When Installing/updating flatpak apps, home and root mounts immediately become read-only. This happens with any app install or update.
for example, running:
flatpak update com.slack.Slack
my home directory becomes read-only and the system quickly becomes unusable. If I save the output of mount before and running flatpak as above, I receive a diff similar to this:
< /dev/mapper/luks-c7792035-1f6a-4a92-8bcf-4cccf9fd8755 on / type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=256,subvol=/root)
---
> /dev/mapper/luks-c7792035-1f6a-4a92-8bcf-4cccf9fd8755 on / type btrfs (ro,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=256,subvol=/root)
22c22
< /dev/mapper/luks-c7792035-1f6a-4a92-8bcf-4cccf9fd8755 on /home type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=257,subvol=/home)
---
> /dev/mapper/luks-c7792035-1f6a-4a92-8bcf-4cccf9fd8755 on /home type btrfs (ro,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=257,subvol=/home)
51c51
< /dev/mapper/luks-c7792035-1f6a-4a92-8bcf-4cccf9fd8755 on /run/timeshift/backup type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=5,subvol=/)
---
> /dev/mapper/luks-c7792035-1f6a-4a92-8bcf-4cccf9fd8755 on /run/timeshift/backup type btrfs (ro,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=5,subvol=/)
Notice the mount point modes changing from rw to ro in the above diff after running the flatpak command.
The output of running flatpak update -vvv com.slack.Slack can be found below. I can’t see anything that alludes to a possible next place to look at why this might be happening. The only errors I see here are relating to it encountering read-only locations.
I’m running Fedora 36 (Linux 5.19.16-200.fc36.x86_64)
I’ve tried running sudo restorecon -vR / in order to see if correctly labelling everything for selinux helps but that doesn’t stop this observed behaviour.
So at this point I’m looking for suggestions of next steps in trying to resolve this issue.
[~] flatpak update -vvv com.slack.Slack 9:16:41
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/will/.local/share/flatpak
Looking for updates…
F: Fetching summary index file for remote ‘flathub’
F: Loading https://dl.flathub.org/repo/summary.idx using libsoup
F: Received 2737 bytes
F: Loaded indexed summary file 6a3e8c02f7f0f88ffd9e085e26ed9ae1dc44b84c1d16ec9593fe7f6c8f3bc60c from cache for remote ‘flathub’
F: Transaction: update flathub:app/com.slack.Slack/x86_64/stable[*]
F: Looking for remote metadata updates for flathub
F: marking op update:app/com.slack.Slack/x86_64/stable resolved to cb44e08354a5dcb8b5799a0d2c05ca2470d1e2998e45e816afd21a2165ecc187
F: Calling system helper: GenerateOciSummary
Required runtime for com.slack.Slack/x86_64/stable (runtime/org.freedesktop.Platform/x86_64/22.08) found in remote flathub
Do you want to install it? [Y/n]:
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform/x86_64/22.08[$old]
F: marking op install/update:runtime/org.freedesktop.Platform/x86_64/22.08 resolved to 253961492abde2982b4c8b9b1e7d45acd72e08e8c84ee7bdc45b491e966072ca
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/22.08[$old]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.Locale/x86_64/22.08[/en]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.VAAPI.Intel/x86_64/22.08[$old]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.openh264/x86_64/2.2.0[$old]
F: marking op install/update:runtime/org.freedesktop.Platform.openh264/x86_64/2.2.0 resolved to 435b1135f46af01c742f7680e92a2ca2b63ef7f5cb6b75030caff3cdd80481a9
F: marking op install/update:runtime/org.freedesktop.Platform.VAAPI.Intel/x86_64/22.08 resolved to cb45563d49f0dacf53d4512e60350a286ff20838abc96150b99c425cfd037040
F: marking op install/update:runtime/org.freedesktop.Platform.Locale/x86_64/22.08 resolved to 6db488be45f93406a265d5d8cb294b5ae492c8041f964e8f545702a11e230f46
F: marking op install/update:runtime/org.freedesktop.Platform.GL.default/x86_64/22.08 resolved to 6062874bd1737b867b0c9a538f5f77b454ba1d05365192165136322e8a20959b
1. org.freedesktop.Platform.GL.default 22.08 i flathub < 131.0 MB
2. org.freedesktop.Platform.Locale 22.08 i flathub < 332.9 MB (partial)
3. org.freedesktop.Platform.VAAPI.Intel 22.08 i flathub < 10.8 MB
4. org.freedesktop.Platform.openh264 2.2.0 i flathub < 944.3 kB
5. org.freedesktop.Platform 22.08 i flathub < 214.3 MB
6. com.slack.Slack stable u flathub < 72.7 MB
Proceed with these changes to the system installation? [Y/n]:
Installing 1/6…
F: Calling system helper: GetRevokefsFd
F: Calling system helper: GetRevokefsFd
Warning: Cannot create repo on revokefs mountpoint /var/tmp/flatpak-cache-FIVCU1/org.freedesktop.Platform.GL.default-RFVCU1: Creating temp file: Permission denied
F: Calling system helper: CancelPull
F: Calling system helper: CancelPull
F: flatpak_dir_pull: Using commit 6062874bd1737b867b0c9a538f5f77b454ba1d05365192165136322e8a20959b for pull of ref runtime/org.freedesktop.Platform.GL.default/x86_64/22.08 from remote flathub
Installing 1/6… 0% 0 bytes/s
Installing 1/6… ████████████████████ 100%
F: Calling system helper: Deploy
Warning: Error deploying: Read-only file system
Installing 2/6…
F: Calling system helper: GetRevokefsFd
F: Calling system helper: GetRevokefsFd
Warning: Failed to get revokefs-fuse socket from system-helper: Failed to create new cache-dir at /var/lib/flatpak/repo/tmp: Read-only file system
Warning: Read-only file system
Installing 3/6…
F: Calling system helper: GetRevokefsFd
F: Calling system helper: GetRevokefsFd
Warning: Failed to get revokefs-fuse socket from system-helper: Failed to create new cache-dir at /var/lib/flatpak/repo/tmp: Read-only file system
Warning: Read-only file system
Installing 4/6…
F: Calling system helper: GetRevokefsFd
F: Calling system helper: GetRevokefsFd
Warning: Failed to get revokefs-fuse socket from system-helper: Failed to create new cache-dir at /var/lib/flatpak/repo/tmp: Read-only file system
Warning: Read-only file system
Installing 5/6…
F: Calling system helper: GetRevokefsFd
F: Calling system helper: GetRevokefsFd
Warning: Failed to get revokefs-fuse socket from system-helper: Failed to create new cache-dir at /var/lib/flatpak/repo/tmp: Read-only file system
Error: Read-only file system
Info: com.slack.Slack was skipped
Changes complete.
error: There were one or more errors
thread 'main' panicked at 'McFly error: DELETE from selected_commands to work (attempt to write a readonly database)', src/history/history.rs:158:17
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
[~]
