System apps don't work after in-place upgrade

[Penobscot]

I used the instructions at https://mxlinux.org/wiki/system/upgradi ... nstalling/ to go from 21 to 23. Most of the system apps, such as the package installer and cleanup, no longer start. Even when I run system information I get the message, "pkexec must be setuid root." What can I do? Thanks

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System:    Kernel: 6.1.0-10-amd64 [6.1.38-2] x86_64 bits: 64 compiler: gcc v: 12.2.0 
           parameters: BOOT_IMAGE=/boot/vmlinuz-6.1.0-10-amd64 root=UUID=<filter> ro quiet splash 
           Desktop: Xfce 4.18.1 tk: Gtk 3.24.36 info: xfce4-panel wm: xfwm 4.18.0 
           dm: LightDM 1.26.0 Distro: MX-21.3_x64 Libretto September 18  2022 
           base: Debian GNU/Linux 12 (bookworm) 
Machine:   Type: Unknown Mobo: FreeBSD model: BHYVE v: 1.0 serial: <filter> UEFI: BHYVE v: 13.0 
           date: 11/10/2020 
CPU:       Info: 2x Dual Core model: Intel Xeon E5-2620 v2 bits: 64 type: MT SMP arch: Ivy Bridge 
           family: 6 model-id: 3E (62) stepping: 4 microcode: N/A cache: L2: 30 MiB 
           flags: avx lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 bogomips: 33572 
           Speed: 2098 MHz min/max: N/A Core speeds (MHz): 1: 2098 2: 2098 3: 2098 4: 2098 5: 2098 
           6: 2098 7: 2098 8: 2098 
           Vulnerabilities: Type: itlb_multihit status: KVM: VMX unsupported 
           Type: l1tf mitigation: PTE Inversion 
           Type: mds mitigation: Clear CPU buffers; SMT Host state unknown 
           Type: meltdown mitigation: PTI 
           Type: mmio_stale_data status: Unknown: No mitigations 
           Type: retbleed status: Not affected 
           Type: spec_store_bypass status: Vulnerable 
           Type: spectre_v1 mitigation: usercopy/swapgs barriers and __user pointer sanitization 
           Type: spectre_v2 
           mitigation: Retpolines, STIBP: disabled, RSB filling, PBRSB-eIBRS: Not affected 
           Type: srbds status: Not affected 
           Type: tsx_async_abort status: Not affected 
Graphics:  Device-1: driver: N/A bus-ID: 00:1d.0 chip-ID: fb5d:40fb class-ID: 0300 
           Display: x11 server: X.Org 1.21.1.7 compositor: xfwm4 v: 4.18.0 driver: loaded: N/A 
           unloaded: fbdev display-ID: :10.0 screens: 1 
           Screen-1: 0 s-res: 1920x1080 s-dpi: 96 s-size: 508x286mm (20.0x11.3") 
           s-diag: 583mm (23") 
           Monitor-1: rdp0 res: 1920x1080 hz: 50 
           OpenGL: renderer: llvmpipe (LLVM 15.0.6 256 bits) v: 4.5 Mesa 22.3.6 direct render: Yes 
Audio:     Message: No device data found. 
           Sound Server-1: PulseAudio v: 16.1 running: yes 
Network:   Device-1: Red Hat Virtio network driver: virtio-pci v: 1 modules: virtio_pci port: 2080 
           bus-ID: 00:04.0 chip-ID: 1af4:1000 class-ID: 0200 
           IF: eth0 state: up speed: -1 duplex: unknown mac: <filter> 
Drives:    Local Storage: total: 70 GiB used: 23.93 GiB (34.2%) 
           ID-1: /dev/vda maj-min: 254:0 model: N/A size: 70 GiB block-size: physical: 65536 B 
           logical: 512 B type: N/A serial: N/A scheme: GPT 
           SMART Message: Unknown smartctl error. Unable to generate data. 
Partition: ID-1: / raw-size: 44.93 GiB size: 44.05 GiB (98.04%) used: 23.09 GiB (52.4%) fs: ext4 
           dev: /dev/vda2 maj-min: 254:2 
           ID-2: /boot/efi raw-size: 256 MiB size: 252 MiB (98.46%) used: 415 KiB (0.2%) fs: vfat 
           dev: /dev/vda1 maj-min: 254:1 
           ID-3: /home raw-size: 23.31 GiB size: 22.84 GiB (97.98%) used: 858.1 MiB (3.7%) 
           fs: ext4 dev: /dev/vda4 maj-min: 254:4 
Swap:      Kernel: swappiness: 15 (default 60) cache-pressure: 100 (default) 
           ID-1: swap-1 type: partition size: 1.5 GiB used: 0 KiB (0.0%) priority: -2 
           dev: /dev/vda3 maj-min: 254:3 
Sensors:   Message: No sensor data found. Is lm-sensors configured? 
Repos:     Packages: note: see --pkg apt: 2224 lib: 1148 flatpak: 0 
           No active apt repos in: /etc/apt/sources.list 
           Active apt repos in: /etc/apt/sources.list.d/debian-stable-updates.list 
           1: deb http://nyc.mirrors.clouvider.net/debian/ bookworm-updates main contrib non-free
           Active apt repos in: /etc/apt/sources.list.d/debian.list 
           1: deb http://nyc.mirrors.clouvider.net/debian/ bookworm main contrib non-free non-free-firmware
           2: deb http://security.debian.org/debian-security bookworm-security main contrib non-free non-free-firmware
           Active apt repos in: /etc/apt/sources.list.d/mx.list 
           1: deb http://mxlinux.mirrors.tds.net/mxlinux/mx/repo/ bookworm main non-free
           Active apt repos in: /etc/apt/sources.list.d/temp.list 
           1: deb http://mxrepo.com/mx/repo/ temp main
Info:      Processes: 243 Uptime: 31m wakeups: 1 Memory: 3.82 GiB used: 2.24 GiB (58.8%) 
           Init: SysVinit v: 3.06 runlevel: 5 default: 5 tool: systemctl Compilers: gcc: 12.2.0 
           alt: 10/12 Client: shell wrapper v: 5.2.15-release inxi: 3.3.06 
Boot Mode: UEFI

[dolphin_oracle]

I would check to make sure all updates are finished, including the kernel.

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sudo dpkg --configure -a

[Penobscot]

Setting up polkitd (122-3) ...
Failed to check if group polkitd already exists: Connection refused
id: ‘polkitd’: no such user
chown: invalid user: ‘polkitd:root’
dpkg: error processing package polkitd (--configure):
installed polkitd package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
polkitd

[dolphin_oracle]

I guess you could try making the group manually

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sudo addgroup --system polkitd
sudo adduser --system --disable-login --ingroup polkitd --no-create-home polkitd

[Penobscot]

I kinda, sorta, got it to work, but at this point I'm going to restore it to the pre-upgrade snapshot and do a fresh install on a new VM.