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Type: Bug
Resolution: Fixed
Priority: Medium
Fix Version/s: 11.0.0
Affects Version/s: 9.12.2, 9.12.14, 9.12.15, 10.0.0, 10.2.0, 10.3.2
Component/s: Installation
Labels:
- FY24RRD
- boosters
- whl-fy25q1
- whl-fy25q2
- whl-fy25q3
- whl-fy25q4
- whl-fy25q4-40

Introduced in Version:
9.12
Support reference count:
23
Symptom Severity:
Severity 3 - Minor
UIS:
16
Current Status:

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Atlassian Update – 17 April 2025

Dear Customers,

We're happy to announce that this issue is fixed in the 11.0.0 release. Learn more about the release

Best regards

Dino Costantini

Principal Software Engineer

Show
Atlassian Update – 17 April 2025 Dear Customers, We're happy to announce that this issue is fixed in the 11.0.0 release. Learn more about the release Best regards Dino Costantini Principal Software Engineer

Issue Summary

Even on a fresh install of Jira 9.12.2 you will get WARN log messages for Duplicate Packages.

This is reproducible on Data Center: Yes

Steps to Reproduce

Fresh install of Jira 9.12.2.

1. Upgrade into it will also show the WARNs.

Expected Results

Don't show any warning messages about these duplicate packages.

Actual Results (Jira 9.12.14):

The below warnings is thrown in the atlassian-jira.log file:

2024-01-25 09:44:24,432-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.protocol' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-store-3.2.2.jar'
2024-01-25 09:44:24,433-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.utils' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-store-3.2.2.jar'
2024-01-25 09:44:24,433-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.cipher' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-store-3.2.2.jar'
2024-01-25 09:44:24,433-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: atlassian-secrets-api-3.2.2.jar and password-cipher-base-1.4.0.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-api-3.2.2.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
2024-01-25 09:44:24,434-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-api-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-api-3.2.2.jar'
2024-01-25 09:44:24,434-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.protocol' with different versions. Files: atlassian-secrets-store-3.2.2.jar and password-cipher-base-1.4.0.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-store-3.2.2.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
2024-01-25 09:44:24,434-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.utils' with different versions. Files: atlassian-secrets-store-3.2.2.jar and password-cipher-base-1.4.0.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-store-3.2.2.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
2024-01-25 09:44:24,434-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.cipher' with different versions. Files: atlassian-secrets-store-3.2.2.jar and password-cipher-base-1.4.0.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/atlassian-secrets-store-3.2.2.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/lib/password-cipher-base-1.4.0.jar'
2024-01-25 09:44:24,435-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.protocol' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/atlassian-secrets-store-3.2.2.jar'
2024-01-25 09:44:24,435-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.utils' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/atlassian-secrets-store-3.2.2.jar'
2024-01-25 09:44:24,435-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.cipher' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/atlassian-secrets-store-3.2.2.jar'
2024-01-25 09:44:24,435-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.activation' with different versions. Files: jakarta.activation-1.2.1.jar and jakarta.activation-api-1.2.2.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.activation-1.2.1.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.activation-api-1.2.2.jar'
2024-01-25 09:44:24,436-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.activation' with different versions. Files: javax.activation-api-1.2.0.jar and jakarta.activation-1.2.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/javax.activation-api-1.2.0.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.activation-1.2.1.jar'
2024-01-25 09:44:24,436-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.activation' with different versions. Files: activation-1.1.1.jar and javax.activation-api-1.2.0.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/activation-1.1.1.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/javax.activation-api-1.2.0.jar'
2024-01-25 09:44:24,436-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: atlassian-secrets-api-3.2.2.jar and password-cipher-api-1.4.0.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/atlassian-secrets-api-3.2.2.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/password-cipher-api-1.4.0.jar'
2024-01-25 09:44:24,436-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.xml.bind.helpers' with different versions. Files: jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.xml.bind-api-2.3.3.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jaxb-api-2.3.1.jar'
2024-01-25 09:44:24,437-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.xml.bind.annotation.adapters' with different versions. Files: jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.xml.bind-api-2.3.3.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jaxb-api-2.3.1.jar'
2024-01-25 09:44:24,437-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.xml.bind.annotation' with different versions. Files: jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.xml.bind-api-2.3.3.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jaxb-api-2.3.1.jar'
2024-01-25 09:44:24,437-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.xml.bind.util' with different versions. Files: jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.xml.bind-api-2.3.3.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jaxb-api-2.3.1.jar'
2024-01-25 09:44:24,437-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.xml.bind.attachment' with different versions. Files: jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.xml.bind-api-2.3.3.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jaxb-api-2.3.1.jar'
2024-01-25 09:44:24,437-0300 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'javax.xml.bind' with different versions. Files: jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jakarta.xml.bind-api-2.3.3.jar'
      '/Users/adminuser/jira/atlassian-jira-software-9.12.2-standalone/atlassian-jira/WEB-INF/lib/jaxb-api-2.3.1.jar

