After upgrading to F39, no longer able to upgrade packges

[stephanlamoureux]

dnf upgrade fails for me because of this transaction test error:

Error: Transaction test error:
  file /usr/share/doc/gstreamer1/NEWS from install of gstreamer1-1.22.7-1.fc39.i686 conflicts with file from package gstreamer1-1.22.6-1.fc39.x86_64
  file /usr/share/doc/gstreamer1/RELEASE from install of gstreamer1-1.22.7-1.fc39.i686 conflicts with file from package gstreamer1-1.22.6-1.fc39.x86_64
  file /usr/share/doc/libgusb/NEWS from install of libgusb-0.4.8-1.fc39.i686 conflicts with file from package libgusb-0.4.7-1.fc39.x86_64
  file /usr/share/doc/p11-kit/NEWS from install of p11-kit-0.25.3-1.fc39.i686 conflicts with file from package p11-kit-0.25.2-1.fc39.x86_64
  file /usr/share/man/man1/trust.1.gz from install of p11-kit-0.25.3-1.fc39.i686 conflicts with file from package p11-kit-0.25.2-1.fc39.x86_64
  file /usr/share/man/man5/pkcs11.conf.5.gz from install of p11-kit-0.25.3-1.fc39.i686 conflicts with file from package p11-kit-0.25.2-1.fc39.x86_64
  file /usr/share/man/man8/p11-kit.8.gz from install of p11-kit-0.25.3-1.fc39.i686 conflicts with file from package p11-kit-0.25.2-1.fc39.x86_64

When I first upgraded to 39 everything seemed fine, however, after booting up again I kept getting stuck on a black screen and had to choose an older kernel version to get my DE to load. Today I was able to get to my desktop with the latest kernel I have (6.5.11) but there was a message stating Nvidia kernel module missing falling back to nouveau and when I try to run sudo dnf upgrade it fails because the above error. Those look like codecs from rpm fusion I believe. Any advice would be appreciated!

[computersavvy (Jeff V)]

Those packages with conflicts all have an i686 package with version that is conflicting with the x86_64 version.

It may be simple to remove the i686 version and eliminate the conflicts.

For example dnf remove gstreamer1*i686

[stephanlamoureux]

Thanks @computersavvy, using dnfdragora made it a little easier to eliminate all the 686 packages. That was able to fix the dnf errors, but I am still booting into a black screen unless I hit the ‘e’ key at the grub menu and remove the nouveau blacklist.

dnf list installed \*nvidia\* returns:

Installed Packages
akmod-nvidia.x86_64                                  3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
kmod-nvidia-6.5.11-300.fc39.x86_64.x86_64            3:545.29.06-1.fc39             @@commandline                   
kmod-nvidia-6.6.2-201.fc39.x86_64.x86_64             3:545.29.06-1.fc39             @@commandline                   
libva-nvidia-driver.x86_64                           0.0.11-1.fc39                  @updates                        
nvidia-gpu-firmware.noarch                           20231111-1.fc39                @updates                        
nvidia-modprobe.x86_64                               3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
nvidia-persistenced.x86_64                           3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
nvidia-settings.x86_64                               3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
nvidia-texture-tools.x86_64                          2.1.2-7.fc39                   @fedora-modular                 
xorg-x11-drv-nvidia.x86_64                           3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-cuda.x86_64                      3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-cuda-libs.i686                   3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-cuda-libs.x86_64                 3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-kmodsrc.x86_64                   3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-libs.i686                        3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-libs.x86_64                      3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver
xorg-x11-drv-nvidia-power.x86_64                     3:545.29.06-1.fc39             @rpmfusion-nonfree-nvidia-driver

so the drivers are there, and then I tested mokutil -l which displays that my keys are enrolled:

