java.io.FileNotFoundException - Upgrade Jira Core 7.2.6

Hello,

after upgrading JIRA Core to Version 7.2.6 we get multiple file not found errors on several jar files in the atlassian-jira.log file:

java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\commons-cli.jar
java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\jts1_0.jar
java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\carol.jar
java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\jonas_timer.jar
java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\idb.jar
java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\classes12.jar
java.io.FileNotFoundException: C:\Program Files\Atlassian\JIRA\lib\p6psy.jar

Those files do not exist in the requested path. They even have not been there in the previous version from which we did the update (V.7.2.4).

Does anyone has an idea, why these files are missing or at least why they are reported missing? It seems as if the application is working properly, we cannot see any error.

Thanks for any help.

Rgds.
Stefan 

8 answers

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We used the same user for the upgrade, which is used for starting the application-service (it's a windows installation). The user has administrative privileges on the system and so write-access to all the necessary directories, program- and home-directories. So I cannot image, what could be wrong in the way, we did the upgrade.

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Yilin Mo Atlassian Team Feb 24, 2017

The root cause of the issue is that we switch to Tomcat 8 since JIRA 7 and the JAR manifest scan is turn on by default. Since we customised Tomcat to fit JIRA application, we disable this feature on Tomcat by adding the following line in the file server.xml before the end of Context tag:

<JarScanner scanManifest="false"/>

so that it will not showing any warning message during the startup

I don't think the original poster had been hacking an unsupported Tomcat config.

Yilin Mo Atlassian Team Feb 24, 2017

This usually happens when upgrading JIRA, as the administrator copy the configuration files (such as setenv.sh, server.xml etc) from the old version to the new version.  Especially upgrade from JIRA 6.4 to 7.x.

That's not the right way to upgrade them, it's not a surprise you have problems when you do it that way, on an unsupported configuration.

I am seeing this exception too when developing plugins during startup with atlas-run even after atlas-clean. This is annoying since it might hide real problems during development in a spam of exceptions.

Has anyone come up with a solution for this... it is really becoming a nuisance. The proposed solution is not viable. It would mean we would have to do a modification to the server.xml EVERY time we do a clean. Is there a way to set it permanently in the POM or something?

Has anyone come up with a solution for this... it is really becoming a nuisance. The proposed solution is not viable. It would mean we would have to do a modification to the server.xml EVERY time we do a clean. Is there a way to set it permanently in the POM or something?

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I'm seeing the exact same behavior with this upgrade, these file not found errors seem to only occur at startup, they don't exist in prior installations, but also cannot determine if there absence is causing some other problem.  It's a bummer that it seems the public has to QA these releases more and more since Atlassian is not.

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This is a symptom of the installation being done incorrectly (I think there are other ways to do it, but this is the one I've seen).  You need to ensure the right users are used to do the installation over the upgraded system and that they have all the full permissions to all the installation and data directories.

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I've installed JIRA from tar.gz archive and I have the same error too. 

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If anyone is still experiencing this kind of problem: Our error messages of missing jar-files have disappeared after doing the migration to Jira-Core 7.3.0.

Maybe a hint to anyone, who has the same problems.

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I upgraded to  7.3 in QA today but still see the same missing files errors, but am unable to determine if something is actually not working.   Since there are several plugins not yet compatible, I'm going to wait before creating a support ticket.

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I just upgraded to 7.3 from 7.2.3 which had JIRA Core as part of the server along with JIRA Software.The upgraded 7.3 lists Jira Core, but it now requires a license. The upgrade was performed using the instructions here https://confluence.atlassian.com/adminjiraserver071/upgrading-jira-applications-using-a-rapid-upgrade-method-802592264.html, using "sudo ./atlassian-jira-X.Y.bin".

I've raised a support case as the files being reported by FilenotFoundException are not physically located in the directory and they also were not in Lib directory of the previous install of 7.2.3, by looking in the jira-7.2.3-backup.zip file.

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