Unable to upgrade flatpak, passt, and conmon packages after upgrading to fedora 41

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1

RPM says its unable to unpack their respective packages during installation. Trying to upgrade using dnf update --refresh .

image
image1282×569 144 KB

Also, unable to install any new flatpak apps as a result.

2

Try cleaning the caches with dnf clean all then repeat the update with dnf upgrade so it downloads both the metadata and the actual rpm files new.

3

Removed flatpak

4

Added dnf

5

tried it. still nothing changed

6

Any way I can download the .rpm files so I can try installing them manually?

7

You can download them from Koji:
passt: passt-0^20240906.g6b38f07-1.fc41 | Build Info | koji
flatpak: flatpak-1.15.10-1.fc41 | Build Info | koji
conmon: conmon-2.1.12-3.fc41 | Build Info | koji

8

Manual installation using rpm renders this error;

image
image1150×146 23.9 KB

9

Fixed the issue finally! ChatGPT helped a lot.

I gave above screenshot to chat gpt and it suggested that this might be an SELinux issue.
I might have changed the SELinux policies in the past and then forgot about it, so thought GPT might be on to something here.
It asked me to check the current profile settings using sestatus, and the ouput is as follows:-
image

After this, it asked me to set the policy to permissive with sudo setenforce 0.

My SELinux status after the change :-
image

Then I tried to update the system again, and this time there were no errors.

But, going by the first output of the sestatus command, everything seems to be set to default, then why did this issue occur at the first place?

10

Thanks everyone for helping me out!

11

This seems either an selinux issue or a packaging issue for those packages. Switching to permissive allowed the packages to be installed but enforcing did not. It seems something is wrong with the way the policy is written or the required permissions of the apps when installing.

It also may be something in the selinux context of the system that has not been properly updated and is interfering. To ensure that is not the case and verify that the entire file system has the proper selinux context you can either use sudo restorecon -R / and keep the computer active until it completes relabeling the entire file system, or use sudo touch /.autorelabel and it will do the relabel during the next boot (and take some time completing that before the system is usable).

1 Like
12

I am glad you found a workaround but changing SELinux from enforcing to permissive cannot be the solution.

Something else is wrong. Please follow above suggestion provided by @computersavvy

13

I’ve had a similar but slightly different problem. After F41 beta update:

  1. packages crun and conmon failed to update
  2. flatpak-system-helper crashed and blocked flatpak operations

both of which were related to SELinux (resolved in permissive mode). I’ve tried the sudo touch /.autorelabel method but this resulted in SELinux completely breaking (systemd: unable to fix selinux security context of file <xyz>: permission denied) and the system did not boot. I had to set it to permissive to have a working system.

dnf update error log 
...
2024-09-18T07:43:32+0000 [13163] INFO RPM callback transaction start, total 4
2024-09-18T07:43:33+0000 [13163] INFO RPM callback transaction stop, total 4
2024-09-18T07:43:33+0000 [13163] INFO RPM callback open file "/var/cache/libdnf5/updates-testing-752f7cecfe924db6/packages/crun-1.17-1.fc41.x86_64.rpm"
2024-09-18T07:43:33+0000 [13163] INFO RPM callback close file
2024-09-18T07:43:33+0000 [13163] INFO RPM callback open file "/var/cache/libdnf5/updates-testing-752f7cecfe924db6/packages/conmon-2.1.12-3.fc41.x86_64.rpm"
2024-09-18T07:43:33+0000 [13163] INFO RPM callback close file
2024-09-18T07:43:33+0000 [13163] INFO RPM callback verify start, total 2
2024-09-18T07:43:33+0000 [13163] INFO RPM callback open file "/var/cache/libdnf5/updates-testing-752f7cecfe924db6/packages/crun-1.17-1.fc41.x86_64.rpm"
2024-09-18T07:43:33+0000 [13163] INFO RPM callback close file
2024-09-18T07:43:33+0000 [13163] INFO RPM callback open file "/var/cache/libdnf5/updates-testing-752f7cecfe924db6/packages/conmon-2.1.12-3.fc41.x86_64.rpm"
2024-09-18T07:43:33+0000 [13163] INFO RPM callback close file
2024-09-18T07:43:33+0000 [13163] INFO RPM callback verify stop, total 2
2024-09-18T07:43:33+0000 [13163] INFO RPM callback transaction start, total 4
2024-09-18T07:43:33+0000 [13163] INFO RPM callback transaction stop, total 4
2024-09-18T07:43:34+0000 [13163] INFO RPM callback open file "/var/cache/libdnf5/updates-testing-752f7cecfe924db6/packages/crun-1.17-1.fc41.x86_64.rpm"
2024-09-18T07:43:34+0000 [13163] INFO RPM callback install start "crun-0:1.17-1.fc41.x86_64" total 533260
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] lsetfilecon: (36 /usr/bin/crun;66ea84a5, system_u:object_r:container_runtime_exec_t:s0) Invalid argument
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] Plugin selinux: hook fsm_file_prepare failed
2024-09-18T07:43:34+0000 [13163] INFO RPM callback install stop "crun-0:1.17-1.fc41.x86_64" amount 533260 total 533260
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] unpacking of archive failed on file /usr/bin/crun;66ea84a5: cpio: (error 0x2)
2024-09-18T07:43:34+0000 [13163] ERROR RPM callback unpack error "crun-0:1.17-1.fc41.x86_64"
2024-09-18T07:43:34+0000 [13163] INFO RPM callback close file
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] crun-1.17-1.fc41.x86_64: install failed
2024-09-18T07:43:34+0000 [13163] INFO RPM callback open file "/var/cache/libdnf5/updates-testing-752f7cecfe924db6/packages/conmon-2.1.12-3.fc41.x86_64.rpm"
2024-09-18T07:43:34+0000 [13163] INFO RPM callback install start "conmon-2:2.1.12-3.fc41.x86_64" total 171824
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] lsetfilecon: (36 /usr/bin/conmon;66ea84a5, system_u:object_r:conmon_exec_t:s0) Invalid argument
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] Plugin selinux: hook fsm_file_prepare failed
2024-09-18T07:43:34+0000 [13163] INFO RPM callback install stop "conmon-2:2.1.12-3.fc41.x86_64" amount 171824 total 171824
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] unpacking of archive failed on file /usr/bin/conmon;66ea84a5: cpio: (error 0x2)
2024-09-18T07:43:34+0000 [13163] ERROR RPM callback unpack error "conmon-2:2.1.12-3.fc41.x86_64"
2024-09-18T07:43:34+0000 [13163] INFO RPM callback close file
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] conmon-2:2.1.12-3.fc41.x86_64: install failed
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] crun-1.15-2.fc41.x86_64: erase skipped
2024-09-18T07:43:34+0000 [13163] ERROR [rpm] conmon-2:2.1.12-2.fc41.x86_64: erase skipped
flatpak-system-helper error log 
systemd[1]: Starting flatpak-system-helper.service - flatpak system helper...
(m-helper)[6575]: flatpak-system-helper.service: Unable to locate executable '/usr/libexec/flatpak-system-helper': Permission denied
(m-helper)[6575]: flatpak-system-helper.service: Failed at step EXEC spawning /usr/libexec/flatpak-system-helper: Permission denied
systemd[1]: flatpak-system-helper.service: Main process exited, code=exited, status=203/EXEC
systemd[1]: flatpak-system-helper.service: Failed with result 'exit-code'.
systemd[1]: Failed to start flatpak-system-helper.service - flatpak system helper.