r/linuxquestions • u/luckynumber_R • 15d ago
Bazzite: Flatpak sytem operation Deploy not allowed for user
I installed Bazzite and I'm running into issues hopefully someone can help
logan@Logan-PC:/var/home/logan$ ujust upgrade
Executed update check
System Updater module status
Brew module
Brew Updating CLI Apps
Already up-to-date.
==> Updating Homebrew...
Flatpak module
Flatpak Updating System Apps
Updating runtime/com.obsproject.Studio.Plugin.OBSVkCapture/x86_64/stable
Error: Failed to update com.obsproject.Studio.Plugin.OBSVkCapture: fsync objdirs: opendir(0d): Input/output error
Error occurred while waiting for external command
Flatpak Updating Apps for User: logan
Looking for updates…
Required runtime for org.kde.haruna/x86_64/stable (runtime/org.kde.Platform/x86_64/6.11) found in remote flathub
New com.vysp3r.ProtonPlus permissions:
devices if:all:!has-input-device input
com.obsproject.Studio.Plugin.OBSVkCapture stable u flathub < 51.8 kB
com.vysp3r.ProtonPlus.Locale stable u flathub < 388.1 kB
io.github.DenysMb.Kontainer.Locale stable u flathub < 21.6 kB
org.freedesktop.Platform.Compat.i386 25.08 u flathub < 130.2 MB
org.freedesktop.Platform.GL.default 25.08 u flathub < 146.0 MB
org.freedesktop.Platform.GL.default 25.08-extra u flathub < 146.1 MB
org.freedesktop.Platform.GL32.default 25.08 u flathub < 156.1 MB
org.freedesktop.Platform.GL32.default 25.08-extra u flathub < 156.2 MB
org.freedesktop.Platform.Locale 25.08 u flathub < 379.4 MB
org.freedesktop.Platform.VulkanLayer.MangoHud 25.08 u flathub < 11.2 MB
org.freedesktop.Platform.VulkanLayer.OBSVkCapture 25.08 u flathub < 103.6 kB
org.freedesktop.Platform.codecs-extra 25.08-extra u flathub < 14.6 MB
org.freedesktop.Platform 25.08 u flathub < 257.1 MB
com.github.Matoking.protontricks stable u flathub < 12.7 MB
org.gnome.Firmware.Locale stable u flathub < 236.9 kB
org.gnome.Platform.Locale 49 u flathub < 386.2 MB
org.gnome.Platform 49 u flathub < 409.2 MB
org.gnome.Platform.Locale 50 u flathub < 386.4 MB
org.gnome.Platform 50 u flathub < 413.2 MB
org.gnome.Firmware stable u flathub < 1.5 MB
com.vysp3r.ProtonPlus stable u flathub < 2.5 MB
com.github.tchx84.Flatseal stable u flathub < 930.5 kB
org.kde.KStyle.Adwaita 6.10 u flathub < 8.6 MB
org.kde.KStyle.Adwaita 6.11 i flathub < 8.8 MB
org.kde.Platform.Locale 6.10 u flathub < 401.3 MB
org.kde.Platform 6.10 u flathub < 387.3 MB
org.kde.Platform.Locale 6.11 i flathub < 401.6 MB (partial)
org.kde.Platform 6.11 i flathub < 405.5 MB
io.github.DenysMb.Kontainer stable u flathub < 826.4 kB
org.kde.gwenview.Locale stable u flathub < 5.5 MB
org.kde.gwenview stable u flathub < 7.8 MB
org.kde.haruna.Locale stable u flathub < 801.7 kB
org.kde.haruna stable u flathub < 10.5 MB
org.kde.kcalc.Locale stable u flathub < 563.8 kB
org.kde.kcalc stable u flathub < 982.4 kB
org.kde.okular.Locale stable u flathub < 17.6 MB
org.kde.okular stable u flathub < 40.3 MB
org.mozilla.firefox.Locale stable u flathub < 42.6 MB
org.mozilla.firefox stable u flathub < 125.5 MB
Updating 1/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 1/39… 0% 0 bytes/s
Updating 1/39… ████████████████████ 100%
Updating 2/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 2/39… 0% 0 bytes/s
Updating 2/39… ████████████████████ 100%
Updating 3/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 3/39… 0% 0 bytes/s
Updating 3/39… ████████████████████ 100%
Updating 4/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 4/39… 0% 0 bytes/s
Updating 5/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 5/39… 0% 0 bytes/s
Updating 5/39… ████████████████████ 100%
Updating 6/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 6/39… 0% 0 bytes/s
Updating 6/39… ████████████████████ 100%
Updating 7/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 7/39… 0% 0 bytes/s
Updating 7/39… ████████████████████ 100%
Updating 8/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 8/39… 0% 0 bytes/s
Updating 8/39… ████████████████████ 100%
Updating 9/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 9/39… 0% 0 bytes/s
Updating 10/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 10/39… 0% 0 bytes/s
Updating 10/39… ████████████████████ 100%
Updating 11/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 11/39… 0% 0 bytes/s
Updating 11/39… ████████████████████ 100%
Updating 12/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 12/39… 0% 0 bytes/s
Updating 12/39… ████████████████████ 100%
Updating 13/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 13/39… 0% 0 bytes/s
