Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Story Points:5
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Epic Link:
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Sprint:Summer 1 2023 May 15, Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10
Description
Situation: We have reached a blocker in the upgrade to java 11 as IGB will not start but there are no additional errors. I think there may be an issue with the OSGI wiring, but we need a way to check if that is the issue keeping IGB from running or if it is a java 11 issue.
Task: Update the various project dependencies for IGB in Java 8. Ensure that IGB starts and that all of the bundles are able to load.
Attachments
Issue Links
Activity
Merged and the new main-JDK8 branch installers are deployed to BioViz early access section.
I have pushed the new development branch. It is ready to receive your PR.
See:
https://bitbucket.org/lorainelab/integrated-genome-browser/src/main-JDK8/
OK - I will make the target branch and push it to the team repository shortly.
Side note:
While attempting to install netbeans version 11.3, I ran into a bug where the installer will fail because it cannot find the jdk. The steps here fixed the issue.
The problem seems to be the fact that /usr/libexec/java_home seems to be broken in BigSur (see here: https://developer.apple.com/forums/thread/666681).
The Netbeans installer checks if the JDK is installed by using /usr/libexec/java_home, gets the wrong answer and quits with an error.
One way to fix that behaviour is to patch the installer. It can be done as follows:
assuming there is no directory called "a" in tmp:
Open the dmg, but do not run the installer
In a shell give the following command:
pkgutil --expand /Volumes/NetBeans\ 8.2\ RC/NetBeans\ 8.2\ RC.pkg /tmp/a
(if your Netbeans installer has a different name, change the command to reflect the actual name of your installer)
This opens the package, and copies it s content in /tmp/a.
Edit the installation script. Using a text editor, open the file /tmp/a/Distribution.
on line 13, replace:
var java_result = checkJavaVersion();
with
var java_result = true;
and save the file. This will skip the check on the Java version. It is your responsibility to make sure you have JDK 8 or following on your machine, and that this version is used when you use the java command. You can make sure that's fine by checking with the command
java -version
Let's wrap it up:
pkgutil --flatten /tmp/a ~/a.pkgAt this point you have in your home directory a package called a.pkg. Double click on it, and the Netbeans installer will do its job.
Tested in local. all 95/95 bundles are active, I am able to load data and everything else looks fine. closing this ticket