My Manjaro Xfce machine won't install today's (2024_5-13) updates

Over an hour ago, pamac showed that I have 581 available updates, 2.3 GB worth.

The update process hardly started and failed, as shown below.

Preparing...
Synchronizing package databases...
Checking shiboken2 dependencies...
Checking pyside2 dependencies...
Checking pyside2-tools dependencies...
Checking python-shiboken2 dependencies...
Checking python-hid-parser dependencies...
Resolving dependencies...
Checking inter-conflicts...
Failed to prepare transaction:
could not satisfy dependencies:
- unable to satisfy dependency 'clang=16.0.6' required by shiboken2
Cloning shiboken2 build files...
Generating shiboken2 information...
Failed to prepare transaction:
Failed to clone shiboken2 build files

I searched Manjaro.org and the web but have found nothing yet.

Pamac shows that I have clang 16.0.6-2 installed.

My machine info is as follows:

[ultra@ultra-ms7b86 ~]$ inxi -zv8
System:
  Kernel: 6.5.13-7-MANJARO arch: x86_64 bits: 64 compiler: gcc v: 13.2.1
    clocksource: tsc avail: hpet,acpi_pm
    parameters: BOOT_IMAGE=/boot/vmlinuz-6.5-x86_64
    root=UUID=121a5a27-095d-4c7a-8853-3a2b6e097b5c rw quiet splash apparmor=1
    security=apparmor udev.log_priority=3
  Desktop: Xfce v: 4.18.1 tk: Gtk v: 3.24.36 wm: xfwm4 v: 4.18.0
    with: xfce4-panel tools: light-locker vt: 7 dm: LightDM v: 1.32.0
    Distro: Manjaro base: Arch Linux
Machine:
  Type: Desktop System: Micro-Star product: MS-7B86 v: 3.0
    serial: <superuser required>
  Mobo: Micro-Star model: B450 GAMING PLUS MAX (MS-7B86) v: 3.0
    serial: <superuser required> uuid: <superuser required> UEFI: American
    Megatrends LLC. v: H.D3 date: 09/28/2021
Battery:
  Device-1: hidpp_battery_0 model: Logitech Wireless Mouse serial: <filter>
    charge: 55% (should be ignored) rechargeable: yes status: discharging
  Device-2: hidpp_battery_1 model: Logitech K520 serial: <filter>
    charge: 70% (should be ignored) rechargeable: yes status: discharging
Memory:
  System RAM: total: 16 GiB available: 15.54 GiB used: 1.97 GiB (12.7%)
  Message: For most reliable report, use superuser + dmidecode.
  Array-1: capacity: 128 GiB slots: 4 modules: 2 EC: None
    max-module-size: 32 GiB note: est.
  Device-1: Channel-A DIMM 0 type: no module installed
  Device-2: Channel-A DIMM 1 type: DDR4 detail: synchronous unbuffered
    (unregistered) size: 8 GiB speed: 2933 MT/s volts: note: check curr: 1
    min: 1 max: 1 width (bits): data: 64 total: 64 manufacturer: G.Skill
    part-no: F4-3200C16-8GVKB serial: N/A
  Device-3: Channel-B DIMM 0 type: no module installed
  Device-4: Channel-B DIMM 1 type: DDR4 detail: synchronous unbuffered
    (unregistered) size: 8 GiB speed: 2933 MT/s volts: note: check curr: 1
    min: 1 max: 1 width (bits): data: 64 total: 64 manufacturer: G.Skill
    part-no: F4-3200C16-8GVKB serial: N/A
PCI Slots:
  Permissions: Unable to run dmidecode. Root privileges required.
CPU:
  Info: model: AMD Ryzen 5 2600 bits: 64 type: MT MCP arch: Zen+ gen: 2
    level: v3 note: check built: 2018-21 process: GF 12nm family: 0x17 (23)
    model-id: 8 stepping: 2 microcode: 0x800820D
  Topology: cpus: 1x cores: 6 tpc: 2 threads: 12 smt: enabled cache:
