AppImage can't see file system after upgrade Debian from 11->12 (and added libfuse2)

BIG PICTURE QUESTION: Has anyone gotten cryptomator appimage to work on Debian 12?

Details;
I have 2 different Debian containers on my chromebook.

The first is Debian 11. It works just fine to use the appimage cryptomator-1.11.0-x86_64.AppImage

The second container is Debian 12 (newly created). It does not run the same app image. Upon first attempt to launch the appimage from terminal it never started, only gave an error that it needed fuse:

  • dlopen(): error loading libfuse.so.2
  • AppImages require FUSE to run.
  • You might still be able to extract the contents of this AppImage if you run it with the --appimage-extract option.
  • See FUSE · AppImage/AppImageKit Wiki · GitHub for more information

So I checked fuse packages (using apt list --installed | grep fuse) and saw the following were installed

  • fuse3/stable,now 3.14.0-4 amd64 [installed,automatic]
  • libfuse3-3/stable,now 3.14.0-4 amd64 [installed,automatic]

My first container (Debian 11, the one that is working with cryptomator) has the above two fuse3 related packages, plus two additional fuse related packages that seem to be associated with fuse2. So I decided to install the first of these additional fuse related packages into my my Debian 12 container as follows:

  • sudo apt install libfuse2

As far as I can tell, that proceeded without error. Then I launched cryptomator and this time the graphical user interface appeared. However upon trying to navigate to an existing vault, it could not see my file system.

I then proceeded to install the other fuse-related package (that was in my working Debian 11 container) into my Debian 12 container

  • sudo apt install gvfs-fuse

There were a handful of errors during the process

    • Setting up udisks2 (2.9.4-4) …
  • vda: Failed to write ‘change’ to ‘/sys/devices/pci0000:00/0000:00:04.0/virtio3/block/vda/uevent’: Permission denied
  • vdb: Failed to write ‘change’ to ‘/sys/devices/pci0000:00/0000:00:05.0/virtio4/block/vdb/uevent’: Permission denied
  • pmem0: Failed to write ‘change’ to ‘/sys/devices/pci0000:00/0000:00:06.0/virtio5/ndbus0/region0/namespace0.0/block/pmem0/uevent’: Permission denied
  • loop0: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop0/uevent’: Permission denied
  • loop1: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop1/uevent’: Permission denied
  • loop2: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop2/uevent’: Permission denied
  • loop3: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop3/uevent’: Permission denied
  • loop4: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop4/uevent’: Permission denied
  • loop5: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop5/uevent’: Permission denied
  • loop6: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop6/uevent’: Permission denied
  • loop7: Failed to write ‘change’ to ‘/sys/devices/virtual/block/loop7/uevent’: Permission denied

I attempted to run crypomator apimage again from terminal again. The results were the same as before (the GUI launched but could not access the file system). Among the stuff displayed in my terminal:

  • 21:29:52.427 [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libayatana-appindicator3.so.1 failed to load
  • 21:29:52.428 [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libappindicator3 failed to load

Other details

  • Other appimages like bitwarden work fine in my Debian 12 container
  • I have never been able to get the crytpomator flatpak to work. It actually has similar symptom as above that the GUI launches but it can’t see the files. I granted File permission access in Flatseal but that didn’t help. I also tried installing as a system flatpak app rather than a user flatpak app. And flatpak has never worked for me, including in Debian 11.

Any advice would be appreciated. I captured more of the output than I posted above (to save space). I recorded alll the output after “sudo apt install gvfs-fuse”. And I recorded all the output from running cryptomator. But everything else looked normal to me within there so I didn’t post it. But I’d be glad to post any of that if it would be helpful. Also I can start from scratch with another Debian 12 container if there is something I should do different or somethingI should record along the way. Thanks!

Sorry this is a long post.

