[Bug]: flatpak update takes 6 minutes to exit when it has nothing to do

[matt32106]

Checklist

• I agree to follow the Code of Conduct that this project adheres to.
• I have searched the issue tracker for a bug that matches the one I want to file, without success.
• If this is an issue with a particular app, I have tried filing it in the appropriate issue tracker for the app (e.g. under https://github.com/flathub/) and determined that it is an issue with Flatpak itself.
• This issue is not a report of a security vulnerability (see here if you need to report a security issue).

Flatpak version

1.12.7

What Linux distribution are you using?

Ubuntu

Linux distribution version

22.04

What architecture are you using?

x86_64

How to reproduce

2024-03-07 19:07hippo@hippo-camp2:~$ time flatpak update
Looking for updates…
Nothing to do.

real	6m2,990s
user	0m0,144s
sys	0m0,030s
2024-03-07 19:13hippo@hippo-camp2:~$ time flatpak update
Looking for updates…
Nothing to do.

real	6m2,956s
user	0m0,131s
sys	0m0,058s
2024-03-07 19:25hippo@hippo-camp2:~$ 

Expected Behavior

Exit just after writiing "Nothing to do."

Actual Behavior

Takes more than 6 min to do so.

Additional Information

No response

[chrisawi]

Please share the output with -vv:

flatpak update -vv &> flatpak.log

[matt32106]

here you are:

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/hippo/.local/share/flatpak
Looking for updates…
F: Fetching summary index file for remote ‘flathub’
F: Loading https://dl.flathub.org/repo/summary.idx using libsoup
F: Received 10001 bytes
F: Loaded indexed summary file 43438e791ec2e9f5331c04518a07a7e0a818fde2682c0ad48aebc2d190e8f3f4 from cache for remote ‘flathub’
F: Transaction: update flathub:app/com.calibre_ebook.calibre/x86_64/stable[*]
F: Transaction: update flathub:app/io.freetubeapp.FreeTube/x86_64/stable[*]
F: Transaction: update flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08[*]
F: Transaction: update flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08-extra[*]
F: Transaction: update flathub:runtime/org.freedesktop.Platform.GL.nvidia-535-161-07/x86_64/1.4[*]
F: Transaction: update flathub:runtime/org.freedesktop.Platform.Locale/x86_64/23.08[/en, /fr]
F: Transaction: update flathub:runtime/org.freedesktop.Platform.openh264/x86_64/2.2.0[*]
F: Transaction: update flathub:runtime/org.freedesktop.Platform/x86_64/23.08[*]
F: Transaction: update flathub:runtime/org.gtk.Gtk3theme.Yaru-dark/x86_64/3.22[*]
F: Transaction: update flathub:runtime/org.gtk.Gtk3theme.Yaru/x86_64/3.22[*]
F: Looking for remote metadata updates for flathub
F: marking op update:runtime/org.gtk.Gtk3theme.Yaru/x86_64/3.22 resolved to 4b1e043544efb4a6d0278a3a2deaede9f6ff61034589bdb380054121aa098952
F: marking op update:runtime/org.gtk.Gtk3theme.Yaru-dark/x86_64/3.22 resolved to d4b294293b4367fa158814d79eaf4fa2fb482f1cbf4c3e490acf5f42eb11b59f
F: marking op update:runtime/org.freedesktop.Platform/x86_64/23.08 resolved to 315f529f41050948b4e202d16193d539b6b7f499e7b435725be3987ea113e29c
F: marking op update:runtime/org.freedesktop.Platform.openh264/x86_64/2.2.0 resolved to bf24f23f3ba385f6e8c9215ed94d979db99814b0b614504a23a6d0751dc5f063
F: marking op update:runtime/org.freedesktop.Platform.Locale/x86_64/23.08 resolved to ddbe7b0c793a718ca16c27ef6fde04f8cd43f637e98f1faf82dcfbd5cdd865a7
F: marking op update:runtime/org.freedesktop.Platform.GL.nvidia-535-161-07/x86_64/1.4 resolved to 1754d056c6a8a3b1798a71e127fa6dac13e6bb4bb18275a9978088fd1ee39b4c
F: marking op update:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08-extra resolved to bec59c350d6e8126c99da5c8c5979d8493878147e7831f78113f66c237154397
F: marking op update:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08 resolved to 4b66ef1c8cde895ff24105cb34bdabb2896471318bbcb601399d4b8d60a5ae3d
F: marking op update:app/io.freetubeapp.FreeTube/x86_64/stable resolved to 7869a90dd4ae09be42c15e77e3bae5e689a021ee8029a37dbf2882a0f22df684
F: marking op update:app/com.calibre_ebook.calibre/x86_64/stable resolved to 810bbc60f573c90b67e7cd353fba056762b4bf91ca1d041d1efdf39eae674a7c
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08[*]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08-extra[*]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.GL.nvidia-535-161-07/x86_64/1.4[*]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.Locale/x86_64/23.08[/en, /fr]
F: Transaction: install/update flathub:runtime/org.gtk.Gtk3theme.Yaru-dark/x86_64/3.22[*]
F: Transaction: install/update flathub:runtime/org.gtk.Gtk3theme.Yaru/x86_64/3.22[*]
F: Transaction: install/update flathub:runtime/org.freedesktop.Platform.openh264/x86_64/2.2.0[*]
Nothing to do.
F: flathub:x86_64 appstream age 15953 is less than ttl 86400
F: flathub:x86_64 appstream age 67798740 is greater than ttl 86400
F: Updating appstream data for user remote flathub
F: Fetching summary index file for remote ‘flathub’
F: Loading https://dl.flathub.org/repo/summary.idx using libsoup
F: Received 10001 bytes
F: Loading https://dl.flathub.org/repo/summaries/7ba4a074df07f93409501735aab2b47f2d0aaa7953c2405eb6c1b701ee003314.idx.sig using libsoup
F: Received 592 bytes
F: Fetching indexed summary delta d7a6e9a2638f06951888ed2e6ec161cea952713be4275ecaae381c3ce938d257-43438e791ec2e9f5331c04518a07a7e0a818fde2682c0ad48aebc2d190e8f3f4.delta for remote ‘flathub’
F: Loading https://dl.flathub.org/repo/summaries/d7a6e9a2638f06951888ed2e6ec161cea952713be4275ecaae381c3ce938d257-43438e791ec2e9f5331c04518a07a7e0a818fde2682c0ad48aebc2d190e8f3f4.delta using libsoup
F: Received 31276 bytes
F: flatpak_dir_pull: Using commit c0b66c143c01609e0a1e9da4ad4fe538316225001331fba3f1778bafeffc40b6 for pull of ref appstream2/x86_64 from remote flathub
F: Error updating: Opening content object 65de53b5263fba526878d527da8bb61bb293aae02c8ec539f2811b59ef881b86: fgetxattr(user.ostreemeta): No data available
F: gnome:x86_64 appstream age 18446744073709551615 is greater than ttl 86400
F: Updating appstream data for user remote gnome
F: Fetching summary index file for remote ‘gnome’
F: Loading http:https://sdk.gnome.org/repo/summary.idx using libsoup
F: Should retry request (remaining: 5 retries), due to transient error: Error resolving “sdk.gnome.org”: Name or service not known
F: Loading http:https://sdk.gnome.org/repo/summary.idx using libsoup
F: Should retry request (remaining: 4 retries), due to transient error: Error resolving “sdk.gnome.org”: Name or service not known
F: Loading http:https://sdk.gnome.org/repo/summary.idx using libsoup
F: Should retry request (remaining: 3 retries), due to transient error: Error resolving “sdk.gnome.org”: Name or service not known
F: Loading http:https://sdk.gnome.org/repo/summary.idx using libsoup
F: Should retry request (remaining: 2 retries), due to transient error: Error resolving “sdk.gnome.org”: Name or service not known
F: Loading http:https://sdk.gnome.org/repo/summary.idx using libsoup
F: Should retry request (remaining: 1 retries), due to transient error: Error resolving “sdk.gnome.org”: Name or service not known
F: Loading http:https://sdk.gnome.org/repo/summary.idx using libsoup
F: Failed to download optional summary index: Error resolving “sdk.gnome.org”: Name or service not known
F: Error updating: Error updating appstream2: No such ref 'appstream2/x86_64' in remote gnome; Error updating appstream: No such ref 'appstream/x86_64' in remote gnome
F: pitivi:x86_64 appstream age 18446744073709551615 is greater than ttl 86400
F: Updating appstream data for user remote pitivi
F: Fetching summary index file for remote ‘pitivi’
F: Loading http:https://flatpak.pitivi.org/summary.idx using libsoup
F: Should retry request (remaining: 5 retries), due to transient error: Could not connect: Socket I/O timed out
F: Loading http:https://flatpak.pitivi.org/summary.idx using libsoup
F: Should retry request (remaining: 4 retries), due to transient error: Could not connect: Socket I/O timed out
F: Loading http:https://flatpak.pitivi.org/summary.idx using libsoup
F: Should retry request (remaining: 3 retries), due to transient error: Could not connect: Socket I/O timed out
F: Loading http:https://flatpak.pitivi.org/summary.idx using libsoup
F: Should retry request (remaining: 2 retries), due to transient error: Could not connect: Socket I/O timed out
F: Loading http:https://flatpak.pitivi.org/summary.idx using libsoup
F: Should retry request (remaining: 1 retries), due to transient error: Could not connect: Socket I/O timed out
F: Loading http:https://flatpak.pitivi.org/summary.idx using libsoup
F: Failed to download optional summary index: Could not connect: Socket I/O timed out
F: Error updating: Error updating appstream2: No such ref 'appstream2/x86_64' in remote pitivi; Error updating appstream: No such ref 'appstream/x86_64' in remote pitivi

