Flatpak not updating

myviolinsings · September 23, 2023, 10:04am

I have had this issue for some time where an update for older version will not update. This week it is for Freedesktop Platform 23.08. Notification in Linux Mint for update:
Freedesktop Platform 23.08.0
org.gnome.Platform aaabdc8963

I tried updating in terminal with the following results:

myviolinsings@mint-desktop:~$ flatpak update
Looking for updates…
Info: org.gnome.Platform//42 is end-of-life, with reason:
   The GNOME 42 runtime is no longer supported as of March 21, 2023. Please ask your application developer to migrate to a supported platform.
Applications using this runtime:
   com.github.alainm23.planner
Info: org.gnome.Platform//41 is end-of-life, with reason:
   The GNOME 41 runtime is no longer supported as of September 17, 2022. Please ask your application developer to migrate to a supported platform.
Applications using this runtime:
   com.github.needleandthread.vocal
Info: org.gnome.Platform//3.36 is end-of-life, with reason:
   The GNOME 3.36 runtime is no longer supported as of February 13, 2021. Please ask your application developer to migrate to a supported platform.
Applications using this runtime:
   com.github.bajoja.indicator-kdeconnect
Info: org.freedesktop.Platform.GL.default//19.08 is end-of-life, with reason:
   The Freedesktop SDK 19.08 runtime is no longer supported as of September 1, 2021. Please ask your application developer to migrate to a supported version


        ID                                  Branch Op Remote  Download
 1. [✗] org.freedesktop.Platform.GL.default 19.08  i  flathub     1.0 kB / 89.1 MB
 2. [✗] org.gnome.Platform                  44     u  flathub    74.4 MB / 326.8 MB
 3. [✗] org.freedesktop.Platform            21.08  u  flathub < 202.1 MB

Got the following errors:

Warning: Error deploying: While trying to checkout 37b81fce15ca2b5e8fe43de35c11510153f19731a1be37cb8214de21e56df134 into /var/lib/flatpak/runtime/org.freedesktop.Platform.GL.default/x86_64/19.08/.37b81fce15ca2b5e8fe43de35c11510153f19731a1be37cb8214de21e56df134-LJ6QB2: No such metadata object 197368830d307d6c719b215b851e4caec8a13faad97f9231cbeab4cf33e4e9e7.dirtree
Error: While pulling runtime/org.gnome.Platform/x86_64/44 from remote flathub: opcode set-read-source: Opening content object 00b482713c5fbaafabf97656534de6c18840f99e6468580a8c9494cd8960a81a: Opening content object 00b482713c5fbaafabf97656534de6c18840f99e6468580a8c9494cd8960a81a: Couldn't find file object '00b482713c5fbaafabf97656534de6c18840f99e6468580a8c9494cd8960a81a'
Error: While pulling runtime/org.freedesktop.Platform/x86_64/21.08 from remote flathub: No such metadata object 11e8bc9200e9c2bdf65c60fc7bdb58efa8ba4f27b120d01cb360f2b59807fc50.commit
Changes complete.
error: There were one or more errors

List of Flatpaks installed:

myviolinsings@mint-desktop:~$ flatpak list
Name         Application ID          Version  Branch      Origin   Installation
Bitwarden    com.bitwarden.desktop   2023.9.0 stable      flathub  system
CalenGoo     …lengoo.calengoodesktop 943      1.0         calengoo system
teams-for-l… …rtinez.teams_for_linux 1.3.5    stable      flathub  system
Planner      …ithub.alainm23.planner 3.0.10   stable      flathub  system
Indicator-K… …a.indicator-kdeconnect 0.9.4    stable      flathub  system
Vocal        ….needleandthread.vocal 2.4.2    stable      flathub  system
Heroic Game… …eroicgameslauncher.hgl v2.9.2   stable      flathub  system
Notesnook    com.notesnook.Notesnook 2.6.4    stable      flathub  system
Peek         …m.uploadedlobster.peek 1.5.1    stable      flathub  system
Sticky Notes com.vixalien.sticky     0.2.4    stable      flathub  system
Joplin       …t.cozic.joplin_desktop 2.12.17  stable      flathub  system
Mullvad Bro… …mullvad.MullvadBrowser 12.5.4   stable      flathub  system
Scribus      net.scribus.Scribus     1.5.8    stable      flathub  system
PDF Chain    …t.sourceforge.pdfchain 0.4.4.2  stable      flathub  system
Freedesktop… …g.freedesktop.Platform 21.08.19 21.08       flathub  system
Freedesktop… …g.freedesktop.Platform 22.08.15 22.08       flathub  system
ClInfo       …esktop.Platform.ClInfo          22.08       flathub  system
i386         …p.Platform.Compat.i386          22.08       flathub  system
Mesa         …op.Platform.GL.default 21.3.9   21.08       flathub  system
Mesa         …op.Platform.GL.default 23.1.6   22.08       flathub  system
Mesa (Extra) …op.Platform.GL.default 23.1.6   22.08-extra flathub  system
Mesa         …op.Platform.GL.default 23.1.7   23.08       flathub  system
Mesa (Extra) …op.Platform.GL.default 23.1.7   23.08-extra flathub  system
nvidia-535-… …rm.GL.nvidia-535-86-05          1.4         flathub  system
Mesa         ….Platform.GL32.default 23.1.6   22.08       flathub  system
nvidia-535-… ….GL32.nvidia-535-86-05          1.4         flathub  system
openh264     …ktop.Platform.openh264 2.1.0    2.0         flathub  system
openh264     …ktop.Platform.openh264 2.1.0    2.2.0       flathub  system
GNOME Appli… org.gnome.Platform               3.36        flathub  system
GNOME Appli… org.gnome.Platform               41          flathub  system
GNOME Appli… org.gnome.Platform               42          flathub  system
GNOME Appli… org.gnome.Platform               44          flathub  system
GNOME Appli… org.gnome.Platform               45          flathub  system
Mint-Y-Aqua… ….Gtk3theme.Mint-Y-Aqua          3.22        flathub  system
Mint-Y-Dark… …theme.Mint-Y-Dark-Teal          3.22        flathub  system
Mint-Y-Teal… ….Gtk3theme.Mint-Y-Teal          3.22        flathub  system
KDE Applica… org.kde.Platform                 5.15-22.08  flathub  system
Midori Web … ….midori_browser.Midori 9.0      stable      flathub  system
Cider        sh.cider.Cider          v1.6.2   stable      flathub  system

