I’m running the latest version of nexus, nexus-3.89.1-02, and since recently removing an rpm from our custom yum repository we’ve been getting errors when rebuilding metadata. The rebuild task states our repository is null with our repository depth set to 2 on the repository settings and when browsing the UI I can see that the proper depth is set:
Error from “rebuild metadata task” in our logs:
2026-02-23 11:04:05,297-0600 ERROR [quartz-12-thread-7] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Failed to rebuild metadata yum-isp-apps : /8/x86_64/ - null
2026-02-23 11:04:05,307-0600 ERROR [quartz-12-thread-7] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Failed to rebuild metadata yum-isp-apps : /9/x86_64/ - null
to identity if this is known issue with nexus-3.89.1-02 version
I will need to confirm what’s the exception, the current logging level set doesn’t give us enough information. could you please set the logging level for this class to DEBUG?
Steps
Go to settings → Support → Logging → create logger button
inside the form fill the logger name as org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet and set the logging level to DEBUG.
Run the rebuild metadata task again it should show the exception stack trace
Here is the full trace. It looks like the rebuild is attempting to remove packages from the directories.
Blockquote
2026-02-27 10:39:43,716-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /8/x86_64/bind-subscription-9.18.43-01WIN.el8.x86_64.rpm metadata if this file does not exist in repository
2026-02-27 10:39:43,717-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /8/x86_64/bind-subscription-9.18.43-01WIN.el8.x86_64.rpm found in the repository. Skip it.
2026-02-27 10:39:43,717-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Rebuilding metadata yum-isp-apps:/8/x86_64/
2026-02-27 10:39:43,717-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Starting rebuilding metadata at yum-isp-apps : /8/x86_64/
2026-02-27 10:39:43,780-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Completed metadata rebuild in 63
2026-02-27 10:39:43,780-0600 ERROR [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Failed to rebuild metadata yum-isp-apps : /8/x86_64/
java.lang.NullPointerException: null
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:903)
at org.sonatype.nexus.repository.view.payloads.PathPayload.(PathPayload.java:40)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuilder.getFileList(YumMetadataRebuilder.java:174)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.writeMetadata(YumHostedMetadataFacet.java:491)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.doRebuildMetadata(YumHostedMetadataFacet.java:475)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.lambda$12(YumHostedMetadataFacet.java:430)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.perform(ScopedCooperation2Support.java:86)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.performCall(CooperatingFuture.java:126)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.call(CooperatingFuture.java:68)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.cooperate(ScopedCooperation2Support.java:103)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.rebuildMetadata(YumHostedMetadataFacet.java:432)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.invalidateMetadataWithoutWaiting(YumHostedMetadataFacet.java:305)
at org.sonatype.nexus.repository.yum.internal.createrepo.task.YumCreateRepoTask.execute(YumCreateRepoTask.java:35)
at org.sonatype.nexus.repository.RepositoryTaskSupport.execute(RepositoryTaskSupport.java:90)
at org.sonatype.nexus.scheduling.TaskSupport.call(TaskSupport.java:107)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.doExecute(QuartzTaskJob.java:147)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.execute(QuartzTaskJob.java:110)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.sonatype.nexus.quartz.internal.QuartzThreadPool.lambda$0(QuartzThreadPool.java:145)
at org.sonatype.nexus.thread.internal.MDCAwareRunnable.run(MDCAwareRunnable.java:40)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
2026-02-27 10:39:43,781-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Start cleaning metadata datastore entries for missed RPMs for repoLocation /9/x86_64/
2026-02-27 10:39:43,782-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/telegraf-1.35.2-1.x86_64.rpm metadata if this file does not exist in repository
2026-02-27 10:39:43,783-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/telegraf-1.35.2-1.x86_64.rpm found in the repository. Skip it.
2026-02-27 10:39:43,783-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/ncat-7.97-1.x86_64.rpm metadata if this file does not exist in repository
2026-02-27 10:39:43,783-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/ncat-7.97-1.x86_64.rpm found in the repository. Skip it.
2026-02-27 10:39:43,784-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/nmap-7.97-1.x86_64.rpm metadata if this file does not exist in repository
2026-02-27 10:39:43,784-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/nmap-7.97-1.x86_64.rpm found in the repository. Skip it.
2026-02-27 10:39:43,785-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/nping-7.97-1.x86_64.rpm metadata if this file does not exist in repository
2026-02-27 10:39:43,785-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/nping-7.97-1.x86_64.rpm found in the repository. Skip it.
2026-02-27 10:39:43,785-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/zenmap-7.97-1.noarch.rpm metadata if this file does not exist in repository
2026-02-27 10:39:43,786-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/zenmap-7.97-1.noarch.rpm found in the repository. Skip it.
