Purpose of /var/lib/flatpak/.removed, needs documentation

[hackel]

I recently discovered /var/lib/flatpak/.removed contained 610M in two removed-{hash} directories. I cannot find this documented anywhere other than the source code. What is the purpose of this directory? Why doesn't Flatpak automatically clean them out? Can I assume it is safe to remove manually? These directories are dated over a year ago, so I can't tell you what version I was running then. I'm currently on Flatpak 0.99.2-flatpak1~bionic on Ubuntu 18.04.

[alexlarsson]

The .removed directory contains apps/runtimes that are removed (typically due to an update), but are still in use. Each time you update something all unused things in this directory will be cleaned up.

[alexlarsson]

It the actual subdirectories are that old its unlikely that they are in use, a simple "flatpak update" should theoretically remove them. If not, something is going wrong and needs debugging.

[alexlarsson]

I believe a flatpak update will fix this, but no reply, so closing. Re-open if it fails.

[erralb]

@alexlarsson
Hi, just tried "flatpak update" but it's not working, the .removed folder still contains files

[hlev]

Flatpak 1.0.4 does not seem to remove the contents of this directory either, even with uninstall --unused, despite every app in the installation was removed beforehand.

It keeps the org.freedesktop.Platform runtime and a couple of extensions are listed in metadata that seem to have been dependencies of the previously installed applications.

[matthiasclasen]

the code for removing is here: https://github.com/flatpak/flatpak/blob/master/common/flatpak-dir.c#L8922

It gets called during install and update. it skips subdirectories of .removed that 'locked', which is indicated by having a .removed/XYZ/files/.ref file. Is that the case for your subdirectories ?

[tjanez]

It gets called during install and update. it skips subdirectories of .removed that 'locked', which is indicated by having a .removed/XYZ/files/.ref file. Is that the case for your subdirectories ?

I will try to fill-in for @hlev since I appear to be experiencing the same issue.

[tadej@toronto files]$ ls /var/lib/flatpak/.removed
org.freedesktop.Platform-73e812f33b03b170bda57c577a2ff9f15f6fe88f6b16d43415311c72751d7693
[tadej@toronto files]$ ls -al /var/lib/flatpak/.removed/org.freedesktop.Platform-73e812f33b03b170bda57c577a2ff9f15f6fe88f6b16d43415311c72751d7693/files/.ref 
-rw-r--r--. 1 root root 0 Oct  6 22:03 /var/lib/flatpak/.removed/org.freedesktop.Platform-73e812f33b03b170bda57c577a2ff9f15f6fe88f6b16d43415311c72751d7693/files/.ref

So, indeed, it appears that org.freedesktop.Platform-73e812f33b03b170bda57c577a2ff9f15f6fe88f6b16d43415311c72751d7693 is somehow locked?

Here is the list of Flatpaks I have on the system:

[tadej@toronto ~]$ flatpak list -d
Ref                                                   Origin                   Active commit Latest commit Installed size Options       
com.slack.Slack/x86_64/stable                         flathub                  af79c7981276  -               2.8 MB       system,current
org.daa.NeovimGtk/x86_64/master                       org.daa.NeovimGtk-origin bcdaf15ce78a  -               1.9 GB       system,current
org.signal.Signal/x86_64/stable                       flathub                  52833ac7c1b7  -             276.8 MB       system,current
us.zoom.Zoom/x86_64/stable                            flathub                  d67055d67ba4  -             151.0 kB       system,current
org.freedesktop.Platform.Icontheme.Adwaita/x86_64/1.0 flathub                  6e589c240937  -              25.6 MB       system,runtime
org.freedesktop.Platform.VAAPI.Intel/x86_64/1.6       flathub                  82006efc71d3  -               8.7 MB       system,runtime
org.freedesktop.Platform.VAAPI.Intel/x86_64/18.08     flathub                  cbf3d3cf9782  -               8.1 MB       system,runtime
org.freedesktop.Platform.ffmpeg/x86_64/1.6            flathub                  d757f762489e  -               7.7 MB       system,runtime
org.freedesktop.Platform.html5-codecs/x86_64/18.08    flathub                  1f2e4a4769ab  -               7.9 MB       system,runtime
org.freedesktop.Platform/x86_64/18.08                 flathub                  34c5f0a8f28a  89f04c10a9f5  935.5 MB       system,runtime
org.gnome.Platform/x86_64/3.28                        flathub                  6d1d0ebbd724  -               1.3 GB       system,runtime

Any ideas what is going on?

