All Flatpak apps fail to open (Permission denied error)

I’ve just started using Fedora 31, and I am unable to successfully open flatpak apps. I added flathub as a remote for flatpak, so flatpak apps are showing up in GNOME software. Whether I install an app from the command line or from the software app, trying to open the app by clicking the icon in the dash results in nothing happening at all. So far this has been the case with Spotify and Slack. If I click “Launch” in the software app, I get a message that says:
“Sorry, something went wrong:
mkdir(/home/user/.var/app/com.spotify.Client): Permission denied”

Apps installed from the Fedora repositories open just fine. Any idea how I can resolve this issue?

OK, I have solved my problem by doing a fresh install. The problem was connected to having transferred over my home directory from a different linux distro (elementary). I never figured out what the exact issue was, but it wasn’t fixed by removing and reinstalling flatpak or clearing flatpak’s caches. So I did a fresh install of Fedora, formatting the old home partition this time, and the issue is now gone (as well as some other unrelated issues).

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When you move the home directory over, you will need to ensure that the permissions are correctly updated too. Generally, some chmod or chown is required, and it’s a good idea to run restorecon to reset the selinux context on files too—which may have changed during the move.

Flatpak uses a lot of other bits such as dbus and so on which also require permissions to be correctly set up. So, I’m not surprised that restalling flatpak didn’t fix it.

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