Permission issues #136
Description
Hi! I use uBlue Aurora (rebased from fresh fedora kinoite) and I woke up this morning with an error regarding uupd having failed. I checked the logs and I found the following:
Feb 02 04:05:27 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"System Updater module status","enabled":false}
Feb 02 04:05:27 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Brew module","module_name":"Brew","module_configuration":{"Title":"Brew","Description":"CLI Apps","Enabled":true,"MultiUser":false,"DryRun":false,"UserDescription":null}}
Feb 02 04:05:27 ThinkMercury uupd[184128]: {"level":"INFO","msg":"Updating","title":"Brew","description":"CLI Apps","progress":0,"total":2,"step_progress":0,"overall":33}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"==> Updating Homebrew..."}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"\u0007==> Homebrew collects anonymous analytics."}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Read the analytics documentation (and how to opt-out) here:"}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" https://docs.brew.sh/Analytics"}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"No analytics have been recorded yet (nor will be during this `brew` run)."}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"==> Homebrew is run entirely by unpaid volunteers. Please consider donating:"}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" https://github.com/Homebrew/brew#donations"}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updated 1 tap (homebrew/cask)."}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"==> New Casks"}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"commander: AI agent operator"}
Feb 02 04:05:32 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"elegoo-slicer: Open-source slicer for FDM 3D printers"}
Feb 02 04:05:35 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Flatpak module","module_name":"Flatpak","module_configuration":{"Title":"Flatpak","Description":"System Apps","Enabled":true,"MultiUser":true,"DryRun":false,"UserDescription":"Apps for User:"}}
Feb 02 04:05:35 ThinkMercury uupd[184128]: {"level":"INFO","msg":"Updating","title":"Flatpak","description":"System Apps","progress":1,"total":2,"step_progress":0,"overall":67}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.kde.Platform is end-of-life, with reason: We strongly recommend moving to the latest stable version of the Platform and SDK"}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.kde.Platform is end-of-life, with reason: We strongly recommend moving to the latest stable version of the Platform and SDK"}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.kde.Platform.Locale is end-of-life, with reason: We strongly recommend moving to the latest stable version of the Platform and SDK"}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.kde.Platform.Locale is end-of-life, with reason: We strongly recommend moving to the latest stable version of the Platform and SDK"}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.freedesktop.Platform.VAAPI.Intel is end-of-life, with reason: org.freedesktop.Platform 23.08 is no longer receiving fixes and security updates. Please update to a supported runtime version."}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.freedesktop.Platform.GL.default is end-of-life, with reason: org.freedesktop.Platform 23.08 is no longer receiving fixes and security updates. Please update to a supported runtime version."}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: org.freedesktop.Platform.GL.default is end-of-life, with reason: org.freedesktop.Platform 23.08 is no longer receiving fixes and security updates. Please update to a supported runtime version."}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"error: Cannot autolaunch D-Bus without X11 $DISPLAY"}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"WARN","msg":"Error occurred while waiting for external command","error":"exit status 1"}
Feb 02 04:05:38 ThinkMercury uupd[184128]: {"level":"INFO","msg":"Updating","title":"Flatpak","description":"Apps for User: linkpuff","progress":2,"total":2,"step_progress":0,"overall":100}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Looking for updates…"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: runtime org.kde.Platform branch 6.8 is end-of-life, with reason:"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" We strongly recommend moving to the latest stable version of the Platform and SDK"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: applications using this runtime:"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" com.obsproject.Studio"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: (pinned) runtime org.kde.Platform branch 5.15-23.08 is end-of-life, with reason:"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" We strongly recommend moving to the latest stable version of the Platform and SDK"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: runtime org.freedesktop.Platform.VAAPI.Intel branch 23.08 is end-of-life, with reason:"}
