java.lang.StringIndexOutOfBoundsException: String index out of range: 65

Atlassian JIRA | Sultan Maiyaki | 3 years ago
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  1. 0

    {code} [ChainExecutionManagerImpl] Exception during merge: String index out of range: 65 java.lang.StringIndexOutOfBoundsException: String index out of range: 65 at java.lang.String.<init>(String.java:211) at java.lang.StringBuilder.toString(StringBuilder.java:430) at com.atlassian.bamboo.plugins.git.GitCommandProcessor$LoggingOutputHandler.getStdout(GitCommandProcessor.java:623) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:493) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runMergeCommand(GitCommandProcessor.java:512) at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.merge(NativeGitOperationHelper.java:240) at com.atlassian.bamboo.plugins.git.GitRepository.mergeWorkspaceWith(GitRepository.java:520) at com.atlassian.bamboo.plan.branch.BranchIntegrationHelperImpl.merge(BranchIntegrationHelperImpl.java:114) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.doVcsMerge(ChainExecutionManagerImpl.java:951) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.access$1300(ChainExecutionManagerImpl.java:97) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl$5.run(ChainExecutionManagerImpl.java:601) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:321) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.execute(ChainExecutionManagerImpl.java:584) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.tryStartChainState(ChainExecutionManagerImpl.java:288) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.start(ChainExecutionManagerImpl.java:171) at sun.reflect.GeneratedMethodAccessor1133.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at com.sun.proxy.$Proxy101.start(Unknown Source) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:476) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:469) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.inlineProcessLocks(PlanExecutionLockServiceImpl.java:99) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithInlineProcessLock(PlanExecutionManagerImpl.java:680) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$400(PlanExecutionManagerImpl.java:123) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:468) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:449) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:81) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:725) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.startConditionalBuild(PlanExecutionManagerImpl.java:448) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:519) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:536) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:137) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:124) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) at com.atlassian.bamboo.build.pipeline.concurrent.NamedThreadFactory$2.run(NamedThreadFactory.java:55) at java.lang.Thread.run(Thread.java:680) : at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at com.sun.proxy.$Proxy101.start(Unknown Source) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:476) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:469) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.inlineProcessLocks(PlanExecutionLockServiceImpl.java:99) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithInlineProcessLock(PlanExecutionManagerImpl.java:680) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$400(PlanExecutionManagerImpl.java:123) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:468) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:449) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:81) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:725) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.startConditionalBuild(PlanExecutionManagerImpl.java:448) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:519) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:536) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:137) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:124) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) at com.atlassian.bamboo.build.pipeline.concurrent.NamedThreadFactory$2.run(NamedThreadFactory.java:55) at java.lang.Thread.run(Thread.java:680) {code} hypothesis: race condition between background process still wrtiting to stream and Bamboo trying to read stream

    Atlassian JIRA | 3 years ago | Sultan Maiyaki [Atlassian]
    java.lang.StringIndexOutOfBoundsException: String index out of range: 65
  2. 0