    L1: 576 KiB desc: d-6x32 KiB; i-6x64 KiB L2: 3 MiB desc: 6x512 KiB
    L3: 16 MiB desc: 2x8 MiB
  Speed (MHz): avg: 1783 high: 3400 min/max: 1550/3400 boost: enabled
    scaling: driver: acpi-cpufreq governor: schedutil cores: 1: 3400 2: 1391
    3: 1550 4: 1550 5: 1550 6: 1550 7: 2800 8: 1550 9: 1550 10: 1550 11: 1410
    12: 1550 bogomips: 81625
  Flags: 3dnowprefetch abm adx aes aperfmperf apic arat avic avx avx2 bmi1
    bmi2 bpext clflush clflushopt clzero cmov cmp_legacy constant_tsc cpb
    cpuid cr8_legacy cx16 cx8 de decodeassists extapic extd_apicid f16c
    flushbyasid fma fpu fsgsbase fxsr fxsr_opt ht hw_pstate ibpb irperf
    lahf_lm lbrv lm mca mce misalignsse mmx mmxext monitor movbe msr mtrr
    mwaitx nonstop_tsc nopl npt nrip_save nx osvw overflow_recov pae pat
    pausefilter pclmulqdq pdpe1gb perfctr_core perfctr_llc perfctr_nb
    pfthreshold pge pni popcnt pse pse36 rapl rdrand rdseed rdtscp rep_good
    sep sev sev_es sha_ni skinit smap smca smep ssbd sse sse2 sse4_1 sse4_2
    sse4a ssse3 succor svm svm_lock syscall tce topoext tsc tsc_scale
    v_vmsave_vmload vgif vmcb_clean vme vmmcall wdt xgetbv1 xsave xsavec
    xsaveerptr xsaveopt
  Vulnerabilities:
  Type: gather_data_sampling status: Not affected
  Type: itlb_multihit status: Not affected
  Type: l1tf status: Not affected
  Type: mds status: Not affected
  Type: meltdown status: Not affected
  Type: mmio_stale_data status: Not affected
  Type: retbleed mitigation: untrained return thunk; SMT vulnerable
  Type: spec_rstack_overflow mitigation: Safe RET
  Type: spec_store_bypass mitigation: Speculative Store Bypass disabled via
    prctl
  Type: spectre_v1 mitigation: usercopy/swapgs barriers and __user pointer
    sanitization
  Type: spectre_v2 mitigation: Retpolines, IBPB: conditional, STIBP:
    disabled, RSB filling, PBRSB-eIBRS: Not affected
  Type: srbds status: Not affected
  Type: tsx_async_abort status: Not affected
Graphics:
  Device-1: NVIDIA GP107 [GeForce GTX 1050 Ti] vendor: Gigabyte
    driver: nouveau v: kernel non-free: 545.xx+ status: current (as of 2024-04;
    EOL~2026-12-xx) arch: Pascal code: GP10x process: TSMC 16nm
    built: 2016-2021 pcie: gen: 1 speed: 2.5 GT/s lanes: 16 link-max: gen: 3
    speed: 8 GT/s ports: active: HDMI-A-1 empty: DP-1,DVI-D-1 bus-ID: 26:00.0
    chip-ID: 10de:1c82 class-ID: 0300 temp: 49.0 C
  Display: x11 server: X.org v: 1.21.1.12 compositor: xfwm4 v: 4.18.0
    driver: X: loaded: modesetting alternate: fbdev,vesa dri: nouveau
    gpu: nouveau display-ID: :0.0 note: <missing: xdpyinfo/xrandr>
  Monitor-1: HDMI-A-1 model: HP w2207 serial: <filter> built: 2007
    res: 1680x1050 dpi: 90 gamma: 1.2 chroma: red: x: 0.647 y: 0.337 green:
    x: 0.290 y: 0.604 blue: x: 0.145 y: 0.063 white: x: 0.314 y: 0.329
    size: 473x296mm (18.62x11.65") diag: 558mm (22") ratio: 16:10
    modes: 1680x1050, 1920x1080, 1920x1080i, 1600x1000, 1280x1024, 1440x900,
    1280x960, 1152x864, 1280x720, 1152x720, 1024x768, 832x624, 800x600,
    720x576, 720x480, 640x480, 720x400
  API: EGL v: 1.5 hw: drv: nvidia nouveau platforms: device: 0 drv: nouveau
    device: 1 drv: swrast gbm: drv: nouveau surfaceless: drv: nouveau x11:
    drv: nouveau inactive: wayland
