Error on rpm-ostree upgrade: openssl-libs, hardlinking file already exists

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1

I’m blocked from upgrading with rpm-ostree. Any clues on what’s happening or how to diagnose or fix it?

➤ rpm-ostree upgrade
2 metadata, 0 content objects fetched; 788 B transferred in 2 seconds; 0 bytes content written
Checking out tree 64353f6... done
Enabled rpm-md repositories: fedora-cisco-openh264 updates fedora rpmfusion-free-updates rpmfusion-free rpmfusion-nonfree-updates rpmfusion-nonfree google-chrome rpmfusion-nonfree-nvidia-driver rpmfusion-nonfree-steam gitlab.com_paulcarroty_vscodium_repo code updates-archive
Importing rpm-md... done
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2023-03-14T10:57:01Z solvables: 4
rpm-md repo 'updates' (cached); generated: 2023-11-27T01:46:21Z solvables: 14021
rpm-md repo 'fedora' (cached); generated: 2023-11-01T00:12:39Z solvables: 70825
rpm-md repo 'rpmfusion-free-updates' (cached); generated: 2023-11-24T19:24:24Z solvables: 91
rpm-md repo 'rpmfusion-free' (cached); generated: 2023-11-04T16:49:08Z solvables: 445
rpm-md repo 'rpmfusion-nonfree-updates' (cached); generated: 2023-11-24T19:44:29Z solvables: 29
rpm-md repo 'rpmfusion-nonfree' (cached); generated: 2023-11-04T17:26:32Z solvables: 208
rpm-md repo 'google-chrome' (cached); generated: 2023-11-22T17:04:48Z solvables: 3
rpm-md repo 'rpmfusion-nonfree-nvidia-driver' (cached); generated: 2023-11-24T21:19:35Z solvables: 29
rpm-md repo 'rpmfusion-nonfree-steam' (cached); generated: 2023-08-10T16:27:35Z solvables: 2
rpm-md repo 'gitlab.com_paulcarroty_vscodium_repo' (cached); generated: 2023-11-15T22:02:52Z solvables: 5
rpm-md repo 'code' (cached); generated: 2023-11-24T17:16:39Z solvables: 491
rpm-md repo 'updates-archive' (cached); generated: 2023-11-26T03:04:34Z solvables: 12832
Resolving dependencies... done
Checking out packages... done
error: Checkout openssl-libs-1:3.1.1-4.fc39.i686: Hardlinking 81/9f6442e7e151abe15dc8b9c6e7b4f08d46c5e98e6a159006593f5b9243c276.file to ct_log_list.cnf: El fichero ya existe
2

Any issue with rpm-ostree commands must come with the output of rpm-ostree status otherwise it’s impossible to diagnose.

3

I’m also getting that same error message.

10:24:19 james@HP-Z840 ~ → rpm-ostree status
State: idle
Deployments:
● fedora:fedora/39/x86_64/silverblue
                  Version: 39.20231122.0 (2023-11-22T00:53:20Z)
               BaseCommit: ef07dc3e0b12825f7e2527699aee9808517ef6ef55889c778fe552c28180065b
             GPGSignature: Valid signature by E8F23996F23218640CB44CBE75CF5AC418B8E74C
      RemovedBasePackages: libpostproc-free libswscale-free libavformat-free libavcodec-free libswresample-free libavfilter-free libavutil-free 6.0.1-1.fc39
          LayeredPackages: akmod-nvidia borgbackup ffmpeg ffmpegthumbnailer langpacks-en lnav podman-compose rpmfusion-free-release rpmfusion-nonfree-release steam steam-devices
                           xorg-x11-drv-nvidia xorg-x11-drv-nvidia-cuda
4 
10:28:02 james@HP-Z840 ~ → rpm-ostree status -v
State: idle
AutomaticUpdates: disabled
Deployments:
● fedora:fedora/39/x86_64/silverblue (index: 0)
                  Version: 39.20231122.0 (2023-11-22T00:53:20Z)
               BaseCommit: ef07dc3e0b12825f7e2527699aee9808517ef6ef55889c778fe552c28180065b
                           ├─ repo-0 (2023-11-01T00:12:39Z)
                           ├─ repo-1 (2023-11-22T00:17:14Z)
                           └─ repo-2 (2023-11-22T00:22:10Z)
                   Commit: e29189b46ae445c14c3240ff9f6281aecc11071d000d5385cd2784a71eb4de6f
                   Staged: no
                StateRoot: fedora
             GPGSignature: 1 signature
                           Signature made Tue 21 Nov 2023 05:53:25 PM MST using RSA key ID 75CF5AC418B8E74C
                           Good signature from "Fedora <fedora-39-primary@fedoraproject.org>"
      RemovedBasePackages: libpostproc-free libswscale-free libavformat-free libavcodec-free libswresample-free libavfilter-free libavutil-free 6.0.1-1.fc39
          LayeredPackages: akmod-nvidia borgbackup ffmpeg ffmpegthumbnailer langpacks-en lnav podman-compose rpmfusion-free-release rpmfusion-nonfree-release steam steam-devices
                           xorg-x11-drv-nvidia xorg-x11-drv-nvidia-cuda
5