[chrisawi]

You have the defunct gnome remote added. You can just delete it: flatpak remote-delete gnome.

I expect the long delay is the pitivi remote. I don't know if it's still active and temporarily offline or if it's abandoned. It's still referenced on their website.

Flatpak 1.15.6 behaves the same way. Maybe a shorter timeout than 30s would be appropriate. Flatpak probably should be more verbose here by default.

[matt32106]

I get an error trying to remove the remote:

2024-03-08 01:11hippo@hippo-camp2:~$ flatpak remote-delete gnome
error: Listing refs: opendir(refs/heads): No such file or directory

[chrisawi]

It looks like one of your flatpak installations is corrupted. You can try sudo flatpak repair and flatpak repair --user. If that doesn't help, please feel free to make a post on the Flathub Discourse.

[hfiguiere]

The action here would be to:

1. probably not retry, and just skip
2. to make the timeout error visible without -v

Also does flatpak remote-delete --force gnome work?

[matt32106]

--force gives the same error:

2024-03-08 09:31hippo@hippo-camp2:~$ flatpak remote-delete --force gnome
error: Listing refs: opendir(refs/heads): No such file or directory
2024-03-08 09:32hippo@hippo-camp2:~$ 

[matt32106]

and the repairs fail too:

2024-03-08 09:35hippo@hippo-camp2:~$ flatpak repair --user -vv
F: Opening user flatpak installation at path /home/hippo/.local/share/flatpak
Working on the user installation at /home/hippo/.local/share/flatpak
error: Listing refs: opendir(refs/heads): No such file or directory
2024-03-08 09:35hippo@hippo-camp2:~$ sudo flatpak repair -vv
[sudo] password for hippo: 
F: Opening system flatpak installation at path /var/lib/flatpak
Working on the system installation at /var/lib/flatpak
[2/21] Verifying flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08-extra…
[3/21] Verifying flathub:runtime/org.gtk.Gtk3theme.Yaru-dark/x86_64/3.22…
[5/21] Verifying flathub:runtime/org.freedesktop.Platform.GL.nvidia-535-161-07/x86_64/1.4…
[11/21] Verifying flathub:runtime/org.freedesktop.Platform/x86_64/23.08…
[12/21] Verifying flathub:app/com.calibre_ebook.calibre/x86_64/stable…
[14/21] Verifying flathub:runtime/org.freedesktop.Platform.Locale/x86_64/23.08…
[15/21] Verifying flathub:runtime/org.gtk.Gtk3theme.Yaru/x86_64/3.22…
[16/21] Verifying flathub:runtime/org.freedesktop.Platform.openh264/x86_64/2.2.0…
[19/21] Verifying flathub:app/io.freetubeapp.FreeTube/x86_64/stable…
[21/21] Verifying flathub:runtime/org.freedesktop.Platform.GL.default/x86_64/23.08…
Checking remotes...
Pruning objects
F: Pruning repo
F: Pruned 19291/0 objects, size 0 bytes
Erasing .removed
F: No installations directory in /etc/flatpak/installations.d. Skipping
2024-03-08 09:36hippo@hippo-camp2:~$ flatpak repair --user -vv
F: Opening user flatpak installation at path /home/hippo/.local/share/flatpak
Working on the user installation at /home/hippo/.local/share/flatpak
error: Listing refs: opendir(refs/heads): No such file or directory

[matt32106]

As flatpak remote-delete was not working, I vi-removed gnome and pitivi from flatpak/repo/config and now it only takes a few seconds after writing (but still a few seconds not zero see point 2 below).
This solves my issue, however some problems remain:

1- flatpak remote-delete --force gnome` should not be stopped by a semi-borked configuration, IMO it should remove what it can and especially the lines in config file

2- I don't get the logic of printing to the user "Nothing to do." when flatpak update is run and then starting to do something else (check all the lines in -vv mode that occur after "Nothing to do."). This should be changed.