  API: OpenGL v: 4.5 compat-v: 4.3 vendor: mesa v: 24.0.2-manjaro1.1
    glx-v: 1.4 direct-render: yes renderer: NV137 device-ID: 10de:1c82
    memory: 3.9 GiB unified: no
Audio:
  Device-1: NVIDIA GP107GL High Definition Audio vendor: Gigabyte
    driver: snd_hda_intel v: kernel pcie: gen: 1 speed: 2.5 GT/s lanes: 16
    link-max: gen: 3 speed: 8 GT/s bus-ID: 26:00.1 chip-ID: 10de:0fb9
    class-ID: 0403
  Device-2: AMD Family 17h HD Audio vendor: Micro-Star MSI
    driver: snd_hda_intel v: kernel pcie: gen: 3 speed: 8 GT/s lanes: 16
    bus-ID: 28:00.3 chip-ID: 1022:1457 class-ID: 0403
  API: ALSA v: k6.5.13-7-MANJARO status: kernel-api with: aoss
    type: oss-emulator tools: alsactl,alsamixer,amixer
  Server-1: JACK v: 1.9.22 status: off tools: N/A
  Server-2: PipeWire v: 1.0.3 status: off with: pipewire-media-session
    status: active tools: pw-cli
  Server-3: PulseAudio v: 17.0 status: active with: pulseaudio-alsa
    type: plugin tools: pacat,pactl,pavucontrol
Network:
  Device-1: Realtek RTL8111/8168/8211/8411 PCI Express Gigabit Ethernet
    vendor: Micro-Star MSI RTL8111/8168/8411 driver: r8169 v: kernel pcie:
    gen: 1 speed: 2.5 GT/s lanes: 1 port: f000 bus-ID: 22:00.0
    chip-ID: 10ec:8168 class-ID: 0200
  IF: enp34s0 state: up speed: 100 Mbps duplex: full mac: <filter>
  IP v4: <filter> type: dynamic noprefixroute scope: global
    broadcast: <filter>
  IP v6: <filter> type: noprefixroute scope: link
  Info: services: mld,NetworkManager
  WAN IP: <filter>
Bluetooth:
  Message: No bluetooth data found.
Logical:
  Message: No logical block device data found.
RAID:
  Message: No RAID data found.
Drives:
  Local Storage: total: 2.5 TiB used: 1.73 TiB (69.2%)
  SMART Message: Required tool smartctl not installed. Check --recommends
  ID-1: /dev/sda maj-min: 8:0 vendor: Crucial model: CT250MX500SSD1
    size: 232.89 GiB block-size: physical: 4096 B logical: 512 B speed: 6.0 Gb/s
    tech: SSD serial: <filter> fw-rev: 043 scheme: GPT
  ID-2: /dev/sdb maj-min: 8:16 vendor: Seagate model: ST3500418AS
    size: 465.76 GiB block-size: physical: 512 B logical: 512 B speed: 1.5 Gb/s
    tech: HDD rpm: 7200 serial: <filter> fw-rev: CC46 scheme: MBR
  ID-3: /dev/sdc maj-min: 8:32 vendor: Hitachi model: HUA723020ALA641
    size: 1.82 TiB block-size: physical: 512 B logical: 512 B speed: 6.0 Gb/s
    tech: HDD rpm: 7200 serial: <filter> fw-rev: A840 scheme: MBR
  Optical-1: /dev/sr0 vendor: HL-DT-ST model: DVDRAM GH24NSC0 rev: LI00
    dev-links: cdrom
  Features: speed: 12 multisession: yes audio: yes dvd: yes
    rw: cd-r,cd-rw,dvd-r,dvd-ram state: running
Partition:
  ID-1: / raw-size: 232.59 GiB size: 227.88 GiB (97.98%)
    used: 104.48 GiB (45.8%) fs: ext4 dev: /dev/sda2 maj-min: 8:2 label: N/A
    uuid: 121a5a27-095d-4c7a-8853-3a2b6e097b5c
  ID-2: /boot/efi raw-size: 300 MiB size: 299.4 MiB (99.80%)
    used: 288 KiB (0.1%) fs: vfat dev: /dev/sda1 maj-min: 8:1 label: N/A
    uuid: 2C95-A40A
  ID-3: /run/media/ultra/DDrive2 raw-size: 232.88 GiB
    size: 228.17 GiB (97.98%) used: 580.9 MiB (0.2%) fs: ext4 dev: /dev/sdb2
    maj-min: 8:18 label: DDrive2 uuid: 353601dc-0eb6-45f9-9475-50f8fb8def2c
  ID-4: /run/media/ultra/Ht1 raw-size: 550 GiB size: 540.3 GiB (98.24%)
