Universal Blue•2w ago

Getting "Read-Only File System" Error everywhere after updating any flatpak

I'm not sure if this is a bug or something I've done wrong, but I wanted to check if anyone else was experiencing this or knew what was up before escalating a bug on GitHub I noticed anytime I update any flatpak package (through the UI, through the terminal, or through ujust update) the whole root filesystem appears to become read only:

[username]@Nemesis:~$ flatpak update org.musicbrainz.Picard
Looking for updates…


        ID                                                Branch      Op     Remote      Download
 2. [✗] org.musicbrainz.Picard.Locale                     stable      u      flathub      < 2.2 MB (partial)
 3. [✗] org.musicbrainz.Picard                            stable      u      flathub     < 22.5 MB

Warning: Unable to remove old checkout: Removing /home/[username]/.local/share/flatpak/.removed/org.kde.Platform-4d49c450514df9f8cfa5fe1a83b9e5cebe1fc2c9b958e8cabe4b1a23f4068d7c: unlinkat(look): Read-only file system
Warning: Read-only file system
Error: Read-only file system
Updates complete.
error: There were one or more errors

[username]@Nemesis:~$ flatpak update org.musicbrainz.Picard
Looking for updates…


        ID                                                Branch      Op     Remote      Download
 2. [✗] org.musicbrainz.Picard.Locale                     stable      u      flathub      < 2.2 MB (partial)
 3. [✗] org.musicbrainz.Picard                            stable      u      flathub     < 22.5 MB

Warning: Unable to remove old checkout: Removing /home/[username]/.local/share/flatpak/.removed/org.kde.Platform-4d49c450514df9f8cfa5fe1a83b9e5cebe1fc2c9b958e8cabe4b1a23f4068d7c: unlinkat(look): Read-only file system
Warning: Read-only file system
Error: Read-only file system
Updates complete.
error: There were one or more errors

Soon after, just about every application starts to throw errors, such as Dolphin:

Configuration file "/var/home/[username]/.config/dolphinrc" not writable.
Please contact your system administrator.

Configuration file "/var/home/[username]/.config/dolphinrc" not writable.
Please contact your system administrator.

And errors even pop up when trying to open the restart menu on the computer:

Configuration file "/var/home/[username]/.config/ksmserver-logout-greeterrc" not writable.
Please contact your system administrator.

Configuration file "/var/home/[username]/.config/ksmserver-logout-greeterrc" not writable.
Please contact your system administrator.

If I were to try and update through ujust update all the following steps would throw similar errors (brew,rustup,etc). Even trying to save txt files of the logs to write this report would fail unless I wrote them to a separately mounted drive The system seems completely stable as long as I don't try to update any flatpaks, and my laptop running Aurora doesn't have this issue, so I'm not sure if the issue lies with Bazzite, or Flatpak, or something else. Any help would be greatly appreciated!

9 Replies

Linus Xu•2w ago

/home going ro tends to be some btrfs error Best bet is to check your logs for kernel oops or io errors

DylancycloneOP•2w ago

Unfortunately all logs stop as soon as I try to update a flatpak. A running journalctl -f just stops giving output, and none of the logs seem to survive the reboot Aha tried it again just in case and something did pop up:

Feb 17 21:11:00 kernel: ------------[ cut here ]------------
Feb 17 21:11:00 kernel: WARNING: CPU: 18 PID: 56650 at fs/btrfs/extent-tree.c:3219 __btrfs_free_extent.isra.0+0x726/0xa10
Feb 17 21:11:00 kernel: Modules linked in: hid_playstation ff_memless led_class_multicolor rfcomm snd_seq_dummy snd_hrtimer nf_conntrack_netbios_ns nf_conntrack_broadcast nft_fib_inet nft_fib_ipv4 nft_fib_ipv6 nft_fib nft_reject_inet nf_reject_ipv4 nf_reject_ipv6 nft_reject nft_ct nft_chain_nat nf_nat nf_conntrack >
Feb 17 21:11:00 kernel:  crct10dif_pclmul crc32_pclmul nvme crc32c_intel polyval_clmulni polyval_generic ghash_clmulni_intel sha512_ssse3 sha256_ssse3 nvme_core sha1_ssse3 sp5100_tco nvme_auth nvidia_uvm(POE) nvidia_drm(POE) nvidia_modeset(POE) nvidia(POE) amdgpu amdxcp drm_exec gpu_sched drm_suballoc_helper drm_tt>
Feb 17 21:11:00 kernel: Unloaded tainted modules: nvidia_peermem(POE):1
Feb 17 21:11:00 kernel: CPU: 18 UID: 0 PID: 56650 Comm: kworker/u98:6 Tainted: P        W  OE      6.12.12-207.bazzite.fc41.x86_64 #1
Feb 17 21:11:00 flatpak[61352]: user: Updated runtime/org.freedesktop.Platform.GL.nvidia-570-86-16/x86_64/1.4 from flathub