    {code} [ChainExecutionManagerImpl] Exception during merge: String index out of range: 65 java.lang.StringIndexOutOfBoundsException: String index out of range: 65 at java.lang.String.<init>(String.java:211) at java.lang.StringBuilder.toString(StringBuilder.java:430) at com.atlassian.bamboo.plugins.git.GitCommandProcessor$LoggingOutputHandler.getStdout(GitCommandProcessor.java:623) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:493) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runMergeCommand(GitCommandProcessor.java:512) at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.merge(NativeGitOperationHelper.java:240) at com.atlassian.bamboo.plugins.git.GitRepository.mergeWorkspaceWith(GitRepository.java:520) at com.atlassian.bamboo.plan.branch.BranchIntegrationHelperImpl.merge(BranchIntegrationHelperImpl.java:114) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.doVcsMerge(ChainExecutionManagerImpl.java:951) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.access$1300(ChainExecutionManagerImpl.java:97) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl$5.run(ChainExecutionManagerImpl.java:601) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:321) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.execute(ChainExecutionManagerImpl.java:584) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.tryStartChainState(ChainExecutionManagerImpl.java:288) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.start(ChainExecutionManagerImpl.java:171) at sun.reflect.GeneratedMethodAccessor1133.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at com.sun.proxy.$Proxy101.start(Unknown Source) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:476) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:469) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.inlineProcessLocks(PlanExecutionLockServiceImpl.java:99) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithInlineProcessLock(PlanExecutionManagerImpl.java:680) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$400(PlanExecutionManagerImpl.java:123) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:468) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:449) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:81) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:725) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.startConditionalBuild(PlanExecutionManagerImpl.java:448) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:519) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:536) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:137) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:124) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) at com.atlassian.bamboo.build.pipeline.concurrent.NamedThreadFactory$2.run(NamedThreadFactory.java:55) at java.lang.Thread.run(Thread.java:680) : at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at com.sun.proxy.$Proxy101.start(Unknown Source) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:476) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:469) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.inlineProcessLocks(PlanExecutionLockServiceImpl.java:99) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithInlineProcessLock(PlanExecutionManagerImpl.java:680) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$400(PlanExecutionManagerImpl.java:123) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:468) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:449) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:81) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:725) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.startConditionalBuild(PlanExecutionManagerImpl.java:448) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:519) at com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:536) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:137) at com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:124) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) at com.atlassian.bamboo.build.pipeline.concurrent.NamedThreadFactory$2.run(NamedThreadFactory.java:55) at java.lang.Thread.run(Thread.java:680) {code} hypothesis: race condition between background process still wrtiting to stream and Bamboo trying to read stream

    Atlassian JIRA | 3 years ago | Sultan Maiyaki
    java.lang.StringIndexOutOfBoundsException: String index out of range: 65
  3. 0