SHA1 Fingerprint: 7e:68:65:1d:52:68:5f:7b:f5:8e:a0:1d:78:4d:2f:90:d3:f4:0f:0a
Certificate:
    Data:
        Version: 3 (0x2)
        Serial Number: 2574709492 (0x9976f2f4)
        Signature Algorithm: sha256WithRSAEncryption
        Issuer: CN=Fedora Secure Boot CA
        Validity
            Not Before: Dec  7 16:25:54 2012 GMT
            Not After : Dec  5 16:25:54 2022 GMT
        Subject: CN=Fedora Secure Boot CA
        Subject Public Key Info:
            Public Key Algorithm: rsaEncryption
                Public-Key: (2048 bit)
                Modulus:
                    00:ae:f5:f7:52:81:a9:5c:3e:2b:f7:1d:55:f4:5a:
                    68:84:2d:bc:8b:76:96:85:0d:27:b8:18:a5:cd:c1:
                    83:b2:8c:27:5d:23:0a:d1:12:0a:75:98:a2:e6:5d:
                    01:8a:f4:d9:9f:fc:70:bc:c3:c4:17:7b:02:b5:13:
                    c4:51:92:e0:c0:05:74:b9:2e:3d:24:78:a0:79:73:
                    94:c0:c2:2b:b2:82:a7:f4:ab:67:4a:22:f3:64:cd:
                    c3:f9:0c:26:01:bf:1b:d5:3d:39:bf:c9:fa:fb:5e:
                    52:b9:a4:48:fb:13:bf:87:29:0a:64:ef:21:7b:bc:
                    1e:16:7b:88:4f:f1:40:2b:d9:22:15:47:4e:84:f6:
                    24:1c:4d:53:16:5a:b1:29:bb:5e:7d:7f:c0:d4:e2:
                    d5:79:af:59:73:02:dc:b7:48:bf:ae:2b:70:c1:fa:
                    74:7f:79:f5:ee:23:d0:03:05:b1:79:18:4f:fd:4f:
                    2f:e2:63:19:4d:77:ba:c1:2c:8b:b3:d9:05:2e:d9:
                    d8:b6:51:13:bf:ce:36:67:97:e4:ad:58:56:07:ab:
                    d0:8c:66:12:49:dc:91:68:b4:c8:ea:dd:9c:c0:81:
                    c6:91:5b:db:12:78:db:ff:c1:af:08:16:fc:70:13:
                    97:5b:57:ad:6b:44:98:7e:1f:ec:ed:46:66:95:0f:
                    05:55
                Exponent: 65537 (0x10001)
        X509v3 extensions:
            Authority Information Access: 
                CA Issuers - URI:https://fedoraproject.org/wiki/Features/SecureBoot
            X509v3 Authority Key Identifier: 
                FD:E3:25:99:C2:D6:1D:B1:BF:58:07:33:5D:7B:20:E4:CD:96:3B:42
            X509v3 Extended Key Usage: 
                Code Signing
            X509v3 Subject Key Identifier: 
                FD:E3:25:99:C2:D6:1D:B1:BF:58:07:33:5D:7B:20:E4:CD:96:3B:42
    Signature Algorithm: sha256WithRSAEncryption
    Signature Value:
        37:77:f0:3a:41:a2:1c:9f:71:3b:d6:9b:95:b5:15:df:4a:b6:
        f4:d1:51:ba:0d:04:da:9c:b2:23:f0:f3:34:59:8d:b8:d4:9a:
        75:74:65:80:17:61:3a:c1:96:7f:a7:c1:2b:d3:1a:d6:60:3c:
        71:3a:a4:c4:e3:39:03:02:15:12:08:1f:4e:cd:97:50:f8:ff:
        50:cc:b6:3e:03:7d:7a:e7:82:7a:c2:67:be:c9:0e:11:0f:16:
        2e:1e:a9:f2:6e:fe:04:bd:ea:9e:f4:a9:b3:d9:d4:61:57:08:
        87:c4:98:d8:a2:99:64:de:15:54:8d:57:79:14:1f:fa:0d:4d:
        6b:cd:98:35:f5:0c:06:bd:f3:31:d6:fe:05:1f:60:90:b6:1e:
        10:f7:24:e0:3c:f6:33:50:cd:44:c2:71:18:51:bd:18:31:81:
        1e:32:e1:e6:9f:f9:9c:02:53:b4:e5:6a:41:d6:65:b4:2e:f1:
        cf:b3:b8:82:b0:a3:96:e2:24:d8:83:ae:06:5b:b3:24:74:4d:
        d1:a4:0a:1d:0a:32:1b:75:a2:96:d1:0e:3e:e1:30:c3:18:e8:
        cb:53:c4:0b:00:ad:7e:ad:c8:49:41:ef:97:69:bd:13:5f:ef:
        ef:3c:da:60:05:d8:92:fc:da:6a:ea:48:3f:0e:3e:73:77:fd:
        a6:89:e9:3f

Turning off secure boot is not an option for me.

I have also tried:

sudo depmod -a and then restarting, and also tried:

sudo dnf remove kmod-nvidia-\*
sudo akmods

sudo akmods returns:

Checking kmods exist for 6.6.2-201.fc39.x86_64   

which is the correct kernel version.

modinfo -F version nvidia returns:

545.29.06

so it looks like I have all the things I need…

[computersavvy (Jeff V)]

That does not show your locally created key used to sign the nvidia drivers.

Running secure boot and not having the nvidia drivers signed will prevent them from loading.

1. Creating the key and importing it into the bios is done according to the instructions in /usr/share/doc/akmods/README.secureboot.
   Once the key is created and imported (and verified) then the module needs to be recompiled with the signing key – which is done with 2 additional steps.
2. remove the unsigned module that does not load with sudo dnf remove kmod-nvidia-\*
3. recreate the modules with sudo akmods --force
4. reboot

The signed modules should now load with secure boot enabled.

[stephanlamoureux]

Ok thank you! I will try this out. I never had an issue with this before during any kernel upgrade, is this just something that will need to be done for distribution upgrades?

[computersavvy (Jeff V)]

There is a common issue that may be related.

Third-party modules (e.g. Nvidia) are not rebuilt during system upgrade

Problem If you use a third-party kernel module (the most common is the Nvidia closed driver, but this might also apply to some wireless card drivers, VirtualBox, etc), it won’t be rebuilt during a system upgrade to a newer Fedora version. That means your kernel module (and the affected hardware) might not work directly after the system upgrade. In case of Nvidia, that might mean using a slow fallback graphical driver, or even failing to boot to a graphical environment at all. Note: This proble…