The last time I had a similar problem, it occurred during a cryptomator upgrade. And the answer at that time was that I needed to install libfuse3. Link as follows

This time I started out (in Debian 12 container) with fuse3 already installed, but the cryptomator appimage wouldn’t even launch to the GUI with those. (It didn’t launch to the GUI until I added the fuse2 stuff, and at that point I could get in and verify that it was using fuse rather than webdav, but it couldn’t see my file system).

I removed all the fuse2 stuff, to get back to only the following packages as shown by apt list --installed | grep fuse:

  • fuse3/stable,now 3.14.0-4 amd64 [installed]
  • libfuse3-3/stable,now 3.14.0-4 amd64 [installed,automatic]

(that’s the same place I was at the beginning of this post upon fresh installation of Debian 12, and I got the same results…)

Upon launching the appimage with only the fuse3 stuff in there, the GUI doesn’t launch and the shell reports the following errors:

  • dlopen(): error loading libfuse.so.2
  • AppImages require FUSE to run.
  • You might still be able to extract the contents of this AppImage if you run it with the --appimage-extract option.
  • See FUSE · AppImage/AppImageKit Wiki · GitHub for more information

That “error loading libfuse.so.2” makes it sound like it wants fuse2 (which is the opposite problem of last thread when it needed fuse 3 to work). But when I installed fuse2 along with fuse3 together as reported in original post, it launched the GUI but it never saw the file system. Do I need to uninstall the fuse3 packages?

I’m pretty sure this has something to do with fuse libraries (the first error related to needing a fuse 2 library). So let me restate my question more simply:

What fuse-related libraries should be installed (and not installed) in linux in order to run the latest appimage?

The current appimage needs libfuse2, Cryptomator requires the fuse3 package.

There is the plan to discard the fuse2 dependency, see Appimage: Use static runtime · Issue #3055 · cryptomator/cryptomator · GitHub, but there is no ETA.

I think it is very important to mention, that you are actually running debian 12 in a container on a chromebook. This is not the same as running Debain as the host system.

That said, i cannot tell why on debian 12 you cannot see the unlocked vault. Maybe because you are mounting as a different user. If so, you need to set additional mount flags, see Volume Types — Cryptomator 1.7.0 documentation.

Thanks for your replies. I’m struggling here.

I think it is very important to mention, that you are actually running debian 12 in a container on a chromebook. This is not the same as running Debain as the host system.

Chromebook provides a virtual environment for linux but as far as I can tell everything works the same as linux other than low level hardware access. I believe it should actually provide an advantage in that I can start from scratch in a new Debian 12 container (as I have done several times already) so that none of my previous customizations can disrupt cryptomator (it’s just out of the box Debian 12 updated with sudo apt update/sudo apt upgrade, along with cryptomator and whatever dependencies that crytpomator needs me to install… the part I’m trying to figure out). In theory it seems that should be easier to troubleshoot.

I have 4 other appimages (other applications) that work both on Debian 11 and Debian 12. Cryptomator seems to be the only one that isn’t working on Debian 12. The problem seems related to fuse (that is the first error I got, that it was looking for something from fuse2).

Fuse management is a little strange to me. I have 4 fuse packages on my debian 11 where cryptomator is working. Installing those same fuse packages onto Debian 12 isn’t working for cryptomator. They are not independent packages, for example if I uninstall Fuse 3 (sudo apt remove libfuse3-3) it removes 3 of those packages (it reports Removing gvfs-fuse (1.50.3-1) …Removing fuse3 (3.14.0-4) …Removing libfuse3-3:amd64 (3.14.0-4) ). I have tried every combination of the four that I think of but I think maybe even the order of installing and removing them matters.

debian has some bug related to fuse and bookworm Debian Bug report logs - [#918984]fuse3: provide upgrade path fuse → fuse3 for bookworm I don’t understand all that but I’ll study that, maybe it has some clues.