Each day the same updates appear and do not complete. I even removed the KDEConnect indicator flatpak as it was the only item listed using the older version of Gnome, but that did not fix that update issue.

I don’t know why org.freedesktop.Platform.GL.default is 19.08 vs. 22.08, but I know little about this.

Please assist with resolving these update issues as they have been ongoing for the past few months.

razzeee · September 24, 2023, 5:11pm

Seems like it can’t write or get that file, do you a have space on that disk?

myviolinsings · September 24, 2023, 6:33pm

Yes. About 150 GB available.

myviolinsings · September 28, 2023, 3:25pm

UPDATE: After several days of waiting for this update to complete, I had additional updates today for different versions of the same files along with the original ones. I chose update and it said my system was up to date. Not trusting that, I refreshed and got the following error:

E: dpkg was interrupted, you must manually run 'sudo dpkg --configure -a' to correct the problem. 
E: _cache->open() failed, please report.

I’m not sure what that means, but am reporting here. I watched the entire process because earlier this morning I did the update and left, came back to find the system froze. So watching closely this time, I saw no errors until I refreshed the update manager.

Then I went to terminal with the following results:

sudo dpkg --configure -a
[sudo] password for myviolinsings:          
Setting up nvidia-dkms-535 (535.104.05-0ubuntu0.22.04.4) ...
update-initramfs: deferring update (trigger activated)
INFO:Enable nvidia
DEBUG:Parsing /usr/share/ubuntu-drivers-common/quirks/put_your_quirks_here
DEBUG:Parsing /usr/share/ubuntu-drivers-common/quirks/dell_latitude
DEBUG:Parsing /usr/share/ubuntu-drivers-common/quirks/lenovo_thinkpad
Loading new nvidia-535.104.05 DKMS files...
Building for 5.15.0-84-generic
Building for architecture x86_64
Building initial module for 5.15.0-84-generic
Secure Boot not enabled on this system.
Done.

nvidia.ko:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/5.15.0-84-generic/updates/dkms/

nvidia-modeset.ko:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/5.15.0-84-generic/updates/dkms/

nvidia-drm.ko:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/5.15.0-84-generic/updates/dkms/

nvidia-uvm.ko:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/5.15.0-84-generic/updates/dkms/

nvidia-peermem.ko:
Running module version sanity check.
 - Original module
   - No original module exists within this kernel
 - Installation
   - Installing to /lib/modules/5.15.0-84-generic/updates/dkms/

depmod.....
Setting up libnvidia-encode-535:amd64 (535.104.05-0ubuntu0.22.04.4) ...
Setting up libnvidia-encode-535:i386 (535.104.05-0ubuntu0.22.04.4) ...
Setting up nvidia-driver-535 (535.104.05-0ubuntu0.22.04.4) ...
Processing triggers for libc-bin (2.35-0ubuntu3.3) ...
Processing triggers for man-db (2.10.2-1) ...
Processing triggers for initramfs-tools (0.140ubuntu13.4) ...
update-initramfs: Generating /boot/initrd.img-5.15.0-84-generic
myviolinsings@mint-desktop:~$

If the nvidia driver is causing this, I could just go back to the non-proprietary one provided by system package. But unsure if this is what is completely causing all the initial issues.

myviolinsings · October 5, 2023, 6:55pm

Well, since there doesn’t seem to be any resolution to this, I just removed all flatpaks and grabbed the appimages of my programs. Now computer is up to date.

barthalion · October 5, 2023, 9:01pm

Your dpkg issues have nothing to do with Flatpak whatsoever; ultimately, this is not a support forum. If you are encountering a problem with Flatpak, Flatpak’s issue tracker is the correct place to report it. If you’re having an issue with Flathub, Flathub’s issue tracker is more appropriate.

If AppImages work, more power to you.

barthalion · October 5, 2023, 9:01pm

hub · October 7, 2023, 3:44am