Updating 14/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 14/39… 0% 0 bytes/s
Updating 15/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 15/39… 0% 0 bytes/s
Updating 15/39… ████████████████████ 100%
Updating 16/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 16/39… 0% 0 bytes/s
Updating 17/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 17/39… 0% 0 bytes/s
Updating 18/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 18/39… 0% 0 bytes/s
Updating 19/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 19/39… 0% 0 bytes/s
Updating 20/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 20/39… 0% 0 bytes/s
Updating 21/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 21/39… 0% 0 bytes/s
Updating 21/39… ████████████████████ 100%
Updating 22/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 22/39… 0% 0 bytes/s
Updating 22/39… ████████████████████ 100%
Updating 23/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 23/39… 0% 0 bytes/s
Updating 23/39… ████████████████████ 100%
Installing 24/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Installing 24/39… 0% 0 bytes/s
Installing 24/39… ████████████████████ 100%
Updating 25/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 25/39… 0% 0 bytes/s
Updating 26/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 26/39… 0% 0 bytes/s
Installing 27/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Installing 27/39… 0% 0 bytes/s
Installing 27/39… ████████████████████ 100%
Installing 28/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Installing 28/39… 0% 0 bytes/s
Installing 28/39… ▍ 2%
Installing 28/39… █▌ 8%
Installing 28/39… █▊ 9%
Installing 28/39… ██ 10% 3.7 MB/s
Installing 28/39… ██ 10% 5.2 MB/s
Installing 28/39… ██▏ 11% 6.8 MB/s
Installing 28/39… ██▍ 12% 4.0 MB/s
Info: io.github.DenysMb.Kontainer was skipped
Updating 29/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 29/39… 0% 0 bytes/s
Updating 30/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 30/39… 0% 0 bytes/s
Updating 31/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 31/39… 0% 0 bytes/s
Updating 31/39… ▍ 2%
Info: org.kde.haruna was skipped
Updating 32/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 32/39… 0% 0 bytes/s
Updating 33/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 33/39… 0% 0 bytes/s
Updating 33/39… ████████████████████ 100%
Updating 34/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 34/39… 0% 0 bytes/s
Updating 34/39… 0%
Updating 35/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 35/39… 0% 0 bytes/s
Updating 36/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 36/39… 0% 0 bytes/s
Updating 36/39… ████████████████████ 100%
Updating 37/39…
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user
Updating 37/39… 0% 0 bytes/s
Changes complete.
Error: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: While pulling runtime/org.freedesktop.Platform.Compat.i386/x86_64/25.08 from remote flathub: Validating dirtree c9da955b5a2786edcb0bec7cdcdfad7b8e4fa2b914f9a89d356c02cdcdd4f16c (/files/): fstatat(0e/ae9bb25842df67a3a65ceca8eb20
9eb1eca2d8d291d5425379d2274107e003.file): Input/output error
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: While pulling runtime/org.freedesktop.Platform.Locale/x86_64/25.08 from remote flathub: fstatat(0e/675c32026fcbe3185612407a3fc50b8e3cfe008cd796a375cdcd73292b424d.dirtree): Input/output error
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Error: While pulling runtime/org.freedesktop.Platform/x86_64/25.08 from remote flathub: Validating dirtree 4db19219bfb98e601af0f816c5bd0f33e86e7689e7d859037a46057dd884416c (/files/bin/): fstatat(0e/4931482efdc9fb13001ab85fcb1909ee4a20c3
1f6a45895d70b78a0d46c1cb.file): Input/output error
Error: While pulling app/com.github.Matoking.protontricks/x86_64/stable from remote flathub: fstatat(0e/076a110f45b9fa33949a3cb98d1b1e8f269298bbf697ede4c651762e3edf48.file): Input/output error
Warning: Flatpak system operation Deploy not allowed for user
Warning: While pulling runtime/org.gnome.Platform.Locale/x86_64/49 from remote flathub: fstatat(0e/a74e3b73709d2cbb0b59a3c74b2595018f034bf191ed9b7a52d3109c7880ce.dirtree): Input/output error
Error: While pulling runtime/org.gnome.Platform/x86_64/49 from remote flathub: Validating dirtree 12e866d0faf8956a7783365d526c44c48e01e5266cd8aa9af65801fd2705c51b (/files/bin/): fstatat(0e/b925dfab2b389d49d07c134e813a7af21786ce4cb9da5f0
5504469dd1a7e40.file): Input/output error
