I already narrowed it to the folder “~/Library/Application\ Support/DevonThink\ 3”. I closed DT3, restored this folder from Time Machine, restarted and everything is back to where it was when the Time Machine backup was made (licence registered, abbyy installed, Global Inbox in yesterdays state, but I have this on other Devices and could restore current state with sync).
I have not noticed any other corruption in my ~/Library or anywhere on the system. So I believe it is some DT3-related issue, not system issue.
I’ve checked the Relocated Items from the update and there was only one file that was not related to DT3.
I understand from your comments that the only circumstances under which DT3 would create all these files is if they are not already there, right? What would happen if the “~/Library/Application\ Support/DevonThink\ 3”? is there but the content is somehow corrupted. Files with the correct names there but content is garbage? Would DT3 refuse to start?
Are there any ideas how I could debug this? In all Time Machine backups the folder looks normal, i.e. is in the old state. Unfortunately I can’t reconstruct now in what state it was when DT3 was started after the update, when the vanilla layout was created. The only thing I noticed is that the startup of DT3 took really long then, something like 15 seconds. Even after reboot it usually only takes 2 or 3 seconds on this machine.
Did you check that the filesystem is actually okay and that there’s enough disk space, especially as the macOS update requires additional space for the installation? As far as I remember there was or is a bug in Big Sur that might corrupt data in case of not enough disk space.
Yes, disk space is a problem on this machine. Only 20GB of 500 left after the update was downloaded. And also these numbers are not reliable as MacOS calculates free disk space as if Trash was already emptied and podcasts already deleted while in reality they are not.
But: There is no other indication of file system corruption and “First Aid” in MacOS Recovery checks out fine. So I remain to think: Why only DT3?
Update: I checked again and the free storage computation of MacOS is just totally broken. After enabling “optimize storage” in Photos.App (I have about 100 GB of Photos), there are now 200 GB free. And this makes sense as my home directory totals to about about 230GB… and there are no other users. So with Apps and System 300 full seems about right.
Please ensure that there’s more disk space available before the next update and let me know whether it should happen again (or whether it should happen independent of updates) - thank you!
Well, I think there was enough space, but I understand that you can’t help me because there is no trace of what happened. I’ll report to this thread again, should it happen again. I have another Mac that I’ll update later this week.
That update went just fine. This Mac appears to be similarly constrained in disk space. I have checked a third (non-DT) Mac, and all three Macs show about 20GB free space while there is just not enough user data to get to such a low amount of free space. I think the free space display on Macs that have been used for long is just off. Maybe the OS uses everything except a 20GB margin for caches, TM snapshots and such…?
My best guess is still that the directory “~/Library/Application\ Support/DevonThink\ 3” got corrupted or deleted somehow and was thus recreated when DT started next. That it was recreated is undoubtedly true, the only question is why.
Good question. DEVONthink does never delete, move or rename this folder. In addition, all the files/folders inside this folder are only updated when necessary but never at the same time (e.g. imprints only after using Preferences > Imprint, smart groups only after editing them etc.) and not even by the same code.
For problems with updates and new partition/volumes format issues you can read The Eclectic Light Company – Macs, painting, and more web. This guy knows very deep how new system works, with very reasoned explanations about all this stuff.
(As a summary, since Catalina, and more since Bug Sur, updating is a chance to disaster).
I successfully update my 2 Intel machines and my M1 without any issue, but both Intel put in my desktop one recovered Kernel file related to macOS itself.
And there is a feature with new volumes: once a volume needs expansion (DATA volume for example) first complains about no disk space, then expands. As said by @cgrunenberg, updating a Big Sur with low disk pace increase the chance of disaster.
Very interesting link. But still, there was no desaster on my machine. I think these issues are unrelated.
I’m of course worried about data corruption so I went to some great lengths to compare my “~/Library” with the backups from before the update and except files changing all the time it is completely sane and not changed more than expected. Only DevonThink had this issue (twice now). I don’t see another possibility than it being some corner case bug in DevonThink. Other than that, what’s the likelihood that I had update related file system corruption that leaves no other trace than a missing DT Library Folder? Twice?