flatpak not working at all on new install

[citizen428]

Brand new install of Aurora (NVIDIA). Everything installed fine. I booted into it, ran ujust devmode, all good so far. However, nothing related to flatpak works:

/usr/bin/flatpak (part of Bazaar) has encountered a fatal error and was closed. 

Getting a similar message when trying to start Firefox.

The crash reporter shows a core dump:

 PID: 5963 (flatpak) UID: 1000 (me) GID: 1000 (me) Signal: 6 (ABRT) Timestamp: Wed 2026-03-04 16:44:39 +07 (3s ago) Command Line: /usr/bin/flatpak run --branch=stable --arch=x86_64 --command=bazaar --file-forwarding io.github.kolunmi.Bazaar @@u @@ Executable: /usr/bin/flatpak Control Group: /user.slice/user-1000.slice/user@1000.service/app.slice/app-io.github.kolunmi.Bazaar@4f0e8a8b893b4090b3d0bac85c15d51e.service Unit: user@1000.service User Unit: app-io.github.kolunmi.Bazaar@4f0e8a8b893b4090b3d0bac85c15d51e.service Slice: user-1000.slice Owner UID: 1000 (me) Boot ID: e8d2498d88f64364b8c94a98a0b8694c Machine ID: 5abf48cb3cee47d189e55da2929ea0c2 Hostname: aurora Storage: /var/lib/systemd/coredump/core.flatpak.1000.e8d2498d88f64364b8c94a98a0b8694c.5963.1772617479000000.zst (present) Size on Disk: 478K Message: Process 5963 (flatpak) of user 1000 dumped core. Module libgvfscommon.so from rpm gvfs-1.58.1-1.fc43.x86_64 Module libgvfsdbus.so from rpm gvfs-1.58.1-1.fc43.x86_64 Module libkeyutils.so.1 from rpm keyutils-1.6.3-6.fc43.x86_64 Module libkrb5support.so.0 from rpm krb5-1.22.2-2.fc43.x86_64 Module libcom_err.so.2 from rpm e2fsprogs-1.47.3-2.fc43.x86_64 Module libk5crypto.so.3 from rpm krb5-1.22.2-2.fc43.x86_64 Module libkrb5.so.3 from rpm krb5-1.22.2-2.fc43.x86_64 Module libunistring.so.5 from rpm libunistring-1.1-10.fc43.x86_64 Module libattr.so.1 from rpm attr-2.5.2-6.fc43.x86_64 Module libblkid.so.1 from rpm util-linux-2.41.3-7.fc43.x86_64 Module libgssapi_krb5.so.2 from rpm krb5-1.22.2-2.fc43.x86_64 Module libssl.so.3 from rpm openssl-3.5.4-2.fc43.x86_64 Module libidn2.so.0 from rpm libidn2-2.3.8-2.fc43.x86_64 Module libnghttp2.so.14 from rpm nghttp2-1.66.0-2.fc43.x86_64 Module libbz2.so.1 from rpm bzip2-1.0.8-21.fc43.x86_64 Module liblz4.so.1 from rpm lz4-1.10.0-3.fc43.x86_64 Module libacl.so.1 from rpm acl-2.3.2-4.fc43.x86_64 Module libcap.so.2 from rpm libcap-2.76-3.fc43.x86_64 Module libcomposefs.so.1 from rpm composefs-1.0.8-3.fc43.x86_64 Module libcrypto.so.3 from rpm openssl-3.5.4-2.fc43.x86_64 Module liblzma.so.5 from rpm xz-5.8.1-4.fc43.x86_64 Module libgpg-error.so.0 from rpm libgpg-error-1.55-2.fc43.x86_64 Module libstemmer.so.0 from rpm snowball-3.0.1-8.fc43.x86_64 Module libfyaml.so.0 from rpm libfyaml-0.8-8.fc43.x86_64 Module libxmlb.so.2 from rpm libxmlb-0.3.24-1.fc43.x86_64 Module libffi.so.8 from rpm libffi-3.5.2-1.fc43.x86_64 Module libselinux.so.1 from rpm libselinux-3.9-5.fc43.x86_64 Module libmount.so.1 from rpm util-linux-2.41.3-7.fc43.x86_64 Module libz.so.1 from rpm zlib-ng-2.3.3-1.fc43.x86_64 Module libgmodule-2.0.so.0 from rpm glib2-2.86.4-1.fc43.x86_64 Module libpcre2-8.so.0 from rpm pcre2-10.47-1.fc43.x86_64 Module libwayland-client.so.0 from rpm wayland-1.24.0-1.fc43.x86_64 Module libXau.so.6 from rpm libXau-1.0.12-3.fc43.x86_64 Module libmalcontent-0.so.0 from rpm malcontent-0.13.0-3.fc43.x86_64 Module libzstd.so.1 from rpm zstd-1.5.7-2.fc43.x86_64 Module libxml2.so.2 from rpm libxml2-2.12.10-5.fc43.x86_64 Module libseccomp.so.2 from rpm libseccomp-2.6.0-2.fc43.x86_64 Module libcurl.so.4 from rpm curl-8.15.0-5.fc43.x86_64 Module libarchive.so.13 from rpm libarchive-3.8.4-1.fc43.x86_64 Module libdconf.so.1 from rpm dconf-0.49.0-1.fc43.x86_64 Module libpolkit-gobject-1.so.0 from rpm polkit-126-6.fc43.x86_64 Module libpolkit-agent-1.so.0 from rpm polkit-126-6.fc43.x86_64 Module libsystemd.so.0 from rpm systemd-258.5-1.fc43.x86_64 Module libostree-1.so.1 from rpm ostree-2025.7-1.fc43.x86_64 Module libjson-glib-1.0.so.0 from rpm json-glib-1.10.8-4.fc43.x86_64 Module libappstream.so.5 from rpm appstream-1.1.0-1.fc43.x86_64 Module libgobject-2.0.so.0 from rpm glib2-2.86.4-1.fc43.x86_64 Module libgio-2.0.so.0 from rpm glib2-2.86.4-1.fc43.x86_64 Module libglib-2.0.so.0 from rpm glib2-2.86.4-1.fc43.x86_64 Stack trace of thread 5963: #0 0x00007f47961e93cc __pthread_kill_implementation (libc.so.6 + 0x743cc) #1 0x00007f479618f15e raise (libc.so.6 + 0x1a15e) #2 0x00007f47961766d0 abort (libc.so.6 + 0x16d0) #3 0x00007f4796d7e482 g_assertion_message.cold (libglib-2.0.so.0 + 0x2482) #4 0x00007f4796def7a7 g_assertion_message_expr (libglib-2.0.so.0 + 0x737a7) #5 0x000055e9eb49c66e n/a (/b7/4a16f352fdc74ad69c84ca997e64746198cf5539b261bd4e0927c84b41e53a.file + 0xd866e) #6 0x000055e9eb46eab3 n/a (/b7/4a16f352fdc74ad69c84ca997e64746198cf5539b261bd4e0927c84b41e53a.file + 0xaaab3) #7 0x000055e9eb46a85a n/a (/b7/4a16f352fdc74ad69c84ca997e64746198cf5539b261bd4e0927c84b41e53a.file + 0xa685a) #8 0x000055e9eb43acb4 n/a (/b7/4a16f352fdc74ad69c84ca997e64746198cf5539b261bd4e0927c84b41e53a.file + 0x76cb4) #9 0x000055e9eb3f90b3 n/a (/b7/4a16f352fdc74ad69c84ca997e64746198cf5539b261bd4e0927c84b41e53a.file + 0x350b3) #10 0x00007f47961785b5 __libc_start_call_main (libc.so.6 + 0x35b5) #11 0x00007f4796178668 __libc_start_main@@GLIBC_2.34 (libc.so.6 + 0x3668) #12 0x000055e9eb3fa7e5 n/a (/b7/4a16f352fdc74ad69c84ca997e64746198cf5539b261bd4e0927c84b41e53a.file + 0x367e5) ELF object binary architecture: AMD x86-64 

