path /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess at 77506432
> 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 at 647a5d82
> 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 'picard']
> Keep-alive timer started
> Adding Debian repository to project 'picard'
> Parallel execution is an incubating feature.
> Evaluating root project 'picard' 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''
> build for version:2.27.1
> 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 at 54b0c013
> Loading the Maven rules...
> Replacing com.intel.gkl:gkl:jar:0.8.8 -> com.intel.gkl:gkl:jar:debian
> Replacing com.google.guava:guava:jar:15.0 -> com.google.guava:guava:jar:debian
> Passing through com.google.guava:guava-parent:jar:debian
> Passing through 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-math3:jar:3.5 -> org.apache.commons:commons-math3:jar:debian
> Replacing org.apache.commons:commons-collections4:jar:4.3 -> org.apache.commons:commons-collections4:jar:debian
> Replacing commons-lang:commons-lang:jar:2.6 -> commons-lang:commons-lang:jar:debian
> Replacing com.github.samtools:htsjdk:jar:2.24.1 -> com.github.samtools:htsjdk:jar:debian
> Replacing org.broadinstitute:barclay:jar:4.0.2 -> org.broadinstitute:barclay:jar:debian
> Replacing org.apache.logging.log4j:log4j-api:jar:2.17.1 -> org.apache.logging.log4j:log4j-api:jar:debian
> Passing through org.apache.logging.log4j:log4j:jar:debian
> Replacing org.apache.logging.log4j:log4j-core:jar:2.17.1 -> org.apache.logging.log4j:log4j-core:jar:debian
> Passing through org.apache.commons:commons-lang3:jar:debian
> Passing through org.broadinstitute:gatk-native-bindings:jar:debian
> Passing through org.jsr-305:jsr305:jar:0.x
> Passing through org.apache.commons:commons-jexl:jar:debian
> Passing through commons-logging:commons-logging: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 net.sf.jopt-simple:jopt-simple:jar:debian
> Passing through com.google.code.gson:gson:jar:debian
> Passing through com.google.code.gson:gson-parent:jar:debian
> Passing through org.freemarker:freemarker:jar:debian
> Adding Maven pom generation to project 'picard'
> 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 at 7d1e404f
> Selected primary task 'javadoc' from project :
> Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc']
> Creating new cache for resourceHashesCache, path /<<PKGBUILDDIR>>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess at 77506432
> Creating new cache for taskHistory, path /<<PKGBUILDDIR>>/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess at 1cc3e9c
> Creating new cache for outputFiles, path /<<PKGBUILDDIR>>/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess at 3baad5c0
> :compileJava (Thread[Task worker for ':',5,main]) started.
> :compileJava
> Putting task artifact state for task ':compileJava' into context took 0.003 secs.
> Up-to-date check for task ':compileJava' took 2.058 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/picard/util/help/PicardHelpDocWorkUnitHandler.java:3: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal
> import com.sun.javadoc.FieldDoc;
> ^
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal
> import com.sun.javadoc.ClassDoc;
> ^
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal
> import com.sun.javadoc.RootDoc;
> ^
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:3: warning: [removal] FieldDoc in com.sun.javadoc has been deprecated and marked for removal
> import com.sun.javadoc.FieldDoc;
> ^
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:6: error: cannot find symbol
> import org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler;
> ^
> symbol: class DefaultDocWorkUnitHandler
> location: package org.broadinstitute.barclay.help
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:7: error: cannot find symbol
> import org.broadinstitute.barclay.help.DocWorkUnit;
> ^
> symbol: class DocWorkUnit
> location: package org.broadinstitute.barclay.help
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:9: error: cannot find symbol
> import org.broadinstitute.barclay.help.HelpDoclet;
> ^
> symbol: class HelpDoclet
> location: package org.broadinstitute.barclay.help
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:23: error: cannot find symbol
> public class PicardHelpDocWorkUnitHandler extends DefaultDocWorkUnitHandler {
> ^
> symbol: class DefaultDocWorkUnitHandler
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:36: error: cannot find symbol
> public PicardHelpDocWorkUnitHandler(final HelpDoclet doclet) {
> ^
> symbol: class HelpDoclet
> location: class PicardHelpDocWorkUnitHandler
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:53: error: cannot find symbol
> public String getTemplateName(final DocWorkUnit workUnit) {
> ^
> symbol: class DocWorkUnit
> location: class PicardHelpDocWorkUnitHandler
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDocWorkUnitHandler.java:69: error: cannot find symbol
> protected void addCustomBindings(final DocWorkUnit currentWorkUnit) {
> ^
> symbol: class DocWorkUnit
> location: class PicardHelpDocWorkUnitHandler
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal
> import com.sun.javadoc.ClassDoc;
> ^
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal
> import com.sun.javadoc.RootDoc;
> ^
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:8: error: cannot find symbol
> import org.broadinstitute.barclay.help.DocWorkUnit;
> ^
> symbol: class DocWorkUnit
> location: package org.broadinstitute.barclay.help
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:10: error: cannot find symbol
> import org.broadinstitute.barclay.help.HelpDoclet;
> ^
> symbol: class HelpDoclet
> location: package org.broadinstitute.barclay.help
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:23: error: cannot find symbol
> public class PicardHelpDoclet extends HelpDoclet {
> ^
> symbol: class HelpDoclet
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:56: error: cannot find symbol
> protected DocWorkUnit createWorkUnit(
> ^
> symbol: class DocWorkUnit
> location: class PicardHelpDoclet
> /<<PKGBUILDDIR>>/src/main/java/picard/util/help/PicardHelpDoclet.java:75: error: cannot find symbol
> protected final Map<String, String> getGroupMap(final DocWorkUnit docWorkUnit) {
> ^
> symbol: class DocWorkUnit
> location: class PicardHelpDoclet
> Note: /<<PKGBUILDDIR>>/src/main/java/picard/analysis/CollectOxoGMetrics.java uses or overrides a deprecated API.
> Note: Recompile with -Xlint:deprecation for details.
> 12 errors
> 6 warnings
> :compileJava FAILED
> :compileJava (Thread[Task worker for ':',5,main]) completed. Took 4.317 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 9s
> 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=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar javadoc returned exit code 1
> make[1]: *** [debian/rules:18: override_dh_auto_build] Error 25
The full build log is available from:
http://qa-logs.debian.net/2022/06/24/picard-tools_2.27.1+dfsg-1_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220624;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220624&fusertaguser=lucas@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 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.
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