Feb 02 04:05:39 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" org.freedesktop.Platform 23.08 is no longer receiving fixes and security updates. Please update to a supported runtime version."}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: runtime org.freedesktop.Platform.GL.default branch 23.08-extra is end-of-life, with reason:"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" org.freedesktop.Platform 23.08 is no longer receiving fixes and security updates. Please update to a supported runtime version."}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Info: runtime org.freedesktop.Platform.GL.default branch 23.08 is end-of-life, with reason:"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" org.freedesktop.Platform 23.08 is no longer receiving fixes and security updates. Please update to a supported runtime version."}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" 1.\t \torg.kde.haruna.Locale\tstable\tu\tflathub\t< 534.4 kB (partial)"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":" 2.\t \torg.kde.haruna\tstable\tu\tflathub\t< 9.9 MB"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":""}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 1/2…"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 1/2… 0% 0 bytes/s"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 1/2… ████████████████████ 100%"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 2/2…"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user"}
Feb 02 04:05:40 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 2/2… 0% 0 bytes/s"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 2/2… ███▊ 19%"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updating 2/2… ████████████████████ 100%"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Updates complete."}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.Platform.tessdata/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.Platform.tessdata/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.Platform.VAAPI.nvidia/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.Platform.VAAPI.nvidia/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.Platform.VAAPI.Intel/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.Platform.VAAPI.Intel/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.Platform.Locale/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.Platform.Locale/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.Platform.GL.default/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.Platform.GL.default/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.Platform.CL.default/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.Platform.CL.default/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since runtime/org.fedoraproject.KDE6Platform/x86_64/f43 is already installed: No such ref 'runtime/org.fedoraproject.KDE6Platform/x86_64/f43' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.skanpage/x86_64/stable is already installed: No such ref 'app/org.kde.skanpage/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.okular/x86_64/stable is already installed: No such ref 'app/org.kde.okular/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.krdc/x86_64/stable is already installed: No such ref 'app/org.kde.krdc/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.kolourpaint/x86_64/stable is already installed: No such ref 'app/org.kde.kolourpaint/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.kmines/x86_64/stable is already installed: No such ref 'app/org.kde.kmines/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.kmahjongg/x86_64/stable is already installed: No such ref 'app/org.kde.kmahjongg/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.kcalc/x86_64/stable is already installed: No such ref 'app/org.kde.kcalc/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.gwenview/x86_64/stable is already installed: No such ref 'app/org.kde.gwenview/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"F: Warning: Treating remote fetch error as non-fatal since app/org.kde.elisa/x86_64/stable is already installed: No such ref 'app/org.kde.elisa/x86_64/stable' in remote fedora"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Warning: Flatpak system operation Deploy not allowed for user"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"Error: Flatpak system operation Deploy not allowed for user"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"DEBUG","msg":"error: There were one or more errors"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"WARN","msg":"Error occurred while waiting for external command","error":"exit status 1"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"WARN","msg":"Exited with failed updates."}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"ERROR","msg":"module_fail","output":{"Stdout":"","Failure":true,"Stderr":null,"Context":"System Apps","Cli":["/usr/bin/flatpak","update","-y","--noninteractive"]},"module":"System Apps","cli":"/usr/bin/flatpak update -y --noninteractive"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"ERROR","msg":"module_fail","output":{"Stdout":"","Failure":true,"Stderr":null,"Context":"Apps for User: linkpuff","Cli":["/usr/bin/flatpak","update","-y"]},"module":"Apps for User: linkpuff","cli":"/usr/bin/flatpak update -y"}
Feb 02 04:05:41 ThinkMercury uupd[184128]: {"level":"ERROR","msg":"Updates finished with errors!"}
Feb 02 04:05:41 ThinkMercury systemd[1]: uupd.service: Deactivated successfully.
According to the logs, uupd already succeeded before once, so this is a bit bizarre.
here's the output of my id command:
uid=1000(linkpuff) gid=1000(linkpuff) groups=1000(linkpuff),10(wheel),951(docker),953(incus-admin),956(libvirt),995(plugdev) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023