[inffy]

Does flatpak update from terminal work?

[citizen428]

Oops, should have specified, my bad. All flatpak commands in the terminal also have errors:

flatpak:ERROR:common/flatpak-variant-impl-private.h:2716:var_deploy_data_get_metadata: assertion failed: (end <= v.size) Bail out! flatpak:ERROR:common/flatpak-variant-impl-private.h:2716:var_deploy_data_get_metadata: assertion failed: (end <= v.size) Aborted (core dumped) flatpak update 

The crash reporter shows essentially the same message/core dump.

[citizen428]

I ran this through gdb, just in case it helps:

[Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". Core was generated by `flatpak update'. Program terminated with signal SIGABRT, Aborted. Downloading source file /usr/src/debug/glibc-2.42-10.fc43.x86_64/nptl/pthread_kill.c #0 __pthread_kill_implementation (threadid=<optimized out>, signo=signo@entry=6, no_tid=no_tid@entry=0) at pthread_kill.c:44 44 return INTERNAL_SYSCALL_ERROR_P (ret) ? INTERNAL_SYSCALL_ERRNO (ret) : 0; [Current thread is 1 (Thread 0x7f9385cdde00 (LWP 7401))] Missing file(s), try: dnf --enablerepo='*debug*' install /usr/lib/.build-id/9b/2debb29f07c581b2f290405d33e1d2ef7d45d6 /usr/lib/debug/.build-id/9b/2debb29f07c581b2f290405d33e1d2ef7d45d6.debug 

Unfortunately, I don't have any more time to spare for this right now. But let me know if there's anything else that you need that could make debugging easier and I'll try to get it to you tomorrow.

[renner0e]

So I have a nuclear approach for you:

I don't know how this could've happened but my guess is that something went wrong on the install process, especially something on the copy process. Maybe it didn't actually finish writing to your drive?

Did you do anything while on the live environment that modified this directory?

https://github.com/get-aurora-dev/iso/blob/f035f50202c701e38be66e99325fb63dc6e91910/iso_files/configure_iso_anaconda.sh#L132-L140

sudo rm -rf /var/lib/flatpak flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo ujust install-system-flatpaks sudo systemd-tmpfiles --create 

If you are curious about this you can make a backup of the directory above and poke around.

Seen something similar recently ublue-os/bazzite#4126

[citizen428]

The good news first, this worked, thanks!

I don't know how this could've happened but my guess is that something went wrong on the install process, especially something on the copy process

That's a reasonable assumption. Just to be sure, the ISO downloaded correctly, the checksums match up:

~/Downloads ❯ sha256 aurora-nvidia-open-stable-webui-x86_64.iso SHA256 (aurora-nvidia-open-stable-webui-x86_64.iso) = f75212d496bebb5bcf374d9d1e66739107368f667b533c5f99f29d0ebbac2ef1 ~/Downloads took 5s ❯ cat aurora-nvidia-open-stable-webui-x86_64.iso-CHECKSUM f75212d496bebb5bcf374d9d1e66739107368f667b533c5f99f29d0ebbac2ef1 aurora-nvidia-open-stable-webui-x86_64.iso 

Did you do anything while on the live environment that modified this directory?

No. I booted from it and went straight to starting the installer.

Seen something similar recently ublue-os/bazzite#4126

While I've been a long-time Linux user, I'm not a uBlue expert, but doesn't this suggest a potential upstream issue in one of the shared layers? Both the other user and I got tripped up by the same assertion error ((end <= v.size)).