3- The verbosity of flatpak update should be modified to report Socket IO errors/retries if this code stays in flatpak update.

EDIT : sorrry for the formatting, the GUI is super buggy

[homersimpsons]

For the record, I also had this issue, but I ran a flatpak update today and it is really fast. I do not understand why as there were no flatpak upgrade:

$ flatpak --version
Flatpak 1.12.7

$ time flatpak update
Looking for updates…
Nothing to do.

real	0m0,645s
user	0m0,205s
sys	0m0,046s

Here is my most recent apt upgrade, I suspect one of this upgrade to give a speed boost to flatpak because IIRC yesterday flatpak was still slow (on my machine it was ~10s):

$ sudo apt upgrade
(Reading database ... 263445 files and directories currently installed.)
Preparing to unpack .../libgnutls-dane0_3.7.3-4ubuntu1.5_amd64.deb ...
Unpacking libgnutls-dane0:amd64 (3.7.3-4ubuntu1.5) over (3.7.3-4ubuntu1.4) ...
Preparing to unpack .../libgnutls30_3.7.3-4ubuntu1.5_amd64.deb ...
Unpacking libgnutls30:amd64 (3.7.3-4ubuntu1.5) over (3.7.3-4ubuntu1.4) ...
Setting up libgnutls30:amd64 (3.7.3-4ubuntu1.5) ...
(Reading database ... 263445 files and directories currently installed.)
Preparing to unpack .../gir1.2-webkit2-4.0_2.44.0-0ubuntu0.22.04.1_amd64.deb ...
Unpacking gir1.2-webkit2-4.0:amd64 (2.44.0-0ubuntu0.22.04.1) over (2.42.5-0ubuntu0.22.04.2) ...
Preparing to unpack .../gir1.2-javascriptcoregtk-4.0_2.44.0-0ubuntu0.22.04.1_amd64.deb ...
Unpacking gir1.2-javascriptcoregtk-4.0:amd64 (2.44.0-0ubuntu0.22.04.1) over (2.42.5-0ubuntu0.22.04.2) ...
Preparing to unpack .../libwebkit2gtk-4.0-37_2.44.0-0ubuntu0.22.04.1_amd64.deb ...
Unpacking libwebkit2gtk-4.0-37:amd64 (2.44.0-0ubuntu0.22.04.1) over (2.42.5-0ubuntu0.22.04.2) ...
Preparing to unpack .../libjavascriptcoregtk-4.0-18_2.44.0-0ubuntu0.22.04.1_amd64.deb ...
Unpacking libjavascriptcoregtk-4.0-18:amd64 (2.44.0-0ubuntu0.22.04.1) over (2.42.5-0ubuntu0.22.04.2) ...
Preparing to unpack .../gnutls-bin_3.7.3-4ubuntu1.5_amd64.deb ...
Unpacking gnutls-bin (3.7.3-4ubuntu1.5) over (3.7.3-4ubuntu1.4) ...
Setting up libgnutls-dane0:amd64 (3.7.3-4ubuntu1.5) ...
Setting up libjavascriptcoregtk-4.0-18:amd64 (2.44.0-0ubuntu0.22.04.1) ...
Setting up gir1.2-javascriptcoregtk-4.0:amd64 (2.44.0-0ubuntu0.22.04.1) ...
Setting up libwebkit2gtk-4.0-37:amd64 (2.44.0-0ubuntu0.22.04.1) ...
Setting up gnutls-bin (3.7.3-4ubuntu1.5) ...
Setting up gir1.2-webkit2-4.0:amd64 (2.44.0-0ubuntu0.22.04.1) ...
Processing triggers for man-db (2.10.2-1) ...
Processing triggers for libc-bin (2.35-0ubuntu3.6) ...

$ sudo apt autoremove --purge
(Reading database ... 263445 files and directories currently installed.)
Removing libwpebackend-fdo-1.0-1:amd64 (1.14.2-0ubuntu0.22.04.1) ...
Removing libwpe-1.0-1:amd64 (1.14.0-0ubuntu0.22.04.1) ...
Processing triggers for libc-bin (2.35-0ubuntu3.6) ...
Log ended: 2024-04-16  14:48:30

Edit: I'm not entirely sure about what happens. It looks like the first call of the day is slow while the next ones are fast.

In fact when I run flatpak update the first time it will be slow (seconds to completes) while running it a second time juste after will be fast (0.4s).

This is certainly due to the following line of log:

F: flathub:x86_64 appstream age 158 is less than ttl 86400