    h3. Summary Git Large File Storage (or LFS) is a new, open-source extension to Git that aims to improve handling of large files. Source code checkouts fail in Bamboo when linked to LFS-enabled repositories h3. Steps to Reproduce # Set up a repository with [Git LFS enabled|https://confluence.atlassian.com/display/BitbucketServer/Git+Large+File+Storage#GitLargeFileStorage-repolfsEnablingGitLFSforarepository] # Add file types for LFS to manage and include at least one file of that type in the repository # [Install git-lfs client extension|https://confluence.atlassian.com/display/BitbucketServer/Git+Large+File+Storage#GitLargeFileStorage-InstallingtheGitLFScommandlineclient] on Bamboo server # Link LFS-enabeld repository to build plan with a [source checkout task|https://confluence.atlassian.com/bamboo/checking-out-code-289277060.html] enabled h3. Expected Results Source checkout should complete successfully h3. Actual Results When Bamboo attempts to checkout repositories with git-lfs enabled, the checkout process fails with "Error accessing media" and "smudge filter lfs failed" errors. The following stack trace can be found in *<BAMBOO_INST>/logs/catalina.out*{noformat}2016-01-28 05:04:00,499 ERROR [13-BAM::Default Agent::Agent:pool-28-thread-1] [TaskExecutorImpl] Error occurred while running Task 'Checkout Default Repository(1)' of type com.atlassian.bamboo.plugins.vcs:task.vcs.checkout. java.lang.RuntimeException: com.atlassian.bamboo.repository.RepositoryException: MAV-MBT-JOB1-201: Checkout to revision 6681d2b8c3009b04ab49b949d31832cd03939ad6 has failed.command /usr/bin/git checkout -f master failed with code 128. Working directory was [/var/atlassian/application-data/bamboo_510/xml-data/build-dir/131073/MAV-MBT-JOB1]., stderr: Downloading test3.jpg (12.57 MB) Error accessing media: test3.jpg (24fda5852ed8527b134501db6877591edbefbadb6f4e05ba5c8c4c4c91f73f92) Errors logged to .git/lfs/objects/logs/20160128T050400.487728317.log Use `git lfs logs last` to view the log. error: external filter git-lfs smudge %f failed 2 error: external filter git-lfs smudge %f failed fatal: test3.jpg: smudge filter lfs failed at com.atlassian.bamboo.executor.RetryingTaskExecutor.rerun(RetryingTaskExecutor.java:144) at com.atlassian.bamboo.executor.RetryingTaskExecutor.runTask(RetryingTaskExecutor.java:88) at com.atlassian.bamboo.executor.RetryingTaskExecutor.retry(RetryingTaskExecutor.java:203) at com.atlassian.bamboo.executor.RetryingTaskExecutor.retry(RetryingTaskExecutor.java:188) at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask.execute(VcsCheckoutTask.java:145) at com.atlassian.bamboo.task.TaskExecutorImpl.lambda$executeTasks$121(TaskExecutorImpl.java:273) at com.atlassian.bamboo.task.TaskExecutorImpl.executeTaskWithPrePostActions(TaskExecutorImpl.java:202) at com.atlassian.bamboo.task.TaskExecutorImpl.executeTasks(TaskExecutorImpl.java:273) at com.atlassian.bamboo.task.TaskExecutorImpl.execute(TaskExecutorImpl.java:108) at com.atlassian.bamboo.build.pipeline.tasks.ExecuteBuildTask.call(ExecuteBuildTask.java:74) at com.atlassian.bamboo.v2.build.agent.DefaultBuildAgent.build(DefaultBuildAgent.java:214) at com.atlassian.bamboo.v2.build.agent.BuildAgentControllerImpl$1.call(BuildAgentControllerImpl.java:139) at com.atlassian.bamboo.v2.build.agent.BuildAgentControllerImpl$1.call(BuildAgentControllerImpl.java:130) at com.atlassian.bamboo.variable.CustomVariableContextImpl.withVariableSubstitutor(CustomVariableContextImpl.java:215) at com.atlassian.bamboo.v2.build.agent.BuildAgentControllerImpl.waitAndPerformBuild(BuildAgentControllerImpl.java:129) at com.atlassian.bamboo.v2.build.agent.DefaultBuildAgent$1.run(DefaultBuildAgent.java:136) at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:49) at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:31) at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:20) at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:52) at java.lang.Thread.run(Thread.java:745) Caused by: com.atlassian.bamboo.repository.RepositoryException: MAV-MBT-JOB1-201: Checkout to revision 6681d2b8c3009b04ab49b949d31832cd03939ad6 has failed.command /usr/bin/git checkout -f master failed with code 128. Working directory was [/var/atlassian/application-data/bamboo_510/xml-data/build-dir/131073/MAV-MBT-JOB1]., stderr: Downloading test3.jpg (12.57 MB) Error accessing media: test3.jpg (24fda5852ed8527b134501db6877591edbefbadb6f4e05ba5c8c4c4c91f73f92) Errors logged to .git/lfs/objects/logs/20160128T050400.487728317.log Use `git lfs logs last` to view the log. error: external filter git-lfs smudge %f failed 2 error: external filter git-lfs smudge %f failed fatal: test3.jpg: smudge filter lfs failed at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:368) at com.atlassian.bamboo.plugins.git.GitRepository$2.call(GitRepository.java:479) at com.atlassian.bamboo.plugins.git.GitRepository$2.call(GitRepository.java:446) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312) at com.atlassian.bamboo.plugins.git.GitRepository.retrieveSourceCode(GitRepository.java:445) at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask.fillWorkingDirFromVcs(VcsCheckoutTask.java:273) at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask.access$000(VcsCheckoutTask.java:57) at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask$1.call(VcsCheckoutTask.java:150) at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask$1.call(VcsCheckoutTask.java:146) at com.atlassian.bamboo.executor.RetryingTaskExecutor.rerun(RetryingTaskExecutor.java:108) ... 20 more Caused by: com.atlassian.bamboo.plugins.git.GitCommandException: command /usr/bin/git checkout -f master failed with code 128. Working directory was [/var/atlassian/application-data/bamboo_510/xml-data/build-dir/131073/MAV-MBT-JOB1]., stderr: Downloading test3.jpg (12.57 MB) Error accessing media: test3.jpg (24fda5852ed8527b134501db6877591edbefbadb6f4e05ba5c8c4c4c91f73f92) Errors logged to .git/lfs/objects/logs/20160128T050400.487728317.log Use `git lfs logs last` to view the log. error: external filter git-lfs smudge %f failed 2 error: external filter git-lfs smudge %f failed fatal: test3.jpg: smudge filter lfs failed at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:587) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:530) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCheckoutCommandForBranchOrRevision(GitCommandProcessor.java:337) at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCheckoutCommand(GitCommandProcessor.java:331) at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:352) ... 29 more{noformat} h3.Workaround In order to checkout git-lfs enabled repositories, the checkout must be performed manually via a scripted task. For example, the following script will perform a checkout for the current branch of your configured plan and can be used in place of the source code checkout task (please note this is a very basic example and your needs may require more customisation): {code}git init git remote add -t ${bamboo.planRepository.branchName} -f origin https://username:password@mygitrepo.org/scm/proj/myrepo.git git checkout -f ${bamboo.planRepository.branchName} {code}