I notice the previous deployment has all the repos listed, but not the current deployment:

 fedora:fedora/39/x86_64/silverblue (index: 1)
                  Version: 39.20231122.0 (2023-11-22T00:53:20Z)
               BaseCommit: ef07dc3e0b12825f7e2527699aee9808517ef6ef55889c778fe552c28180065b
                           ├─ repo-0 (2023-11-01T00:12:39Z)
                           ├─ repo-1 (2023-11-22T00:17:14Z)
                           └─ repo-2 (2023-11-22T00:22:10Z)
                   Commit: 9ca5c156009ec8da1e7f44975c51f162227c5397e03f1cd97ea9ea41f32b0966
                           ├─ fedora (2023-11-01T00:12:39Z)
                           ├─ fedora-cisco-openh264 (2023-03-14T10:57:01Z)
                           ├─ google-chrome (2023-11-16T21:05:48Z)
                           ├─ phracek-PyCharm (2023-08-10T15:35:19Z)
                           ├─ rpmfusion-free (2023-11-04T16:49:08Z)
                           ├─ rpmfusion-free-updates (2023-11-21T13:11:57Z)
                           ├─ rpmfusion-nonfree (2023-11-04T17:26:32Z)
                           ├─ rpmfusion-nonfree-nvidia-driver (2023-11-07T15:52:41Z)
                           ├─ rpmfusion-nonfree-steam (2023-08-10T16:27:35Z)
                           ├─ rpmfusion-nonfree-updates (2023-11-21T13:26:18Z)
                           ├─ updates (2023-11-22T01:18:33Z)
                           └─ updates-archive (2023-11-22T01:41:52Z)
                StateRoot: fedora
             GPGSignature: 1 signature
                           Signature made Tue 21 Nov 2023 05:53:25 PM MST using RSA key ID 75CF5AC418B8E74C
                           Good signature from "Fedora <fedora-39-primary@fedoraproject.org>"
      RemovedBasePackages: libpostproc-free libswscale-free libavformat-free libavcodec-free libswresample-free libavfilter-free libavutil-free 6.0.1-1.fc39
          LayeredPackages: akmod-nvidia borgbackup ffmpeg ffmpegthumbnailer firewall-config gnome-tweaks guvcview iftop langpacks-en lnav podman-compose rpmfusion-free-release
                           rpmfusion-nonfree-release shotwell steam steam-devices tmux wl-clipboard xorg-x11-drv-nvidia xorg-x11-drv-nvidia-cuda zsh
6

I have filed a bug report on 2251795 – When updating system i686 libraries continuous problem with Steam installed but I’m having trouble connecting today. Site never loads.

7

Layering i686 packages doesn’t work very well and is thus inadvisable, in part because updates-archive isn’t multilib-enabled.

The akmods issue was reported here. That should probably be reopened if it’s affecting multiple people.

For the error in this topic, I found something similar from F38: conflict with 32 bit openssl-libs · Issue #4439 · coreos/rpm-ostree · GitHub

That one seems to be a general Fedora multilib issue: surprisingly, there doesn’t appear to be anything enforcing that multilib packages match the versions of installed x86_64 packages. Without that, rpm-ostree (or dnf) will blindly try to install a newer i686 package, possibly resulting in file conflicts. In these cases, the absence of i686 packages in updates-archive doesn’t even come into play because the resolver doesn’t know it needs them in the first place.

That said, I can’t figure out why that would be happening now on F39. There haven’t been any updates to openssl since F39 went final. However, I can reproduce the error in a VM trying to layer openssl-libs.i686 , but only when using Silverblue version 39.20231122.0. The composes immediately before and after both work.

I think the only way past this is to unlayer that package, at least temporarily.

Please open an issue here: Issues · fedora-silverblue/issue-tracker · GitHub

8

I layered the steam and steam-devices packages. That’s how I ended up with i686 packages. It runs so much better that the flatpak.

9

Yes, I did realize that. I’d expect that the vast majority of Silverblue users are using the flatpak. What is it about the RPM that runs better?

10

I use the Steam Flatpak mostly without issues. The main limitation I’ve found is that launching other apps from the Steam interface doesn’t work due to the sandbox: Adding a Non-Steam Game that is also a flatpak · Issue #616 · flathub/com.valvesoftware.Steam · GitHub

11

Yes, i noticed during the launching of the ‘steam’ flatpak, it would fail. Which most of the time it would do. I would open ‘System Monitor’ and manually shut it down, then try and launch it again.

Also, with ‘steam’ layered, when rebooting, ‘steam’ will show that is shutting down and saving before the desktop exits and reboots. It has never done that with the flatpak.

I used to use the flatpak, but got frustrated with the fails start-ups. I found on Reddit, by users there that stated they layer it. Better controller responses. I have no way of testing that, except my controller would not get recognized until I layered ‘steam-devices’ so why not layer the actual ‘steam’ package. It seems more responsive. The only drawback is the ‘rpm-ostree upgrade’ fails more often now. Due to i686 packages. Every week, there is a problem.

12

I went to the flatpak repo and saw this pinned issue: AppImage-packed games won't run · Issue #770 · flathub/com.valvesoftware.Steam · GitHub

Also I saw that there’s a list of Tested Games · flathub/com.valvesoftware.Steam Wiki · GitHub where explains that not all work.

Thus, I decided to use the RPM too for now.

13

I wouldn’t assume that most of those issues are specific to the flatpak.