Unchecking an update site does too much

[hinerm]

I accidentally unchecked the "Java 8" update site, then re-checked it. This left me with changes:

Which first of all seems wrong.

Then, after restarting it appears my installation is fundamentally broken:

[ctrueden]

@hinerm Probably the installation of jars/opencensus-contrib-http-util.jar is correct. It was likely not installed locally in your existing installation, but it is part of the Java-8 update site. This can happen because the Updater has some logic surrounding which files from an update site get installed, based on whether they are dependencies of anything else. The opencensus-contrib-http-util library is a dependency only of google-cloud-core-http, which is a dependency of n5-viewer_fiji and google-cloud-storage, the latter of which is a dependency of n5-google-cloud. This is a relatively complex (nested, at least) dependency hierarchy, which the Updater perhaps reasoned about incorrectly, or perhaps there is some other bug resulting in your opencensus-contrib-http-util not being installed when it should have been. But when you check a new update site, I think it marks all files (apart from non-matching platform ones) for installation, which would explain the behavior you saw.

As for the installation being fundamentally broken: that I don't have a guess about. More verbose console logging, and/or directory listings of your Fiji.app tree, would be helpful.

[carandraug]

Someone seems to be facing the same on the forum https://forum.image.sc/t/errors-with-european-mirrors-for-fiji-and-imagej/103355/6 (the thread is a bit long because they found the issue when selecting the European mirrors and thought the issue was with the European mirrors).

How to reproduce step-by-step:

1. start with a fresh "install" of Fiji
2. start the updater
3. click “Manage update sites”
4. unselect the “Java-8” original update site
5. note how the "ImageJ Updater" window behind lists the files that will be removed/updated
6. re-select the “Java-8” original update site
7. note how the "ImageJ Updater" window behind still lists the files to be removed/updated
8. click “Apply and Close”
9. note how the "ImageJ Updater" window now lists no files to be removed/updated
10. since the “ImageJ Updater” window shows no files to be changed, press “Cancel” to close the window
11. Quit Fiji
12. before starting fiji, note the Fiji.app/update directory full of empty files (to be removed by the launcher next time it starts)
13. Start Fiji again (you should now get the Could not find ij.jar in .../Fiji.app/jars/ error)

A few things from this:

• starting ImageJ with --debug does not show the launcher applying the updates (also mentioned on Fiji --dry-run option will still run the updater and remove files apposed/jaunch#58)

• making changes to "Manage update sites" is meant to immediately show what will change on the "ImageJ updater" window behind. In this case, reselecting the "Java-8" update site only changes the "pending" changes after closing the window. I found that weird and maybe is related.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/errors-with-european-mirrors-for-fiji-and-imagej/103355/8