    Atlassian JIRA | 1 year ago | Dave Chevell [Atlassian]
    test3.jpg: smudge filter lfs failed
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  5. 0

    When a plan uses a Git Repository that uses Git Submodules and that plan also has branches with Branch Merging enabled, it will never run the branch plan as Bamboo fails to check out the Submodule. It will remain stuck on 'Queued' for about 10 minutes, then fail, never reaching the Elastic Agent. Disabling Branch Merging will allow the branch plan to run successfully, this also shows that the elastic agent successfully checks out the Submodule (once an SSH key is [present on the agent|https://jira.atlassian.com/browse/BAM-11369]). The Bamboo log itself shows the following error {noformat} 2013-06-14 09:35:11,491 WARN [3-DelayedChangeDetectionThread:pool-6-thread-15] [ChainExecutionManagerImpl] Exception during merge: Checkout to revision 7cdf15301b67473812af4af83d44312ddcd34b06 has failed.command /usr/bin/git submodule update --init --recursive failed with code 1. Working directory was [/data/jirastudio/bamboo/home/xml-data/build-dir/serverSide/RHIN-SBM0-1/mergeWorkspace]., stderr: Submodule 'submodule' (git@bitbucket.org:user/submodule.git) registered for path 'submodule' Cloning into 'submodule'... ssh: connect to host bitbucket.org port 22: Connection timed out fatal: The remote end hung up unexpectedly Clone of 'git@bitbucket.org:user/submodule.git' into submodule path 'submodule' failed com.atlassian.bamboo.repository.RepositoryException: Checkout to revision 7cdf15301b67473812af4af83d44312ddcd34b06 has failed.command /usr/bin/git submodule update --init --recursive failed with code 1. Working directory was [/data/jirastudio/bamboo/home/xml-data/build-dir/serverSide/RHIN-SBM0-1/mergeWorkspace]., stderr: Submodule 'submodule' (git@bitbucket.org:user/submodule.git) registered for path 'submodule' Cloning into 'lock'... ssh: connect to host bitbucket.org port 22: Connection timed out fatal: The remote end hung up unexpectedly Clone of 'git@bitbucket.org:user/submodule.git' into submodule path 'submodule' failed at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:390) at com.atlassian.bamboo.plugins.git.GitRepository$3.call(GitRepository.java:338) at com.atlassian.bamboo.plugins.git.GitRepository$3.call(GitRepository.java:314) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:324) at com.atlassian.bamboo.plugins.git.GitRepository.retrieveSourceCode(GitRepository.java:313) at com.atlassian.bamboo.plugins.hg.BitbucketRepository.retrieveSourceCode(BitbucketRepository.java:296) at com.atlassian.bamboo.plan.branch.BranchIntegrationHelperImpl.merge(BranchIntegrationHelperImpl.java:112) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.doVcsMerge(ChainExecutionManagerImpl.java:911) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.access$700(ChainExecutionManagerImpl.java:93) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl$4.run(ChainExecutionManagerImpl.java:538) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:333) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.execute(ChainExecutionManagerImpl.java:522) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.tryStartChainState(ChainExecutionManagerImpl.java:287) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.delayedStart(ChainExecutionManagerImpl.java:189) {noformat} The Elastic Agent does not show any activity (because it is never invoked by Bamboo) *workaround* Disable 'Use Submodules' add a script task to the plan that performs {{git submodule init}} {{git submodule update}}

