Ubuntu 25.04 Flatpak: "Unable to Allocate Instance ID"

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1

Ubuntu Version: 25.04

Desktop Environment (if applicable): GNOME 48

Problem Description:

I installed flatpak following this guide https://flatpak.org/setup/Ubuntu

sudo apt install flatpak
sudo apt install gnome-software-plugin-flatpak
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

I rebooted.

I installed a few apps via the Software GUI.

zach@zach-desktop:~$ flatpak list
Name                                           Application ID                                   Version                      Branch                Installation
ProtonUp-Qt                                    net.davidotek.pupgui2                            2.12.0                       stable                system
RPCS3                                          net.rpcs3.RPCS3                                  0.0.36-1-b8d1d7cd            stable                system
Mesa                                           org.freedesktop.Platform.GL.default              25.0.3                       24.08                 system
Mesa (Extra)                                   org.freedesktop.Platform.GL.default              25.0.3                       24.08extra            system
Intel VAAPI driver                             org.freedesktop.Platform.VAAPI.Intel                                          24.08                 system
FFmpeg extension with extra codecs             org.freedesktop.Platform.ffmpeg-full                                          24.08                 system
openh264                                       org.freedesktop.Platform.openh264                2.5.1                        2.5.1                 system
Yaru-dark Gtk Theme                            org.gtk.Gtk3theme.Yaru-dark                                                   3.22                  system
KDE Application Platform                       org.kde.Platform                                                              6.8                   system
KDE Application Platform                       org.kde.Platform                                                              6.9                   system

Whenever I try to launch them I get the following error:
Unable to allocate instance id

zach@zach-desktop:~$ flatpak run net.davidotek.pupgui2
error: Unable to allocate instance id

A more verbose output:

zach@zach-desktop:~$ flatpak run --verbose net.davidotek.pupgui2
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: Skipping parental controls check for app/net.davidotek.pupgui2/x86_64/stable since parental controls are disabled globally
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: /var/lib/flatpak/runtime/org.kde.Platform/x86_64/6.8/5a2cd6ab96a55760bb957364e61b018e0ffb08dea80519711c317364e5574fa7/files/lib32 does not exist
error: Unable to allocate instance id

zach@zach-desktop:~$ flatpak run --verbose net.rpcs3.RPCS3
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: Skipping parental controls check for app/net.rpcs3.RPCS3/x86_64/stable since parental controls are disabled globally
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: /var/lib/flatpak/runtime/org.kde.Platform/x86_64/6.9/25f4e90265bbf21753ddf9b5926061cd3f5c40e9298bffbc7121d041e2457d10/files/lib32 does not exist
error: Unable to allocate instance id

Directory Permissions:

drwx------ 4 zach zach 4096 Apr 21 12:15 /home/zach/.local/share/flatpak
drwxr-xr-x 7 root root 4096 Apr 21 13:52 /var/lib/flatpak

Relevant System Information:

System Details Report

Report details

  • Date generated: 2025-04-21 13:34:26

Hardware Information:

  • Hardware Model: ASRock B560M Pro4
  • Memory: 64.0 GiB
  • Processor: 11th Gen Intel® Core™ i9-11900K × 16
  • Graphics: AMD Radeon™ Graphics (RX 9070 XT)
  • Graphics 1: Intel® Graphics (RKL GT1)
  • Disk Capacity: 27.0 TB

Software Information:

  • Firmware Version: P2.30
  • OS Name: Ubuntu 25.04
  • OS Build: (null)
  • OS Type: 64-bit
  • GNOME Version: 48
  • Windowing System: Wayland
  • Kernel Version: Linux 6.14.0-061400-generic

What I’ve Tried:

I have tried completely uninstalling flatpak:

flatpak uninstall --all
sudo apt purge --autoremove flatpak

Rebooting, then reinstalling flatpak:

sudo apt install flatpak
sudo apt install gnome-software-plugin-flatpak
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

I have tried repairing the flatpaks:

zach@zach-desktop:~$ sudo flatpak repair
[sudo] password for zach: 
Working on the system installation at /var/lib/flatpak
[25/25] Verifying flathub:runtime/org.kde.Platform/x86_64/6.8…
Checking remotes...
Pruning objects

I have tried rebooting many times as the only topics I could find online with the same error message seemed to have their problems fixed after a simple reboot.

I have tried disabling wayland and rebooting, but get the same result.