2026-02-27 10:39:43,786-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Rebuilding metadata yum-isp-apps:/9/x86_64/
2026-02-27 10:39:43,786-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Starting rebuilding metadata at yum-isp-apps : /9/x86_64/
2026-02-27 10:39:43,788-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Completed metadata rebuild in 2
2026-02-27 10:39:43,788-0600 ERROR [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Failed to rebuild metadata yum-isp-apps : /9/x86_64/
java.lang.NullPointerException: null
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:903)
at org.sonatype.nexus.repository.view.payloads.PathPayload.(PathPayload.java:40)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuilder.getFileList(YumMetadataRebuilder.java:174)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.writeMetadata(YumHostedMetadataFacet.java:491)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.doRebuildMetadata(YumHostedMetadataFacet.java:475)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.lambda$12(YumHostedMetadataFacet.java:430)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.perform(ScopedCooperation2Support.java:86)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.performCall(CooperatingFuture.java:126)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.call(CooperatingFuture.java:68)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.cooperate(ScopedCooperation2Support.java:103)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.rebuildMetadata(YumHostedMetadataFacet.java:432)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.invalidateMetadataWithoutWaiting(YumHostedMetadataFacet.java:305)
at org.sonatype.nexus.repository.yum.internal.createrepo.task.YumCreateRepoTask.execute(YumCreateRepoTask.java:35)
at org.sonatype.nexus.repository.RepositoryTaskSupport.execute(RepositoryTaskSupport.java:90)
at org.sonatype.nexus.scheduling.TaskSupport.call(TaskSupport.java:107)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.doExecute(QuartzTaskJob.java:147)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.execute(QuartzTaskJob.java:110)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.sonatype.nexus.quartz.internal.QuartzThreadPool.lambda$0(QuartzThreadPool.java:145)
at org.sonatype.nexus.thread.internal.MDCAwareRunnable.run(MDCAwareRunnable.java:40)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
2026-02-27 10:39:43,789-0600 INFO [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.internal.createrepo.task.YumCreateRepoTask - Task complete
I’ve updated to nexus 3.91.1-04 and I’m still seeing issues with the rebuild of our metatdata:
2026-04-22 12:45:14,444-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /8/x86_64/zenmap-7.98-1.noarch.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,445-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /8/x86_64/zenmap-7.98-1.noarch.rpm found in the repository. Skip it.
2026-04-22 12:45:14,445-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /8/x86_64/bind-9.18.43-01WIN.el8.x86_64.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,446-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /8/x86_64/bind-9.18.43-01WIN.el8.x86_64.rpm found in the repository. Skip it.
2026-04-22 12:45:14,446-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /8/x86_64/bind-subscription-9.18.43-01WIN.el8.x86_64.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,446-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /8/x86_64/bind-subscription-9.18.43-01WIN.el8.x86_64.rpm found in the repository. Skip it.
2026-04-22 12:45:14,447-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Rebuilding metadata yum-isp-apps:/8/x86_64/
2026-04-22 12:45:14,447-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Starting rebuilding metadata at yum-isp-apps : /8/x86_64/
2026-04-22 12:45:14,448-0500 ERROR [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Failed to rebuild metadata yum-isp-apps : /8/x86_64/
org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuildException: Failed to initialize yum metadata files for rebuilding metadata at /8/x86_64/
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuilder.start(YumMetadataRebuilder.java:105)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.doRebuildMetadata(YumHostedMetadataFacet.java:457)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.lambda$12(YumHostedMetadataFacet.java:430)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.perform(ScopedCooperation2Support.java:86)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.performCall(CooperatingFuture.java:126)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.call(CooperatingFuture.java:68)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.cooperate(ScopedCooperation2Support.java:103)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.rebuildMetadata(YumHostedMetadataFacet.java:432)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.invalidateMetadataWithoutWaiting(YumHostedMetadataFacet.java:305)
at org.sonatype.nexus.repository.yum.internal.createrepo.task.YumCreateRepoTask.execute(YumCreateRepoTask.java:35)
at org.sonatype.nexus.repository.RepositoryTaskSupport.execute(RepositoryTaskSupport.java:90)
at org.sonatype.nexus.scheduling.TaskSupport.call(TaskSupport.java:107)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.doExecute(QuartzTaskJob.java:147)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.execute(QuartzTaskJob.java:110)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.sonatype.nexus.quartz.internal.QuartzThreadPool.lambda$0(QuartzThreadPool.java:145)
at org.sonatype.nexus.thread.internal.MDCAwareRunnable.run(MDCAwareRunnable.java:40)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.nio.file.AccessDeniedException: ../sonatype-work/nexus3/tmp/filelist15666113519809930930xml.gz
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:261)
at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
at java.base/java.nio.file.Files.createFile(Files.java:658)
at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
at java.base/java.nio.file.Files.createTempFile(Files.java:924)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuilder.start(YumMetadataRebuilder.java:87)
… 23 common frames omitted
2026-04-22 12:45:14,448-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Start cleaning metadata datastore entries for missed RPMs for repoLocation /9/x86_64/
2026-04-22 12:45:14,449-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/connmon-1.0.0-1.el9.noarch.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,449-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/connmon-1.0.0-1.el9.noarch.rpm found in the repository. Skip it.