    Atlassian JIRA | 4 years ago | Ivan Maduro
    com.atlassian.bamboo.repository.RepositoryException: Checkout to revision 7cdf15301b67473812af4af83d44312ddcd34b06 has failed.command /usr/bin/git submodule update --init --recursive failed with code 1. Working directory was [/data/jirastudio/bamboo/home/xml-data/build-dir/serverSide/RHIN-SBM0-1/mergeWorkspace]., stderr: Submodule 'submodule' (git@bitbucket.org:user/submodule.git) registered for path 'submodule' Cloning into 'lock'... ssh: connect to host bitbucket.org port 22: Connection timed out fatal: The remote end hung up unexpectedly Clone of 'git@bitbucket.org:user/submodule.git' into submodule path 'submodule' failed
  6. 0

    When a plan uses a Git Repository that uses Git Submodules and that plan also has branches with Branch Merging enabled, it will never run the branch plan as Bamboo fails to check out the Submodule. It will remain stuck on 'Queued' for about 10 minutes, then fail, never reaching the Elastic Agent. Disabling Branch Merging will allow the branch plan to run successfully, this also shows that the elastic agent successfully checks out the Submodule (once an SSH key is [present on the agent|https://jira.atlassian.com/browse/BAM-11369]). The Bamboo log itself shows the following error {noformat} 2013-06-14 09:35:11,491 WARN [3-DelayedChangeDetectionThread:pool-6-thread-15] [ChainExecutionManagerImpl] Exception during merge: Checkout to revision 7cdf15301b67473812af4af83d44312ddcd34b06 has failed.command /usr/bin/git submodule update --init --recursive failed with code 1. Working directory was [/data/jirastudio/bamboo/home/xml-data/build-dir/serverSide/RHIN-SBM0-1/mergeWorkspace]., stderr: Submodule 'submodule' (git@bitbucket.org:user/submodule.git) registered for path 'submodule' Cloning into 'submodule'... ssh: connect to host bitbucket.org port 22: Connection timed out fatal: The remote end hung up unexpectedly Clone of 'git@bitbucket.org:user/submodule.git' into submodule path 'submodule' failed com.atlassian.bamboo.repository.RepositoryException: Checkout to revision 7cdf15301b67473812af4af83d44312ddcd34b06 has failed.command /usr/bin/git submodule update --init --recursive failed with code 1. Working directory was [/data/jirastudio/bamboo/home/xml-data/build-dir/serverSide/RHIN-SBM0-1/mergeWorkspace]., stderr: Submodule 'submodule' (git@bitbucket.org:user/submodule.git) registered for path 'submodule' Cloning into 'lock'... ssh: connect to host bitbucket.org port 22: Connection timed out fatal: The remote end hung up unexpectedly Clone of 'git@bitbucket.org:user/submodule.git' into submodule path 'submodule' failed at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:390) at com.atlassian.bamboo.plugins.git.GitRepository$3.call(GitRepository.java:338) at com.atlassian.bamboo.plugins.git.GitRepository$3.call(GitRepository.java:314) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:324) at com.atlassian.bamboo.plugins.git.GitRepository.retrieveSourceCode(GitRepository.java:313) at com.atlassian.bamboo.plugins.hg.BitbucketRepository.retrieveSourceCode(BitbucketRepository.java:296) at com.atlassian.bamboo.plan.branch.BranchIntegrationHelperImpl.merge(BranchIntegrationHelperImpl.java:112) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.doVcsMerge(ChainExecutionManagerImpl.java:911) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.access$700(ChainExecutionManagerImpl.java:93) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl$4.run(ChainExecutionManagerImpl.java:538) at com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:333) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.execute(ChainExecutionManagerImpl.java:522) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.tryStartChainState(ChainExecutionManagerImpl.java:287) at com.atlassian.bamboo.chains.ChainExecutionManagerImpl.delayedStart(ChainExecutionManagerImpl.java:189) {noformat} The Elastic Agent does not show any activity (because it is never invoked by Bamboo) *workaround* Disable 'Use Submodules' add a script task to the plan that performs {{git submodule init}} {{git submodule update}}