1 Like
2

I’m not getting that error:

gp
gp1343×543 451 KB

can you try to run it as:

dbus-run-session flatpak run net.davidotek.pupgui2
4

I get this:

zach@zach-desktop:~$ dbus-run-session flatpak run net.davidotek.pupgui2
dbus-daemon[184030]: [session uid=1000 pid=184030 pidfd=5] Activating service name='org.gtk.vfs.Daemon' requested by ':1.0' (uid=1000 pid=184031 comm="flatpak run net.davidotek.pupgui2")
dbus-daemon[184030]: [session uid=1000 pid=184030 pidfd=5] Successfully activated service 'org.gtk.vfs.Daemon'
error: app/net.davidotek.pupgui2/x86_64/master not installed
A connection to the bus can't be made
zach@zach-desktop:~$ fusermount3: failed to access mountpoint /run/user/1000/gvfs: Permission denied
5

Please show this:

stat /run/user/1000/gvfs
6 
zach@zach-desktop:~$ stat /run/user/1000/gvfs
  File: /run/user/1000/gvfs
  Size: 0         	Blocks: 0          IO Block: 4096   directory
Device: 0,81	Inode: 1           Links: 2
Access: (0500/dr-x------)  Uid: ( 1000/    zach)   Gid: ( 1000/    zach)
Access: 2025-04-21 12:51:00.000000000 -0500
Modify: 2025-04-21 12:51:00.000000000 -0500
Change: 2025-04-21 12:51:00.000000000 -0500
 Birth: -
7

This I did not expect, and mine has better permissions ie:

Access: (0700/drwx------)  Uid: ( 1000/      me)   Gid: ( 1000/      me)

The rest of that line on yours looks good.
Have you changed any permissions manually?

8

I haven’t changed any permissions, just an update from 24.10 to 25.04 a few weeks ago.

9

The chmod value of 0600 grants read and write permissions to the owner of the file, while denying all permissions to the group and other users.

The chmod value of 0700 sets the file permissions so that only the owner has read, write, and execute permissions, while the group and others have no permissions.

This setting can be applied to files or directories to control access, enhancing file security by limiting permissions to the owner only.

I have no idea how yours is set to 0500 mine is set @0700
Do you want to try to change it?

10

If changing it could fix it, then yeah, I’m for changing it. Worse case I can always reinstall 25.04.

11

Let’s give it a whirl then:

chmod 0700  /run/user/1000/gvfs

now try your run command.

12

I don’t believe it’s changing?

zach@zach-desktop:~$ chmod 0700  /run/user/1000/gvfs
zach@zach-desktop:~$ flatpak run --verbose net.davidotek.pupgui2
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening user flatpak installation at path /home/zach/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
error: app/net.davidotek.pupgui2/x86_64/master not installed
zach@zach-desktop:~$ stat /run/user/1000/gvfs
  File: /run/user/1000/gvfs
  Size: 0         	Blocks: 0          IO Block: 4096   directory
Device: 0,81	Inode: 1           Links: 2
Access: (0500/dr-x------)  Uid: ( 1000/    zach)   Gid: ( 1000/    zach)
Access: 2025-04-21 12:51:00.000000000 -0500
Modify: 2025-04-21 12:51:00.000000000 -0500
Change: 2025-04-21 12:51:00.000000000 -0500
 Birth: -
zach@zach-desktop:~$ sudo chmod 0700  /run/user/1000/gvfs
[sudo] password for zach: 
chmod: cannot access '/run/user/1000/gvfs': Permission denied
zach@zach-desktop:~$ dbus-run-session flatpak run net.davidotek.pupgui2
dbus-daemon[198070]: [session uid=1000 pid=198070 pidfd=5] Activating service name='org.gtk.vfs.Daemon' requested by ':1.0' (uid=1000 pid=198071 comm="flatpak run net.davidotek.pupgui2")
dbus-daemon[198070]: [session uid=1000 pid=198070 pidfd=5] Successfully activated service 'org.gtk.vfs.Daemon'
error: app/net.davidotek.pupgui2/x86_64/master not installed
A connection to the bus can't be made
zach@zach-desktop:~$ fusermount3: failed to access mountpoint /run/user/1000/gvfs: Permission denied
13

Sorry use sudo chmod 0700 /run/user/1000/gvfs

14 
zach@zach-desktop:~$ sudo chmod 0700 /run/user/1000/gvfs
chmod: cannot access '/run/user/1000/gvfs': Permission denied
15