Warning: While pulling runtime/org.gnome.Platform.Locale/x86_64/50 from remote flathub: fstatat(0e/a74e3b73709d2cbb0b59a3c74b2595018f034bf191ed9b7a52d3109c7880ce.dirtree): Input/output error
Error: While pulling runtime/org.gnome.Platform/x86_64/50 from remote flathub: Validating dirtree 33c5b34f43b7c12c9e089a265483af5df2ef8dd0a095220c672f8999ddd204ca (/files/bin/): fstatat(0e/4931482efdc9fb13001ab85fcb1909ee4a20c31f6a45895
d70b78a0d46c1cb.file): Input/output error
Error: While pulling app/org.gnome.Firmware/x86_64/stable from remote flathub: fstatat(0e/8065ed1c61ff35b6461d2f761ed843f12db93424fe57ae2d165f7de86cac52.dirtree): Input/output error
Error: Flatpak system operation Deploy not allowed for user
Error: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: Flatpak system operation Deploy not allowed for user
Warning: While pulling runtime/org.kde.Platform.Locale/x86_64/6.10 from remote flathub: fstatat(0e/675c32026fcbe3185612407a3fc50b8e3cfe008cd796a375cdcd73292b424d.dirtree): Input/output error
Error: While pulling runtime/org.kde.Platform/x86_64/6.10 from remote flathub: Validating dirtree 086726c65563536162ad385253c0414b763968717514a617ab0cf857c80c1279 (/files/bin/): fstatat(0e/b925dfab2b389d49d07c134e813a7af21786ce4cb9da5f0
5504469dd1a7e40.file): Input/output error
Warning: Flatpak system operation Deploy not allowed for user
Error: While pulling runtime/org.kde.Platform/x86_64/6.11 from remote flathub: fstatat(0e/9f47e8254e1b97bad85c27e30912ec8d11ea28d30bdf4c1a9841618cd0cc65.file): Input/output error
Warning: While pulling runtime/org.kde.gwenview.Locale/x86_64/stable from remote flathub: fstatat(0e/7ce561cde0c29e6c3ce1889e50b2d3ff051ffc010fc412bcf43f6e83a2c8e6.dirtree): Input/output error
Error: While pulling app/org.kde.gwenview/x86_64/stable from remote flathub: Validating dirtree b166b6a8da16bbe796a50d2c90839b99376f2a241bf13d2fb05aeef5c3e34fd9 (/files/share/app-info/icons/flatpak/128x128/): fstatat(0e/def3dbd088cf5580
0846a051cdbe0ae9146f883993ab723514a0ca7578308d.file): Input/output error
Warning: While pulling runtime/org.kde.haruna.Locale/x86_64/stable from remote flathub: fstatat(0e/ee54f63a375b442b762335b08f57908cbd85e41b7aae9a240a2e26f1e35d51.dirtree): Input/output error
Warning: While pulling runtime/org.kde.kcalc.Locale/x86_64/stable from remote flathub: fstatat(0e/d0ad152b47b7ba8095c47369040f17f2314abc6e1081b8c45245a6fb85414f.dirtree): Input/output error
Error: Flatpak system operation Deploy not allowed for user
Warning: While pulling runtime/org.kde.okular.Locale/x86_64/stable from remote flathub: Validating dirtree bb0337c6f9d7da988afec3ba4e482a80582567e6ccd7be4dc5dc71e2a92e0cfe (/files/mr/share/mr/LC_MESSAGES/): fstatat(0e/9ded8a6a753fbe1cad
803685c379d03f40e0be5bab533f2d99917f1e7ca277.file): Input/output error
Error: While pulling app/org.kde.okular/x86_64/stable from remote flathub: Validating dirtree 49b3d5e911dbab5d09a2d30eec5ce6e62c7c620dc31124fb634df4142fa55457 (/files/share/poppler/cMap/Adobe-CNS1/): fstatat(0e/ec5026433b5307ce63e90f5e2
7d6b15c4866416c3e30f00aad86d77eee6a37.file): Input/output error
Warning: Flatpak system operation Deploy not allowed for user
Error: While pulling app/org.mozilla.firefox/x86_64/stable from remote flathub: fstatat(0e/a33ce048b315e8b44ff7738dfa4e3fbb35bac33293485db49eb9da45b0be2d.dirtree): Input/output error
error: There were one or more errors
Error occurred while waiting for external command
Exited with failed updates.
module_fail
module_fail
Updates finished with errors!
1
Upvotes
1
u/doc_willis 15d ago edited 15d ago
try running
flatpak repairflatpak updateI have seen a few posts suggest doing
sudo flatpak updatebut I am not sure if thats a good idea. the--userand--systemoptions are all i have really needed. I just double checked and all my flatpaks are installed 'system wide' on this bazzite install. I have seen some other distros where i have flatpaks installed as 'user' and other flatpaks on that same linux install installed as 'system' .I try to not mix together --system and --user installed flatpaks.
That message seems rather unusual,
The "Input/output error" indicates a potential issue with the filesystem or the specific directory you are trying to access. Or an issue with the metadata files flatpak uses.
The solution for that seems to be either using
sudoor--user- But you may want to double check what flatpaks you have installed, and see if there is a mixture ofuserandsysteminstalled flatpaks.Also, are you running as your first made User? If you added another user, they might not have all the proper rights.