Feb 17 21:11:00 kernel: ------------[ cut here ]------------
Feb 17 21:11:00 kernel: WARNING: CPU: 18 PID: 56650 at fs/btrfs/extent-tree.c:3219 __btrfs_free_extent.isra.0+0x726/0xa10
Feb 17 21:11:00 kernel: Modules linked in: hid_playstation ff_memless led_class_multicolor rfcomm snd_seq_dummy snd_hrtimer nf_conntrack_netbios_ns nf_conntrack_broadcast nft_fib_inet nft_fib_ipv4 nft_fib_ipv6 nft_fib nft_reject_inet nf_reject_ipv4 nf_reject_ipv6 nft_reject nft_ct nft_chain_nat nf_nat nf_conntrack >
Feb 17 21:11:00 kernel:  crct10dif_pclmul crc32_pclmul nvme crc32c_intel polyval_clmulni polyval_generic ghash_clmulni_intel sha512_ssse3 sha256_ssse3 nvme_core sha1_ssse3 sp5100_tco nvme_auth nvidia_uvm(POE) nvidia_drm(POE) nvidia_modeset(POE) nvidia(POE) amdgpu amdxcp drm_exec gpu_sched drm_suballoc_helper drm_tt>
Feb 17 21:11:00 kernel: Unloaded tainted modules: nvidia_peermem(POE):1
Feb 17 21:11:00 kernel: CPU: 18 UID: 0 PID: 56650 Comm: kworker/u98:6 Tainted: P        W  OE      6.12.12-207.bazzite.fc41.x86_64 #1
Feb 17 21:11:00 flatpak[61352]: user: Updated runtime/org.freedesktop.Platform.GL.nvidia-570-86-16/x86_64/1.4 from flathub

Its unlike anything I've seen before, unfortunately

Linus Xu•2w ago

Then maybe try booting a live system and btrfs check from there?

DylancycloneOP•2w ago

Will any live system work? Thank you for your help, this is my first btrfs system :D

Linus Xu•2w ago

As long as they support Btrfs yes

DylancycloneOP•2w ago

btrfs check did report errors:

liveuser@localhost-live:~$ sudo btrfs check /dev/nvme0n1p3
Opening filesystem to check...
Checking filesystem on /dev/nvme0n1p3
UUID: 9f19189c-6b55-44a7-af26-33ea047df10c
[1/8] checking log skipped (none written)
[2/8] checking root items
[3/8] checking extents
data extent[111026114560, 36864] referencer count mismatch (root 257 owner 4424030 offset 0) wanted 0 have 1
data extent[111026114560, 36864] bytenr mimsmatch, extent item bytenr 111026114560 file item bytenr 0
data extent[111026114560, 36864] referencer count mismatch (root 257 owner 9223372036859199838 offset 0) wanted 1 have 0
backpointer mismatch on [111026114560 36864]
ERROR: errors found in extent allocation tree or chunk allocation
[4/8] checking free space tree
[5/8] checking fs roots
[6/8] checking only csums items (without verifying data)
[7/8] checking root refs
[8/8] checking quota groups skipped (not enabled on this FS)
found 880053747712 bytes used, error(s) found
total csum bytes: 841618960
total tree bytes: 5744967680
total fs tree bytes: 4145971200
total extent tree bytes: 576995328
btree space waste bytes: 1052258220
file data blocks allocated: 917605294080
 referenced 1073930858496

liveuser@localhost-live:~$ sudo btrfs check /dev/nvme0n1p3
Opening filesystem to check...
Checking filesystem on /dev/nvme0n1p3
UUID: 9f19189c-6b55-44a7-af26-33ea047df10c
[1/8] checking log skipped (none written)
[2/8] checking root items
[3/8] checking extents
data extent[111026114560, 36864] referencer count mismatch (root 257 owner 4424030 offset 0) wanted 0 have 1
data extent[111026114560, 36864] bytenr mimsmatch, extent item bytenr 111026114560 file item bytenr 0
data extent[111026114560, 36864] referencer count mismatch (root 257 owner 9223372036859199838 offset 0) wanted 1 have 0
backpointer mismatch on [111026114560 36864]
ERROR: errors found in extent allocation tree or chunk allocation
[4/8] checking free space tree
[5/8] checking fs roots
[6/8] checking only csums items (without verifying data)
[7/8] checking root refs
[8/8] checking quota groups skipped (not enabled on this FS)
found 880053747712 bytes used, error(s) found
total csum bytes: 841618960
total tree bytes: 5744967680
total fs tree bytes: 4145971200
total extent tree bytes: 576995328
btree space waste bytes: 1052258220
file data blocks allocated: 917605294080
 referenced 1073930858496

Linus Xu•2w ago

Then add --repair and make sure to read the warning message

DylancycloneOP•2w ago

I'm seeing many warnings that it is dangerous hah Should I not run any kind of fsck first?

Linus Xu•2w ago

Check without repair is just the fsck

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Getting "Read-Only File System" Error everywhere after updating any flatpak

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