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[Bug]: update deadlocks because of reaper #6733

Description

@asg0451

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

1.17.6

What Linux distribution are you using?

Fedora Silverblue

Linux distribution version

Bazzite 43 (Fedora Atomic 44 base, kernel 6.19.14)

What architecture are you using?

x86_64

How to reproduce

run flatpak update. it hangs forever at 1/ 100%

Expected Behavior

i expected update not to hang forever

Actual Behavior

it does hang forever

Additional Information

i asked claude to root cause this for me as i'm not too familiar with flatpaks. his analysis below:

▎ During a 35-ref flatpak update -y --noninteractive, the apply_extra step of fm.reaper.Reaper (extra-data) hangs forever. The extraction (tar xf reaper.tar.xz → xz -d; freedesktop 25.08 runtime, tar 1.35 / xz 5.8.3) sleeps at 0 CPU from the first second — a 13.6 MB tarball that should take ~1s. The tarball is complete (13,599,360 bytes, matches the manifest's extra-data size, sha256 already verified), so this isn't a truncated download.
▎
▎ Since the hung process holds the system installation lock, every other flatpak install/update on the machine blocks. One wedged run went unnoticed for 6 weeks (uupd.service: Consumed 15.705s CPU time over 3w 4d 18h ... wall clock time).

 State at hang time:
▎
▎ uupd(4020370)─flatpak update -y --noninteractive(4021653)
▎   └─bwrap(4022328)─bwrap(4022329)─sh /app/bin/apply_extra(4022330)
▎       └─tar xf reaper.tar.xz -C /app/extra/export/share(4022332)
▎           └─xz -d(4022333)

this reproduces easily.

Activity

  1. mexow182 commented on Jul 18, 2026

    @mexow182

    Great work

  2. asg0451 commented on Aug 8, 2026

    @asg0451
    Author

    anyone avaailable to look at this?

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