2026-04-22 12:45:14,449-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/connmon-1.0.2-1.el9.noarch.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,450-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/connmon-1.0.2-1.el9.noarch.rpm found in the repository. Skip it.
2026-04-22 12:45:14,450-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/telegraf-1.35.2-1.x86_64.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,450-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/telegraf-1.35.2-1.x86_64.rpm found in the repository. Skip it.
2026-04-22 12:45:14,450-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/ncat-7.97-1.x86_64.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,451-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/ncat-7.97-1.x86_64.rpm found in the repository. Skip it.
2026-04-22 12:45:14,451-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/nmap-7.97-1.x86_64.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,452-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/nmap-7.97-1.x86_64.rpm found in the repository. Skip it.
2026-04-22 12:45:14,452-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/nping-7.97-1.x86_64.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,452-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/nping-7.97-1.x86_64.rpm found in the repository. Skip it.
2026-04-22 12:45:14,453-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /9/x86_64/zenmap-7.97-1.noarch.rpm metadata if this file does not exist in repository
2026-04-22 12:45:14,453-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Asset /9/x86_64/zenmap-7.97-1.noarch.rpm found in the repository. Skip it.
2026-04-22 12:45:14,453-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Rebuilding metadata yum-isp-apps:/9/x86_64/
2026-04-22 12:45:14,453-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Starting rebuilding metadata at yum-isp-apps : /9/x86_64/
2026-04-22 12:45:14,454-0500 ERROR [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Failed to rebuild metadata yum-isp-apps : /9/x86_64/
org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuildException: Failed to initialize yum metadata files for rebuilding metadata at /9/x86_64/
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuilder.start(YumMetadataRebuilder.java:105)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.doRebuildMetadata(YumHostedMetadataFacet.java:457)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.lambda$12(YumHostedMetadataFacet.java:430)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.perform(ScopedCooperation2Support.java:86)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.performCall(CooperatingFuture.java:126)
at org.sonatype.nexus.common.cooperation2.datastore.internal.CooperatingFuture.call(CooperatingFuture.java:68)
at org.sonatype.nexus.common.cooperation2.ScopedCooperation2Support$ScopedCooperation2Builder.cooperate(ScopedCooperation2Support.java:103)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.rebuildMetadata(YumHostedMetadataFacet.java:432)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet.invalidateMetadataWithoutWaiting(YumHostedMetadataFacet.java:305)
at org.sonatype.nexus.repository.yum.internal.createrepo.task.YumCreateRepoTask.execute(YumCreateRepoTask.java:35)
at org.sonatype.nexus.repository.RepositoryTaskSupport.execute(RepositoryTaskSupport.java:90)
at org.sonatype.nexus.scheduling.TaskSupport.call(TaskSupport.java:107)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.doExecute(QuartzTaskJob.java:147)
at org.sonatype.nexus.quartz.internal.task.QuartzTaskJob.execute(QuartzTaskJob.java:110)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.sonatype.nexus.quartz.internal.QuartzThreadPool.lambda$0(QuartzThreadPool.java:145)
at org.sonatype.nexus.thread.internal.MDCAwareRunnable.run(MDCAwareRunnable.java:40)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.nio.file.AccessDeniedException: ../sonatype-work/nexus3/tmp/filelist2333225115060907998xml.gz
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:261)
at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
at java.base/java.nio.file.Files.createFile(Files.java:658)
at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
at java.base/java.nio.file.Files.createTempFile(Files.java:924)
at org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumMetadataRebuilder.start(YumMetadataRebuilder.java:87)
… 23 common frames omitted
2026-04-22 12:45:14,454-0500 INFO [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.internal.createrepo.task.YumCreateRepoTask - Task complete
Interesting , we’ve not adjusted any permissions since our initial install of sonatype 3.91-04 which the tarball deploys that directory again with permissions set to
Is it possible you mistakenly ran nexus as root/with sudo? This could cause some files to change ownership.I would suggest doing the following to be safe:
