Bluefin 41 System Update Fails with "SQL statement evaluation failed ... attempt to write a readonly database"

[rexmtorres]

Describe the bug

Whenever I run "System Update", it fails with the said error. Below is the full console output:

── 06:52:01 - System update ────────────────────────────────────────────────────
[sudo] password for rex: 
Updating and loading repositories:
 RPM Fusion for Fedora 41 - Nonfree - Steam                                                                                                                                                                           100% |   7.8 KiB/s |  16.0 KiB |  00m02s
 Scooter Software                                                                                                                                                                                                     100% |   1.4 KiB/s |   3.0 KiB |  00m02s
 RPM Fusion for Fedora 41 - Nonfree - NVIDIA Driver                                                                                                                                                                   100% |  15.4 KiB/s |  17.0 KiB |  00m01s
 Copr repo for PyCharm owned by phracek                                                                                                                                                                               100% |   1.8 KiB/s |   2.1 KiB |  00m01s
 MEGAsync                                                                                                                                                                                                             100% |   2.1 KiB/s |   1.6 KiB |  00m01s
 google-chrome                                                                                                                                                                                                        100% |   4.5 KiB/s |   1.3 KiB |  00m00s
 Fedora 41 - x86_64 - Updates Archive                                                                                                                                                                                 100% |   2.3 KiB/s |   3.4 KiB |  00m01s
 Fedora 41 - x86_64 - Updates                                                                                                                                                                                         100% |  23.7 KiB/s |  34.3 KiB |  00m01s
 google-chrome                                                                                                                                                                                                        100% |   7.4 KiB/s |   3.2 KiB |  00m00s
 Fedora 41 - x86_64 - Updates Archive                                                                                                                                                                                 100% |   1.7 MiB/s |   1.9 MiB |  00m01s
 Fedora 41 - x86_64 - Updates                                                                                                                                                                                         100% | 481.4 KiB/s |   2.1 MiB |  00m04s
Repositories loaded.
Package                                                                            Arch          Version                                                                             Repository                                                           Size
Upgrading:
 fwupd                                                                             x86_64        1.9.28-1.fc41                                                                       updates                                                           7.5 MiB
   replacing fwupd                                                                 x86_64        1.9.26-100.ublue                                                                    copr:copr.fedorainfracloud.org:ublue-os:staging                   7.4 MiB
 fwupd-plugin-flashrom                                                             x86_64        1.9.28-1.fc41                                                                       updates                                                          35.8 KiB
   replacing fwupd-plugin-flashrom                                                 x86_64        1.9.26-100.ublue                                                                    copr:copr.fedorainfracloud.org:ublue-os:staging                  35.8 KiB
 fwupd-plugin-modem-manager                                                        x86_64        1.9.28-1.fc41                                                                       updates                                                         137.3 KiB
   replacing fwupd-plugin-modem-manager                                            x86_64        1.9.26-100.ublue                                                                    copr:copr.fedorainfracloud.org:ublue-os:staging                 137.3 KiB
 fwupd-plugin-uefi-capsule-data                                                    x86_64        1.9.28-1.fc41                                                                       updates                                                           2.0 MiB
   replacing fwupd-plugin-uefi-capsule-data                                        x86_64        1.9.26-100.ublue                                                                    copr:copr.fedorainfracloud.org:ublue-os:staging                   2.0 MiB
 gnome-online-accounts                                                             x86_64        3.53.1-3.fc41                                                                       updates                                                           2.2 MiB
   replacing gnome-online-accounts                                                 x86_64        3.53.0-1.fc41                                                                       <unknown>                                                         2.2 MiB
 gnome-shell                                                                       x86_64        47.3-1.fc41                                                                         updates                                                          13.7 MiB
   replacing gnome-shell                                                           x86_64        47.2-1.fc41.switcheroo.0.0.git.218.d8c42b2e                                         copr:copr.fedorainfracloud.org:ublue-os:staging                  13.7 MiB
 gnome-software                                                                    x86_64        47.4-1.fc41                                                                         updates                                                          12.1 MiB
   replacing gnome-software                                                        x86_64        47.1-101.ublue.fc41                                                                 <unknown>                                                        12.0 MiB
 libX11                                                                            x86_64        1.8.11-1.fc41                                                                       updates                                                           1.3 MiB
   replacing libX11                                                                x86_64        1.8.10-2.fc41                                                                       <unknown>                                                         1.3 MiB
 libX11-common                                                                     noarch        1.8.11-1.fc41                                                                       updates                                                           1.2 MiB
   replacing libX11-common                                                         noarch        1.8.10-2.fc41                                                                       <unknown>                                                         1.1 MiB
 libX11-xcb                                                                        x86_64        1.8.11-1.fc41                                                                       updates                                                          15.0 KiB
   replacing libX11-xcb                                                            x86_64        1.8.10-2.fc41                                                                       <unknown>                                                        15.0 KiB
 libopenjph                                                                        x86_64        0.18.2-1.fc41                                                                       updates                                                         442.5 KiB
   replacing libopenjph                                                            x86_64        0.18.0-1.fc41                                                                       <unknown>                                                       444.9 KiB
 python3-boto3                                                                     noarch        1.36.12-1.fc41                                                                      updates                                                           2.1 MiB
   replacing python3-boto3                                                         noarch        1.36.7-1.fc41                                                                       <unknown>                                                         2.1 MiB
 python3-botocore                                                                  noarch        1.36.12-1.fc41                                                                      updates                                                          99.7 MiB
   replacing python3-botocore                                                      noarch        1.36.7-1.fc41                                                                       <unknown>                                                        99.6 MiB
 tuned                                                                             noarch        2.25.1-1.fc41                                                                       updates                                                           1.6 MiB
   replacing tuned                                                                 noarch        2.25.0-1.fc41                                                                       <unknown>                                                         1.6 MiB
 tuned-ppd                                                                         noarch        2.25.1-1.fc41                                                                       updates                                                           6.9 KiB
   replacing tuned-ppd                                                             noarch        2.25.0-1.fc41                                                                       <unknown>                                                         6.9 KiB
Installing weak dependencies:
 gnome-software-rpm-ostree                                                         x86_64        47.4-1.fc41                                                                         updates                                                         262.4 KiB

Transaction Summary:
 Installing:         1 package
 Upgrading:         15 packages
 Replacing:         15 packages

Total size of inbound packages is 19 MiB. Need to download 10 MiB.
After this operation, 629 KiB extra will be used (install 144 MiB, remove 144 MiB).
[1/1] gnome-software-rpm-ostree-0:47.4-1.fc41.x86_64                                                                                                                                                                  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[1/2] fwupd-0:1.9.28-1.fc41.x86_64                                                                                                                                                                                    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[1/3] fwupd-plugin-flashrom-0:1.9.28-1.fc41.x86_64                                                                                                                                                                    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[1/4] fwupd-plugin-modem-manager-0:1.9.28-1.fc41.x86_64                                                                                                                                                               100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[1/5] fwupd-plugin-uefi-capsule-data-0:1.9.28-1.fc41.x86_64                                                                                                                                                           100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[1/7] gnome-shell-0:47.3-1.fc41.x86_64                                                                                                                                                                                100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[2/8] gnome-software-0:47.4-1.fc41.x86_64                                                                                                                                                                             100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[ 3/12] libopenjph-0:0.18.2-1.fc41.x86_64                                                                                                                                                                             100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               0% [<=>               ] |   0.0   B/s |   0.0   B |  00m00s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               0% [<=>               ] |   0.0   B/s |   0.0   B |  00m00s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               0% [<=>               ] |   0.0   B/s |   0.0   B |  00m00s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               0% [<=>               ] |   0.0   B/s |   0.0   B |  00m00s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               0% [ <=>              ] |   0.0   B/s |   0.0   B |  00m00s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               2% [                  ] |  22.2 KiB/s |  13.8 KiB |  00m23s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                               7% [=                 ] |  22.2 KiB/s |  42.1 KiB |  00m22s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              18% [===               ] |  22.2 KiB/s | 100.1 KiB |  00m19s
[ 4/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              31% [======            ] | 177.7 KiB/s | 172.2 KiB |  00m02s
[ 4/16] libX11-common-0:1.8.11-1.fc41.noarch                                                                                                                                                                          100% | 181.2 KiB/s | 176.1 KiB |  00m01s
[ 5/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              31% [======            ] | 177.7 KiB/s | 172.2 KiB |  00m02s
[ 5/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              48% [=========         ] | 177.7 KiB/s | 259.9 KiB |  00m01s
[ 5/16] libX11-xcb-0:1.8.11-1.fc41.x86_64                                                                                                                                                                             100% |  87.8 KiB/s |  11.8 KiB |  00m00s
[ 6/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              51% [=========         ] | 177.7 KiB/s | 276.8 KiB |  00m01s
[ 6/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              67% [============      ] | 177.7 KiB/s | 364.5 KiB |  00m00s
[ 6/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              83% [===============   ] | 177.7 KiB/s | 452.2 KiB |  00m00s
[ 6/16] libX11-0:1.8.11-1.fc41.x86_64                                                                                                                                                                                 100% | 495.6 KiB/s | 650.3 KiB |  00m01s
[ 7/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                              90% [================  ] | 177.7 KiB/s | 486.1 KiB |  00m00s
[ 7/16] gnome-online-accounts-0:3.53.1-3.fc41.x86_64                                                                                                                                                                  100% | 392.5 KiB/s | 539.3 KiB |  00m01s
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                     29% [=====             ] |   4.0   B/s | 122.7 KiB |  20h46m
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                     32% [======            ] |   4.0   B/s | 136.9 KiB |  19h46m
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                     58% [===========       ] |   4.0   B/s | 244.3 KiB |  12h07m
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                     80% [===============   ] |   4.0   B/s | 334.8 KiB |  05h41m
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                     96% [================= ] |   4.0   B/s | 398.5 KiB |  01h09m
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                     96% [================= ] |   4.0   B/s | 398.5 KiB |  01h09m
[ 8/16] python3-boto3-0:1.36.12-1.fc41.noarch                                                                                                                                                                         100% | 596.9 KiB/s | 414.8 KiB |  00m01s
[ 9/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                   5% [=                 ] |   2.0   B/s | 411.2 KiB |  44d05h
[ 9/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                   8% [=                 ] |   2.0   B/s | 631.8 KiB |  42d21h
[ 9/16] tuned-ppd-0:2.25.1-1.fc41.noarch                                                                                                                                                                              100% | 148.9 KiB/s |  21.2 KiB |  00m00s
[10/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                   8% [==                ] | 708.9 KiB/s | 692.6 KiB |  00m10s
[10/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  10% [==                ] | 708.9 KiB/s | 846.7 KiB |  00m09s
[10/16] tuned-0:2.25.1-1.fc41.noarch                                                                                                                                                                                  100% | 817.7 KiB/s | 533.1 KiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  11% [==                ] | 708.9 KiB/s | 873.6 KiB |  00m09s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  13% [===               ] | 708.9 KiB/s |   1.1 MiB |  00m09s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  16% [===               ] | 708.9 KiB/s |   1.2 MiB |  00m09s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  19% [===               ] | 708.9 KiB/s |   1.5 MiB |  00m08s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  22% [====              ] | 708.9 KiB/s |   1.7 MiB |  00m08s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  25% [=====             ] | 708.9 KiB/s |   1.9 MiB |  00m08s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  28% [=====             ] | 708.9 KiB/s |   2.2 MiB |  00m07s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  31% [======            ] | 708.9 KiB/s |   2.4 MiB |  00m07s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  34% [======            ] | 708.9 KiB/s |   2.6 MiB |  00m07s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  37% [=======           ] |   2.2 MiB/s |   2.9 MiB |  00m02s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  40% [=======           ] |   2.2 MiB/s |   3.1 MiB |  00m02s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  44% [========          ] |   2.2 MiB/s |   3.5 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  49% [=========         ] |   2.2 MiB/s |   3.8 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  53% [==========        ] |   2.2 MiB/s |   4.1 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  56% [==========        ] |   2.2 MiB/s |   4.4 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  61% [===========       ] |   2.2 MiB/s |   4.7 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  65% [============      ] |   2.2 MiB/s |   5.0 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  69% [=============     ] |   2.2 MiB/s |   5.3 MiB |  00m01s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  74% [=============     ] |   2.2 MiB/s |   5.7 MiB |  00m00s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  78% [==============    ] |   3.0 MiB/s |   6.1 MiB |  00m00s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  85% [===============   ] |   3.0 MiB/s |   6.5 MiB |  00m00s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  88% [================  ] |   3.0 MiB/s |   6.8 MiB |  00m00s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  93% [================= ] |   3.0 MiB/s |   7.2 MiB |  00m00s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                  99% [==================] |   3.0 MiB/s |   7.7 MiB |  00m00s
[11/16] python3-botocore-0:1.36.12-1.fc41.noarch                                                                                                                                                                      100% |   2.5 MiB/s |   7.7 MiB |  00m03s
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[16/16] Total                                                                                                                                                                                                         100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
SQL statement evaluation failed: "
    INSERT INTO
        "trans" (
            "dt_begin",
            "dt_end",
            "rpmdb_version_begin",
            "rpmdb_version_end",
            "releasever",
            "user_id",
            "description",
            "comment",
            "state_id",
            "id"
        )
        VALUES
            (1738882355, 0, 'cf281eb3547866ec1531775380a6773f6987525ffbea9b25ded625ada6f9d69c', '', '41', 1000, '/usr/bin/dnf upgrade -y', '', (SELECT "id" FROM "trans_state" WHERE "name" = 'Started'), NULL)
": (8) - attempt to write a readonly database
System update failed: 
   0: Command failed: `/usr/bin/sudo /usr/bin/dnf upgrade -y`
   1: `/usr/bin/sudo` failed: exit status: 1

Location:
   src/steps/os/linux.rs:259
Retry? (y)es/(N)o/(s)hell/(q)uit

What did you expect to happen?

System update should successfully update my system.

Output of bootc status

● Booted ostree
           Commit: a33d7218157bf4f4205cee910c68df722902f7e8503fab2c5d573dbdf35f5a4e

  Rollback ostree
           Commit: 9c383297201dd1d00ab299e7c6d39ccc0265b00045f0442d4db0ddf5e6b9cd54

Output of groups

rex wheel

Extra information or context

I had my system on hibernate for a couple of weeks. When I woke it up, I ran System Update and it updated. However, my layered package "Beyond Compare" did not update. So I manually updated it. Everything seemed fine. The next day, I ran System Update again and started getting that error. I attempted System Update several times and got the same error all the time. After a few days, I attempted System Update again. There were now a few more updates but it still failed with the same error.

[castrojo]

do an rpm-ostree update to manually force the update.

[m2Giles]

Please try running rpm-ostree upgrade