    Atlassian JIRA | 4 years ago | Ivan Maduro
    com.atlassian.bamboo.repository.RepositoryException: Checkout to revision 7cdf15301b67473812af4af83d44312ddcd34b06 has failed.command /usr/bin/git submodule update --init --recursive failed with code 1. Working directory was [/data/jirastudio/bamboo/home/xml-data/build-dir/serverSide/RHIN-SBM0-1/mergeWorkspace]., stderr: Submodule 'submodule' (git@bitbucket.org:user/submodule.git) registered for path 'submodule' Cloning into 'lock'... ssh: connect to host bitbucket.org port 22: Connection timed out fatal: The remote end hung up unexpectedly Clone of 'git@bitbucket.org:user/submodule.git' into submodule path 'submodule' failed

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    Root Cause Analysis

    1. java.lang.StringIndexOutOfBoundsException

      String index out of range: 65

      at java.lang.String.<init>()
    2. Java RT
      StringBuilder.toString
      1. java.lang.String.<init>(String.java:211)
      2. java.lang.StringBuilder.toString(StringBuilder.java:430)
      2 frames
    3. com.atlassian.bamboo
      ChainExecutionManagerImpl$5.run
      1. com.atlassian.bamboo.plugins.git.GitCommandProcessor$LoggingOutputHandler.getStdout(GitCommandProcessor.java:623)
      2. com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:493)
      3. com.atlassian.bamboo.plugins.git.GitCommandProcessor.runMergeCommand(GitCommandProcessor.java:512)
      4. com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.merge(NativeGitOperationHelper.java:240)
      5. com.atlassian.bamboo.plugins.git.GitRepository.mergeWorkspaceWith(GitRepository.java:520)
      6. com.atlassian.bamboo.plan.branch.BranchIntegrationHelperImpl.merge(BranchIntegrationHelperImpl.java:114)
      7. com.atlassian.bamboo.chains.ChainExecutionManagerImpl.doVcsMerge(ChainExecutionManagerImpl.java:951)
      8. com.atlassian.bamboo.chains.ChainExecutionManagerImpl.access$1300(ChainExecutionManagerImpl.java:97)
      9. com.atlassian.bamboo.chains.ChainExecutionManagerImpl$5.run(ChainExecutionManagerImpl.java:601)
      9 frames
    4. com.atlassian.util
      ManagedLocks$ManagedLockImpl.withLock
      1. com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:321)
      1 frame
    5. com.atlassian.bamboo
      ChainExecutionManagerImpl.start
      1. com.atlassian.bamboo.chains.ChainExecutionManagerImpl.execute(ChainExecutionManagerImpl.java:584)
      2. com.atlassian.bamboo.chains.ChainExecutionManagerImpl.tryStartChainState(ChainExecutionManagerImpl.java:288)
      3. com.atlassian.bamboo.chains.ChainExecutionManagerImpl.start(ChainExecutionManagerImpl.java:171)
      3 frames
    6. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor1133.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
      3. java.lang.reflect.Method.invoke(Method.java:597)
      3 frames
    7. Spring AOP
      JdkDynamicAopProxy.invoke
      1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
      2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
      3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
      4. org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89)
      5. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
      6. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
      6 frames
    8. com.sun.proxy
      $Proxy101.start
      1. com.sun.proxy.$Proxy101.start(Unknown Source)
      1 frame
    9. com.atlassian.bamboo
      PlanExecutionManagerImpl$3$2.call
      1. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:476)
      2. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:469)
      2 frames
    10. com.atlassian.util
      ManagedLocks$ManagedLockImpl.withLock
      1. com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312)
      1 frame
    11. com.atlassian.bamboo
      PlanExecutionManagerImpl$3.call
      1. com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.inlineProcessLocks(PlanExecutionLockServiceImpl.java:99)
      2. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithInlineProcessLock(PlanExecutionManagerImpl.java:680)
      3. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$400(PlanExecutionManagerImpl.java:123)
      4. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:468)
      5. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:449)
      5 frames
    12. com.atlassian.util
      ManagedLocks$ManagedLockImpl.withLock