[hlev]

HNY

@matthiasclasen Thanks for highlighting the part of the code responsible for deletion. Unfortunately it wasn't a permalink, so I don't know if and where it goes off track.

Not sure if @tjanez has the same issue, because he has applications installed, my comment was simply related to flatpak 1.0.4 leaving unwanted files around even if you uninstall everything.

1. Install one or more applications
2. Uninstall every application
3. flatpak seems to keep the Platform runtime(s) in this directory, despite nothing possibly using it, since there's nothing installed.

There is no indication, other than decreased disk space, that these files are kept around and the client does not seem to have a command to remove everything. Cleanup has to be done manually.

I haven't used or updatet flatpak since I made the comment so this may have changed.

[BullShark]

I tried doing an update. That didn't remove it.

[plasma ~]# flatpak update Looking for updates… Nothing to do. 
[plasma ~]# sudo find /var/lib/flatpak/.removed -name '*.ref' /var/lib/flatpak/.removed/org.gnome.Platform-6a3d0df724a4617ed3527ac8cd5851f6f26b1535e278d8d23df71b65dd553675/files/.ref /var/lib/flatpak/.removed/com.leinardi.gwe-d386f950fcbcc5e9bb669f1fad167a276733195defecde28a8887cab07888f09/files/.ref 
[plasma ~]# flatpak list -d 
[plasma ~]# flatpak list 
[plasma ~]# du -sh /var/lib/flatpak/.removed    
950M    /var/lib/flatpak/.removed 
[plasma ~]# 

[ludvigng]

Are these safe to remove manually? I currently only have flatpaks installed as --user, but I did accidentally install something as --system which I later removed. These things are still left in /var/lib/flatpak/.removed though.

[khanson679]

Still an issue with Flatpak 1.8.2 (Ubuntu 20.10).

➜  ~ flatpak update                   
Looking for updates…
Nothing to do.
➜  ~ du -sh /var/lib/flatpak/.removed 
866M    /var/lib/flatpak/.removed

[llucax]

Same here. I even removed the .ref file and did a flatpak update and nothing is being removed from /var/lib/flatpak/.removed.

[ghost]

sudo flatpak repair might do the trick.

bach@kubuntu:~$ sudo flatpak repair
[sudo] password for bach: 
[16/33] Verifying flathub:runtime/org.kde.Platform/x86_64/5.14…
Checking remotes...
Pruning objects
Erasing .removed

Original thread

[kjcole]

I've moved (perhaps foolishly) all the user flatpaks to system but still have ~/.local/share/flatpak/.removed/ files even after:

reboot
flatpak update
flatpak repair
sudo flatpak update
sudo flatpak repair

[alxlg]

@kjcole same here but I solved with:

flatpak repair --user

[kjcole]

@alxlg Sometime within the past nine months the problem went away... possibly because I issued that command, but more probably because my flatpaks are now all "system" rather than "user". But thanks.

[nightmareci]

I had this same issue, a lot of space being used up by the .removed directory that I wanted to reclaim. I can confirm that merely sudo flatpak repair completely erased the system packages' .removed directory and contents:

$ sudo flatpak repair
Working on the system installation at /var/lib/flatpak
Checking remotes...
Pruning objects
Erasing .removed

That doesn't do cleanup for user packages though, do flatpak repair --user for user packages as well, to finish cleaning up everything. I ran that too, but it didn't report that .removed was erased/present.