These are the file pairs that contain duplicate implementations of the same packages:

➜  ~ grep "Package Scanner found duplicates for package" x | cut -d':' -f4 | sort -u
 activation-1.1.1.jar and javax.activation-api-1.2.0.jar
 atlassian-secrets-api-3.2.2.jar and password-cipher-api-1.4.0.jar
 atlassian-secrets-api-3.2.2.jar and password-cipher-base-1.4.0.jar
 atlassian-secrets-store-3.2.2.jar and password-cipher-base-1.4.0.jar
 jakarta.activation-1.2.1.jar and jakarta.activation-api-1.2.2.jar
 jakarta.xml.bind-api-2.3.3.jar and jaxb-api-2.3.1.jar
 javax.activation-api-1.2.0.jar and jakarta.activation-1.2.1.jar
 password-cipher-base-1.4.0.jar and atlassian-secrets-api-3.2.2.jar
 password-cipher-base-1.4.0.jar and atlassian-secrets-store-3.2.2.jar

Another bug report was opened for different packages on previous version. Here it is for reference:

Package Scanner found duplicates for atlassian packages - ~~JRASERVER-75078~~

Actual Results (Jira 10.2.0):

2024-11-15 09:49:29,620+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.protocol' with different versions. Files: atlassian-secrets-store-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/lib/atlassian-secrets-store-5.0.6.jar'
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,620+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.utils' with different versions. Files: atlassian-secrets-store-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/lib/atlassian-secrets-store-5.0.6.jar'
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,620+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.cipher' with different versions. Files: atlassian-secrets-store-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/lib/atlassian-secrets-store-5.0.6.jar'
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,620+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: atlassian-secrets-api-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/lib/atlassian-secrets-api-5.0.6.jar'
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,621+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.protocol' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-5.0.6.jar
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
      '/tmp/jira/lib/atlassian-secrets-store-5.0.6.jar'
2024-11-15 09:49:29,621+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.utils' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-5.0.6.jar
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
      '/tmp/jira/lib/atlassian-secrets-store-5.0.6.jar'
2024-11-15 09:49:29,621+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-api-5.0.6.jar
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
      '/tmp/jira/lib/atlassian-secrets-api-5.0.6.jar'
2024-11-15 09:49:29,621+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.cipher' with different versions. Files: password-cipher-base-1.4.0.jar and atlassian-secrets-store-5.0.6.jar
      '/tmp/jira/lib/password-cipher-base-1.4.0.jar'
      '/tmp/jira/lib/atlassian-secrets-store-5.0.6.jar'
2024-11-15 09:49:29,621+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.protocol' with different versions. Files: atlassian-secrets-store-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/atlassian-jira/WEB-INF/lib/atlassian-secrets-store-5.0.6.jar'
      '/tmp/jira/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,621+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.utils' with different versions. Files: atlassian-secrets-store-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/atlassian-jira/WEB-INF/lib/atlassian-secrets-store-5.0.6.jar'
      '/tmp/jira/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,622+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.secrets.tomcat.cipher' with different versions. Files: atlassian-secrets-store-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/atlassian-jira/WEB-INF/lib/atlassian-secrets-store-5.0.6.jar'
      '/tmp/jira/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,622+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: atlassian-secrets-api-5.0.6.jar and password-cipher-base-1.4.0.jar
      '/tmp/jira/atlassian-jira/WEB-INF/lib/atlassian-secrets-api-5.0.6.jar'
      '/tmp/jira/atlassian-jira/WEB-INF/lib/password-cipher-base-1.4.0.jar'
2024-11-15 09:49:29,622+0000 JIRA-Bootstrap WARN      [o.twdata.pkgscanner.ExportPackageListBuilder] Package Scanner found duplicates for package 'com.atlassian.db.config.password' with different versions. Files: password-cipher-api-1.4.0.jar and atlassian-secrets-api-5.0.6.jar
      '/tmp/jira/atlassian-jira/WEB-INF/lib/password-cipher-api-1.4.0.jar'
      '/tmp/jira/atlassian-jira/WEB-INF/lib/atlassian-secrets-api-5.0.6.jar'

Note, that only password-cipher-* and atlassian-secrets-* are listed here, no mention of activation-1.1.1.jar, javax.activation-api-1.2.0.jar, jakarta.activation-1.2.1.jar, jakarta.activation-api-1.2.2.jar, jakarta.xml.bind-api-2.3.3.jar or jaxb-api-2.3.1.jar

Workaround

Currently, there is no known workaround for this behavior. A workaround will be added here when available. For now, you can just ignore these warnings.

relates to

JRASERVER-75078 Package Scanner found duplicates for atlassian packages

Closed

is resolved by: WILDT-89 Loading...

mentioned in: Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...

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Details

Description

Issue Summary

Steps to Reproduce

Expected Results

Actual Results (Jira 9.12.14):

Actual Results (Jira 10.2.0):

Workaround

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