      1. com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312)
      1 frame
    13. com.atlassian.bamboo
      NonBlockingPlanExecutionServiceImpl$3.call
      1. com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:81)
      2. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:725)
      3. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.startConditionalBuild(PlanExecutionManagerImpl.java:448)
      4. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:519)
      5. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:536)
      6. com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:137)
      7. com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:124)
      7 frames
    14. Java RT
      ThreadPoolExecutor$Worker.run
      1. java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
      2. java.util.concurrent.FutureTask.run(FutureTask.java:138)
      3. java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
      4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
      4 frames
    15. com.atlassian.bamboo
      NamedThreadFactory$2.run
      1. com.atlassian.bamboo.build.pipeline.concurrent.NamedThreadFactory$2.run(NamedThreadFactory.java:55)
      1 frame
    16. Java RT
      Thread.run
      1. java.lang.Thread.run(Thread.java:680)
      1 frame
    17. Spring AOP
      JdkDynamicAopProxy.invoke
      1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
      2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
      3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
      4. org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89)
      5. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
      6. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
      6 frames
    18. com.sun.proxy
      $Proxy101.start
      1. com.sun.proxy.$Proxy101.start(Unknown Source)
      1 frame
    19. com.atlassian.bamboo
      PlanExecutionManagerImpl$3$2.call
      1. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:476)
      2. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3$2.call(PlanExecutionManagerImpl.java:469)
      2 frames
    20. com.atlassian.util
      ManagedLocks$ManagedLockImpl.withLock
      1. com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312)
      1 frame
    21. com.atlassian.bamboo
      PlanExecutionManagerImpl$3.call
      1. com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.inlineProcessLocks(PlanExecutionLockServiceImpl.java:99)
      2. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithInlineProcessLock(PlanExecutionManagerImpl.java:680)
      3. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.access$400(PlanExecutionManagerImpl.java:123)
      4. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:468)
      5. com.atlassian.bamboo.plan.PlanExecutionManagerImpl$3.call(PlanExecutionManagerImpl.java:449)
      5 frames
    22. com.atlassian.util
      ManagedLocks$ManagedLockImpl.withLock
      1. com.atlassian.util.concurrent.ManagedLocks$ManagedLockImpl.withLock(ManagedLocks.java:312)
      1 frame
    23. com.atlassian.bamboo
      NonBlockingPlanExecutionServiceImpl$3.call
      1. com.atlassian.bamboo.plan.PlanExecutionLockServiceImpl.lock(PlanExecutionLockServiceImpl.java:81)
      2. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.doWithProcessLock(PlanExecutionManagerImpl.java:725)
      3. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.startConditionalBuild(PlanExecutionManagerImpl.java:448)
      4. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:519)
      5. com.atlassian.bamboo.plan.PlanExecutionManagerImpl.start(PlanExecutionManagerImpl.java:536)
      6. com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:137)
      7. com.atlassian.bamboo.plan.NonBlockingPlanExecutionServiceImpl$3.call(NonBlockingPlanExecutionServiceImpl.java:124)
      7 frames
    24. Java RT
      ThreadPoolExecutor$Worker.run
      1. java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
      2. java.util.concurrent.FutureTask.run(FutureTask.java:138)
      3. java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
      4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
      4 frames
    25. com.atlassian.bamboo
      NamedThreadFactory$2.run
      1. com.atlassian.bamboo.build.pipeline.concurrent.NamedThreadFactory$2.run(NamedThreadFactory.java:55)
      1 frame
    26. Java RT
      Thread.run
      1. java.lang.Thread.run(Thread.java:680)
      1 frame