Object missing and object invalid when i run flatpack repair probleme?

when i do a Flatpack repair, i have this lignes…

Verifying deploy/runtime/org.gimp.GIMP.Manual/x86_64/2.10…

Object missing: c94034116edcf29a5941aba309027232fda04ce3d84967d224a0ec95c0eb7da0.file

Verifying eos:os/eos/amd64/eos3a…
Object invalid: d3fa9214de0816a2cf5475da17be2036ae0eda3df526eff7c1ddee082c6e5b58.file
Object invalid: 85d04a234d7ff52a65cfae1781a3d48015f33513c9005f3a1f5285bffce76ff5.file
Object invalid: 6f1b4296984e75baf6869d4160c6530483ee15dfdc6451c885c3ea55e530b273.file
Object invalid: 2a06f8e41c4bfb16c13db25f15dcb0426e386cef0a865961c8f47702f65e1eb1.file
Object invalid: 450bcbb67e4851b17a6ec2d32200ae97c75ccb1ef3134d1a11b3fbe97cfc1335.file
Object invalid: 6a074f728257f2eca33afdd4710586ebf291146fefa5a4030c4a570eb3489f07.file
Object invalid: 8e6a77eba731b065e30085728662610feffeece8c2a52ab15e6043cc18823a8d.file
Object invalid: 4fcf2bbf64f5987d03dac1e32c81acf946aac0ab7c6ecba86b2c7f5d590255c3.file
Object invalid: 0f96ddb2439841abc052f17c3a7ddb6c6be4aaf619031481ed45dd3835cf3750.file
Object invalid: 77fca35c1377521bf28d8cbb9275cb58c40f8146ca377c9212df00c6d2b11a26.file
Object invalid: 23c0080c3441c1696bccd788273598336f1c41fdc24ee4843ba5a483545c4ea1.file
Object invalid: 96479f5897dfed74e00d536494adcc4e21dd3b84c4fa4a6281e0fd7e642f23a8.file
Object invalid: 4119b1c8767fd1976eef5417b6d98ee1d89a8b8dc566f1b342000006a01bf121.file
Object invalid: 9afc956c9d72edbae0b5914ba141aa5e7c7a88e2312f4e9810558fd65e5bf9ea.file
Object invalid: db6a639642a8c74c9bf7ca3dba24abae5acb25562478afb2232ed242d45a04bd.file
Object invalid: 2d1648bb199268749c166d2a5d4c5f63e1d986f40983caf3c3500ad84e3b8c14.file
Object invalid: c413edcb42f44265b8648a00f933b5ae21f75646f3f7a070135b70c9ca07ccfd.file
Object invalid: 9b3909f90d8bc83a8588c8196e20b841c171f806441a6317796d7d229540a073.file

Verifying ostree/0/1/1…
Object invalid: fd08983d9b33c1ae162a89482a3ebb9ac0885df890441f74da1e46eefdd6e4d5.file
Object invalid: 40da6e480e570ccc17d5fbec123cd624f3deaad15c4f059c2903ab661a73ac94.file
Object invalid: 1457e28f39cfd6f67619a32a71d10076e1464fd29beafdbbb8b82422e1ba4f77.file
Object invalid: 610d1b6c680344805c6c7be6fc0f4fe0306cb054c9ef297d56d2639095d43ce0.file
Object invalid: 4fbe7573d918f90d089fff0945fe0af49b025b75cac0d63506c4adc842dd5856.file

I’m worry about that… what can i do if i must do anything ?

This message normally indicates that there is some corruption in the OSTree repository (this is the place where all operating system files and flatpak applications store their files).

