Yum Metadata Rebuild Failed

post by SamJ on Feb 24

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

UI:

repo settings with Repodata depth of 2 to reflect the // directory structure:

Is there a fix to be able to get our packages under /8/x86_64/ recognized again?

post by SamJ on Feb 26

Note a reversion back to our 3.87.0-03 build has fixed the issue with our metadata rebuild

post by Jacob_Arcila_Cardenas on Feb 26

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

post by SamJ on Mar 2

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 10:39:43,780-0600 DEBUG [quartz-12-thread-11] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Completed metadata rebuild in 63

2026-02-27 10:39:43,788-0600 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/
```plaintext

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$0(QuartzThreadPool.java:145)
at org.nexus.thread.internal.MDCAwareRunnable.run(MDCAwareRunnable.java:40)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.Executors$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] ...

## post by Jacob_Arcila_Cardenas on Mar 3

Thank you for sharing the stack trace. I have filled a ticket internally for it.

## post by SamJ on Mar 18

Just curious if there has been any discovery on the provided stack trace

## post by jzora on Mar 18

Hi, Sam,

This bug was triaged and is being tested this sprint. I’ll make it a point to update you when I know more.

## post by jzora on Mar 24

Sam,

This bug should be fixed in our next major release, 3.91, planned for April.

## post by SamJ on Mar 24

Thank you so much!

## post by SamJ on Apr 22

I’ve updated to nexus 3.91.1-04 and I’m still seeing issues with the rebuild of our metadata:

```plaintext
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 12:45:14,446-0500 DEBUG [quartz-12-thread-13] *TASK org.sonatype.nexus.repository.yum.datastore.internal.createrepo.YumHostedMetadataFacet - Trying to remove RPM /8/x86_64/bind-9.18.43-01WIN.el8.x86_64.rpm metadata if this file does not exist in repository
```plaintext

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.performCall(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$0(QuartzThreadPool.java:145)
at org.nexus.thread.internal.MDCAwareRunnable.run(MDCAwareRunnable.java:40)
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
at java.base/java.util.concurrent.Executors$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.currentThread().getName());

```plaintext
Caused by: java.nio.file.AccessDeniedException: ../sonatype-work/nexus3/tmp/filelist2333225115060907998xml.gz
```plaintext

## post by mpiggott on Apr 23

That error suggests that you have Nexus configured with a tmp directory it doesn’t have permission to write to.

## post by SamJ on Apr 23

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

```plaintext
[root@lnclnekvm674 opt]# ll sonatype-work/nexus3/
total 55312
-rw-r--r-- 1 nexus nexus 36 Sep 4 2024 admin.password
drwxr-xr-x 6 nexus nexus 4096 Sep 4 2024 backup
drwxr-xr-x 4 nexus nexus 61 Jul 29 2025 blobs
drwxr-xr-x 286 nexus nexus 8192 Jul 29 2025 cache
-drwxr-xr-x 7 nexus nexus 171 Aug 6 2025 db
drwxr-xr-x 2 nexus nexus 6 Sep 23 2025 downloads
drwxr-xr-x 3 nexus nexus 36 Dec 24 2019 elasticsearch
drwxr-xr-x 4 nexus nexus 79 Jul 29 2025 etc
drwxr-xr-x 2 nexus nexus 6 Dec 24 2019 generated-bundles
drwxr-xr-x 2 nexus nexus 33 Dec 24 2019 instances
drwxr-xr-x 2 nexus nexus 6 Apr 1 2020 kar
-rw-r--r-- 1 nexus nexus 7 Jul 29 2025 karaf.pid
drwxr-xr-x 3 nexus nexus 18 Dec 24 2019 keystores
-rw-r--r-- 1 nexus nexus 40 Jul 29 2025 lock
drwxr-xr-x 5 root root 8192 Apr 23 10:13 log
drwxr-xr-x 2 nexus nexus 6 May 22 2024 upgrades

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