Dang I just can’t reproduce your error, A new 25.04 Lubuntu KVM

stat /run/user/1000/gvfs
  File: /run/user/1000/gvfs
  Size: 0               Blocks: 0          IO Block: 4096   directory
Device: 0,67    Inode: 1           Links: 2
Access: (0500/dr-x------)  Uid: ( 1000/      me)   Gid: ( 1000/      me)
Access: 2025-04-21 14:25:41.000000000 -0600
Modify: 2025-04-21 14:25:41.000000000 -0600
Change: 2025-04-21 14:25:41.000000000 -0600
 Birth: -

I still show owner as 0600 where yours is locked, and I remember why. (More on that later)

gp2
gp21191×599 226 KB

~$user/.gvfs is the mount point for the FUSE interface to GVFS. GVFS is a virtual filesystem implementation for Gnome, which allows Gnome applications to access resources such as FTP or Samba servers or the content of zip files like local directories. FUSE is a way to implement filesystem drivers as user code (instead of kernel code). The GVFS-FUSE gateway makes GVFS filesystem drivers accessible to all applications, not just the ones using Gnome libraries.
So yes it is untouchable from a user space.

16

I got it lets unmount it:

umount /run/user/1000/gvfs

Now you should be able to change it:

sudo chmod 0700 /run/user/1000/gvfs

My new permissions now look like:

stat /run/user/1000/gvfs
  File: /run/user/1000/gvfs
  Size: 40              Blocks: 0          IO Block: 4096   directory
Device: 0,65    Inode: 107         Links: 2
Access: (0700/drwx------)  Uid: ( 1000/      me)   Gid: ( 1000/      me)
Access: 2025-04-21 14:25:41.123000000 -0600
Modify: 2025-04-21 14:25:41.123000000 -0600
Change: 2025-04-21 14:45:43.942018314 -0600
 Birth: 2025-04-21 14:25:41.123000000 -0600
17

Thanks for keeping at it, I super appreciate it. Unmounting it let me change it, though still the same fate. The error related to gvfs seems to be gone now though. I might just have to reinstall.

zach@zach-desktop:~$ umount /run/user/1000/gvfs
zach@zach-desktop:~$ sudo chmod 0700 /run/user/1000/gvfs
[sudo] password for zach: 
zach@zach-desktop:~$ stat /run/user/1000/gvfs
  File: /run/user/1000/gvfs
  Size: 40        	Blocks: 0          IO Block: 4096   directory
Device: 0,68	Inode: 114         Links: 2
Access: (0700/drwx------)  Uid: ( 1000/    zach)   Gid: ( 1000/    zach)
Access: 2025-04-21 12:51:00.020999639 -0500
Modify: 2025-04-21 12:51:00.020999639 -0500
Change: 2025-04-21 16:03:31.415770758 -0500
 Birth: 2025-04-21 12:51:00.020999639 -0500
zach@zach-desktop:~$ flatpak run net.davidotek.pupgui2
error: Unable to allocate instance id
zach@zach-desktop:~$ dbus-run-session flatpak run net.davidotek.pupgui2
dbus-daemon[220802]: [session uid=1000 pid=220802 pidfd=5] Activating service name='org.gtk.vfs.Daemon' requested by ':1.0' (uid=1000 pid=220803 comm="flatpak run net.davidotek.pupgui2")
dbus-daemon[220802]: [session uid=1000 pid=220802 pidfd=5] Successfully activated service 'org.gtk.vfs.Daemon'
dbus-daemon[220802]: [session uid=1000 pid=220802 pidfd=5] Activating service name='org.freedesktop.Flatpak' requested by ':1.0' (uid=1000 pid=220803 comm="flatpak run net.davidotek.pupgui2")
dbus-daemon[220802]: [session uid=1000 pid=220802 pidfd=5] Successfully activated service 'org.freedesktop.Flatpak'
error: Unable to allocate instance id
A connection to the bus can't be made
18

I’m sure it’s all related to this:

Access: 2025-04-21 12:51:00.020999639 -0500
Modify: 2025-04-21 12:51:00.020999639 -0500
Change: 2025-04-21 16:03:31.415770758 -0500
 Birth: 2025-04-21 12:51:00.020999639 -0500

It dose sound like a good possibility for a new clean install.

1 Like
19

You seem to be mixing up timestamps with permissions, the last block (the -0500 and -0600) in each line is the timezone …

21

Reinstalling 25.04 has fixed the issue, sorry to anyone searching that wanted a more proper fix.

22

I think the right is always with the ‘sudo’ command to the core and: ‘sudo flatpak update’ then ‘verify 2’ this is !!!