Can you please run the following command:

sudo ostree fsck --all 2>&1 | tee -a ~/ostree-fsck.txt

and upload the resulting file (ostree-fsck.txt in your home directory). Additionally, please run a diagnostic (eos-diagnostics) and upload the generated file too.

ostree-fsck.txt (67,6 Ko)
eos-diagnostic-210413_062425_UTC 0200.txt (2,6 Mo)

It seems that your Harddrive has some errors on it:

avril 12 07:58:10 localhost systemd[1]: Starting File System Check on /dev/disk/by-uuid/d44e7b3e-e22d-4c4f-a472-aafa6704984a...
avril 12 07:58:10 localhost systemd-fsck[267]: ostree contains a file system with errors, check forced.
avril 12 07:58:12 localhost systemd-fsck[267]: ostree: Inodes that were part of a corrupted orphan linked list found.
avril 12 07:58:12 localhost systemd-fsck[267]: ostree: UNEXPECTED INCONSISTENCY; RUN fsck MANUALLY.
avril 12 07:58:12 localhost systemd-fsck[267]:         (i.e., without -a or -p options)
avril 12 07:58:12 localhost systemd-fsck[265]: fsck failed with exit status 4.
avril 12 07:58:12 localhost systemd-fsck[265]: Ignoring error.

I would highly recommend you to first make a backup of all necessary data, then boot with a Live EOS USB and run:

sudo blkid

this will give you some output like:

/dev/nvme0n1p1: SEC_TYPE="msdos" UUID="B511-B02E" BLOCK_SIZE="512" TYPE="vfat" PARTUUID="157ca48f-5486-6d40-81e3-b76c4e7661d1"
/dev/nvme0n1p2: PARTUUID="cb3d3173-28b5-544a-91d5-3c93c77efa42"
/dev/nvme0n1p3: LABEL="ostree" UUID="6b4f3d49-aded-42b1-a54c-e097c5c097f6" BLOCK_SIZE="4096" TYPE="ext4" PARTUUID="364abc79-d500-344b-95b1-ee42383b7950"
/dev/sda1: LABEL="backup" UUID="95406185-05e0-4e0d-a7d5-9a167a3b673e" BLOCK_SIZE="4096" TYPE="ext4" PARTLABEL="Linux filesystem" PARTUUID="2453ff92-acdf-46b9-ad32-80c468dc789e"
/dev/zram0: UUID="1f0fabd0-9629-481e-8d88-749c7d70681e" TYPE="swap"

search for the one with the Label “OSTREE” and remember it’s device name (in my case /dev/nvme0n1p3. Then run:

sudo e2fsck -f -p /dev/nvme0n1p3

This may take quite some time. Reboot when finished and run the ostree fsck again.

i do this process.
i join the ostree file.

ostree-fsck.txt (297,2 Ko)

Can you please run:

ostree log 13c0427271adb7a13d6a04bd7d3c41f466ed2cd6a2bb4685342c139a6ba5499e

It seems that the commit in question comes from an old application which isn’t even in the repositories anymore, so we need to find out on your side which application it is.

i do but…

raphael@endless:~$ ostree log 13c0427271adb7a13d6a04bd7d3c41f466ed2cd6a2bb4685342c139a6ba5499e
error: No such metadata object 13c0427271adb7a13d6a04bd7d3c41f466ed2cd6a2bb4685342c139a6ba5499e.commit

OK, the object in question no longer exists in the repository … to fix the issue, run:

sudo ostree fsck --delete

This will remove these orphaned objects from the repository.

ok i do !! but the command don’t finish the process…

raphael@endless:~$ sudo ostree fsck --delete
Validating refs…
Validating refs in collections…
Enumerating objects…
Verifying content integrity of 186 commit objects…
fsck objects (182145/355415) [====== ] 51%Object missing in commits cb87166beb748d43caa897d76e1dcffc8969c7d3438cae6d50c71079a80137b5: 102559e5b7de94c2a8957211f8ef23e101b65831c5c458b937f70707141d77c7.dirtree

error: No such metadata object cb87166beb748d43caa897d76e1dcffc8969c7d3438cae6d50c71079a80137b5.commit

I think your errors come from the filesystem issue which had occured and damaged the repository more than i had hoped.

My recommendation is to back up your data, then verify the amount of damage your HDD has by booting a Live Installer and running:

badblocks -v /dev/sda3

If there are any errors reported, replace the disk before reinstalling the OS. If there are no errors, then they you can reinstall the OS immediatly.

ok … no error on my hdd !!
i gonna reinstall the os !


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