I am unable to update my OS. I get the message “Directory Not Empty”, and I cannot resolve the issue. I’ve tried Rebasing, Rollback, and even reset. Please view the GitHub issue for more details:
opened 11:50PM - 05 Mar 26 UTC
### Describe the bug
This has happened twice now, I've reinstalled twice for th… is same error to occur. It does not happen immediately, I can update the system via "ujust update" but at some point (a few days or so later) something happens and I can no longer update.
### What did you expect to happen?
The update to succeed.
### Session Logs
```shell
journalctl -b is too large, and hhd gets stuck on "Trying to acquire hhd lock..."
```
### Hardware
AMD Ryzen 9 9950x3D, 128GB DDR5 6000Mt, Nvidia RTX 3090
### Extra information or context
```
user@bazzite:~$ ujust update
── 18:42:04 - System update ────────────────────────────────────────────────────
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite-dx-nvidia
Checking out tree b1213aa... done
error: Removing extensions/rpmostree/private/commit: unlinkat(LC_MESSAGES): Directory not empty
System update failed:
0: Command failed: `/usr/bin/rpm-ostree upgrade`
1: `/usr/bin/rpm-ostree` failed: exit status: 1
Location:
src/steps/os/linux.rs:228
root@bazzite:/var/home/user# rpm-ostree reset
Staging deployment... done
error: syscore cleanup: cleaning tmp rootfs: Removing extensions/rpmostree/private/commit: unlinkat(LC_MESSAGES): Directory not empty
```
Drive SMART status:
```
user@bazzite:~$ sudo smartctl -a /dev/nvme2n1
[sudo] password for user:
smartctl 7.5 2025-04-30 r5714 [x86_64-linux-6.17.7-ba25.fc43.x86_64] (local build)
Copyright (C) 2002-25, Bruce Allen, Christian Franke, www.smartmontools.org
=== START OF INFORMATION SECTION ===
Model Number: CT2000P5PSSD8
Serial Number: 21443252CD2E
Firmware Version: P7CR403
PCI Vendor/Subsystem ID: 0xc0a9
IEEE OUI Identifier: 0x00a075
Total NVM Capacity: 2,000,398,934,016 [2.00 TB]
Unallocated NVM Capacity: 0
Controller ID: 0
NVMe Version: 1.4
Number of Namespaces: 1
Namespace 1 Size/Capacity: 2,000,398,934,016 [2.00 TB]
Namespace 1 Formatted LBA Size: 512
Namespace 1 IEEE EUI-64: 00a075 013252cd2e
Local Time is: Thu Mar 5 18:41:16 2026 EST
Firmware Updates (0x14): 2 Slots, no Reset required
Optional Admin Commands (0x0017): Security Format Frmw_DL Self_Test
Optional NVM Commands (0x0057): Comp Wr_Unc DS_Mngmt Sav/Sel_Feat Timestmp
Log Page Attributes (0x1b): S/H_per_NS Cmd_Eff_Lg Telmtry_Lg Pers_Ev_Lg
Maximum Data Transfer Size: 512 Pages
Warning Comp. Temp. Threshold: 80 Celsius
Critical Comp. Temp. Threshold: 82 Celsius
Namespace 1 Features (0x08): No_ID_Reuse
Supported Power States
St Op Max Active Idle RL RT WL WT Ent_Lat Ex_Lat
0 + 8.25W - - 0 0 0 0 0 0
1 + 4.00W - - 1 1 1 1 0 0
2 + 2.00W - - 2 2 2 2 0 0
3 - 0.1000W - - 3 3 3 3 5000 6000
4 - 0.0050W - - 4 4 4 4 12000 35000
Supported LBA Sizes (NSID 0x1)
Id Fmt Data Metadt Rel_Perf
0 + 512 0 0
=== START OF SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED
SMART/Health Information (NVMe Log 0x02, NSID 0x1)
Critical Warning: 0x00
Temperature: 36 Celsius
Available Spare: 100%
Available Spare Threshold: 5%
Percentage Used: 10%
Data Units Read: 204,314,843 [104 TB]
Data Units Written: 289,286,184 [148 TB]
Host Read Commands: 2,636,060,234
Host Write Commands: 2,290,231,955
Controller Busy Time: 5,296
Power Cycles: 346
Power On Hours: 9,907
Unsafe Shutdowns: 163
Media and Data Integrity Errors: 0
Error Information Log Entries: 1,551
Warning Comp. Temperature Time: 0
Critical Comp. Temperature Time: 0
Temperature Sensor 1: 36 Celsius
Error Information (NVMe Log 0x01, 16 of 256 entries)
Num ErrCount SQId CmdId Status PELoc LBA NSID VS Message
0 1551 0 0x0010 0x8004 0x000 0 0 - Invalid Field in Command
Self-test Log (NVMe Log 0x06, NSID 0xffffffff)
Self-test status: No self-test in progress
Num Test_Description Status Power_on_Hours Failing_LBA NSID Seg SCT Code
0 Extended Completed without error 9907 - - - - -
1 Extended Completed without error 9906 - - - - -
2 Short Completed without error 9906 - - - - -
3 Short Completed without error 6800 - - - - -
4 Short Completed without error 6769 - - - - -
```
I am on bazzite-dx-nvidia.
Fastfetch:
```
user@bazzite
bazzite-dx-nvidia:stable
Bazzite
Linux 6.17.7-ba25.fc43.x86_64
1 day, 2 hours, 15 mins
MS-7E85 (1.0)
AMD Ryzen 9 9950X3D (32) @ 5.76 GHz
NVIDIA GeForce RTX 3090 [Discrete]
AMD Radeon Graphics [Integrated]
28.77 GiB / 123.10 GiB (23%)
378.86 GiB / 1.82 TiB (20%) - btrfs
7.84 TiB / 14.55 TiB (54%) - btrfs
15.01 TiB / 18.19 TiB (83%) - btrfs
13.54 TiB / 18.19 TiB (74%) - btrfs
5.78 MiB / 7.28 TiB (0%) - btrfs
68.05 GiB / 931.50 GiB (7%) - btrfs
8.32 GiB / 1.82 TiB (0%) - btrfs
5.78 MiB / 1.82 TiB (0%) - btrfs
1.75 TiB / 3.64 TiB (48%) - btrfs
5.78 MiB / 1.82 TiB (0%) - btrfs
252.32 GiB / 3.64 TiB (7%) - btrfs
2560x1440 in 32", 240 Hz [External]
7680x2160 in 57", 120 Hz [External, HDR] *
Mouse passthrough (absolute)
KDE Plasma 6.6.1
KWin (Wayland)
bash 5.3.0
Ptyxis 49.3
3020 (rpm), 67 (flatpak)
```
It seems fishy that it’s just for the temp directory. I haven’t checked but are you sure it isn’t backed by a RAM drive? In that case you might have bad RAM (or I guess that could be the case either way).