That said, i cannot tell why on debian 12 you cannot see the unlocked vault. Maybe because you are mounting as a different user. If so, you need to set additional mount flags, see Volume Types — Cryptomator 1.7.0 documentation

I’m not sure what you mean by mounting as a different user. I have only one linux user in my container (other than root, which I’m not using). That is the same username that shows on my prompt in the shell where I am launching cryptomator appimage from (in my own home directory). Is there something else I should check to investigate “mounting as a different user”

I have only one option for mount type option showing in cryptomator, which is Fuse (the same as I’ve always used). Are you saying I should try to set up something other than Fuse? If so, I’ll try it but I just want to double check that’s what you’re saying.

I started from scratch with a brand new Debian 12 container, then updated, then added additional libraries to support appimages as suggested here How To Install AppImage on Debian 12 - idroot

Then I launched the appiamge and the GUI launches, but I cannot see my files (same as before), but this time I get a slightly different set of errors:

  • [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libayatana-appindicator3.so.1 failed to load
  • [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libappindicator3 failed to load

apt-cache search libindicator3 shows that the following packages are available for installation:

libappindicator3-0.1-cil - CLI binding for libayatana-appindicator3 using GObject introspection
libappindicator3-0.1-cil-dev - CLI binding for libayatana-appindicator3 using GObject introspection
libayatana-appindicator3-1 - Ayatana Application Indicators (GTK-3+ version)
libayatana-appindicator3-dev - Ayatana Application Indicators (development files, GTK-3+ version)

So from that list I selected one to install sudo apt install libayatana-appindicator3-1

Then I relaunched cryptomator appimage with same results (gui started files not visible) and now the first error above is resolved, but the 2nd remains:

  • [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libayatana-appindicator3.so.1 successfully loaded
  • [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libappindicator3 failed to load

So I typed apt-cache search libappindicator3 and it shows packages available:

libappindicator3-0.1-cil - CLI binding for libayatana-appindicator3 using GObject introspection
libappindicator3-0.1-cil-dev - CLI binding for libayatana-appindicator3 using GObject introspection
libayatana-appindicator3-1 - Ayatana Application Indicators (GTK-3+ version)
libayatana-appindicator3-dev - Ayatana Application Indicators (development files, GTK-3+ version)

Since libayatana-appindicator3-1 is already installed and I don’t think I need either of the dev options, there is only one option left so I tried sudo apt install libappindicator3-0.1-cil. It still gives the same error.

  • [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libayatana-appindicator3.so.1 successfully loaded
  • [JavaFX Application Thread] INFO o.p.appindicator.RuntimeHelper - Native code library libappindicator3 failed to load

I’m at a loss here. there are no remaining packages in the Debian 12 repository matching the name libappindicator3 that are not either already installed, or identified as dev.

ps - I am not particularly fluent at tracking down dependencies. It’s not something I normally need to do. If I should be doing it a different way please let me know.

This is not related to seeing files or not. These are libraries for tray menu support.


I think this is a permission issue on your filesystem/os. You can apparently open the directory selector, but you cannot navigate to your vault storage location, right? Depending on how the vault storage location is integrated into the filesystem, you cannot directly select it.

For example, mounting a web storage inside nautilus, let’s you access the storage from nautilus, but not from your filesystem, making it unsuitable for Cryptomator. You need to use davfs.


If the issue is about accessing an already unlocked vault, did you tried a custom mountpoint directly in your user home directory?

  1. Create empty folder
  2. Lock vault, open vault options, tab “Mounting”
  3. Select custom directory in section “Mountpoint” and select the empty directory
  4. Unlock vault

You should be able to open the vault access point in your filemanager and browse through your vault content. If not, try to use the terminal, to see if this works.

I think this is a permission issue on your filesystem/os. You can apparently open the directory selector, but you cannot navigate to your vault storage location, right?

I can open the directory selector, but it sees nothing. Clicking on the icon labeled “computer” gives nothing, not a single directory or anything. Yes it does seem like a permissions issue of some kind. But I’m the only user.