    used: 451.25 GiB (83.5%) fs: ext4 dev: /dev/sdc2 maj-min: 8:34 label: Ht1
    uuid: 48d40e11-d416-4079-9abd-c3115f9bdfc3
  ID-5: /run/media/ultra/Ht2 raw-size: 640 GiB size: 628.89 GiB (98.26%)
    used: 590.4 GiB (93.9%) fs: ext4 dev: /dev/sdc3 maj-min: 8:35 label: Ht2
    uuid: db9f7c41-b09a-462e-a202-e0cd136c5ee7
  ID-6: /run/media/ultra/Ht3 raw-size: 673.02 GiB size: 661.39 GiB (98.27%)
    used: 626.56 GiB (94.7%) fs: ext4 dev: /dev/sdc4 maj-min: 8:36 label: Ht3
    uuid: dc1ff585-f270-4de5-ae19-45a09aa1bbb7
Swap:
  Kernel: swappiness: 60 (default) cache-pressure: 100 (default) zswap: yes
    compressor: zstd max-pool: 20%
  ID-1: swap-1 type: file size: 512 MiB used: 256 KiB (0.0%) priority: -2
    file: /swapfile
Unmounted:
  ID-1: /dev/sdb1 maj-min: 8:17 size: 232.88 GiB fs: ext4 label: DDrive1
    uuid: 6e4c97b7-826e-445e-8796-72d0e38f7e36
USB:
  Hub-1: 1-0:1 info: hi-speed hub with single TT ports: 10 rev: 2.0
    speed: 480 Mb/s (57.2 MiB/s) lanes: 1 mode: 2.0 chip-ID: 1d6b:0002
    class-ID: 0900
  Device-1: 1-8:2 info: Logitech Unifying Receiver type: keyboard,mouse,HID
    driver: logitech-djreceiver,usbhid interfaces: 3 rev: 2.0
    speed: 12 Mb/s (1.4 MiB/s) lanes: 1 mode: 1.1 power: 98mA
    chip-ID: 046d:c52b class-ID: 0300
  Hub-2: 2-0:1 info: super-speed hub ports: 4 rev: 3.1
    speed: 10 Gb/s (1.16 GiB/s) lanes: 1 mode: 3.2 gen-2x1 chip-ID: 1d6b:0003
    class-ID: 0900
  Hub-3: 3-0:1 info: hi-speed hub with single TT ports: 4 rev: 2.0
    speed: 480 Mb/s (57.2 MiB/s) lanes: 1 mode: 2.0 chip-ID: 1d6b:0002
    class-ID: 0900
  Hub-4: 4-0:1 info: super-speed hub ports: 4 rev: 3.0
    speed: 5 Gb/s (596.0 MiB/s) lanes: 1 mode: 3.2 gen-1x1 chip-ID: 1d6b:0003
    class-ID: 0900
Sensors:
  System Temperatures: cpu: 41.1 C mobo: N/A gpu: nouveau temp: 49.0 C
  Fan Speeds (rpm): N/A gpu: nouveau fan: 0
Repos:
  Packages: 1598 pm: pacman pkgs: 1557 libs: 385 tools: pamac pm: flatpak
    pkgs: 41
  Active pacman repo servers in: /etc/pacman.d/mirrorlist
    1: https://forksystems.mm.fcix.net/manjaro/stable/$repo/$arch
    2: https://coresite.mm.fcix.net/manjaro/stable/$repo/$arch
    3: https://mirrors.gigenet.com/manjaro/stable/$repo/$arch
    4: https://southfront.mm.fcix.net/manjaro/stable/$repo/$arch
    5: https://irltoolkit.mm.fcix.net/manjaro/stable/$repo/$arch
    6: https://ridgewireless.mm.fcix.net/manjaro/stable/$repo/$arch
    7: https://opencolo.mm.fcix.net/manjaro/stable/$repo/$arch
    8: http://mirror.fcix.net/manjaro/stable/$repo/$arch
Processes:
  CPU top: 5 of 469
  1: cpu: 200% command: ps pid: 18112 mem: 4.36 MiB (0.0%)
  2: cpu: 7.5% command: 1 started-by: firefox pid: 17501
    mem: 408.4 MiB (2.5%)
  3: cpu: 3.2% command: firefox pid: 17607 mem: 160.1 MiB (1.0%)
  4: cpu: 3.0% command: Xorg pid: 896 mem: 110.5 MiB (0.6%)
  5: cpu: 2.9% command: xfce4-terminal pid: 18074 mem: 47.6 MiB (0.2%)
  Memory top: 5 of 469
  1: mem: 408.4 MiB (2.5%) command: 1 started-by: firefox pid: 17501
    cpu: 7.5%
  2: mem: 258.6 MiB (1.6%) command: firefox pid: 17728 cpu: 1.1%
  3: mem: 160.1 MiB (1.0%) command: firefox pid: 17607 cpu: 3.2%
  4: mem: 160.0 MiB (1.0%) command: firefox pid: 17665 cpu: 0.3%
  5: mem: 110.5 MiB (0.6%) command: Xorg pid: 896 cpu: 3.0%
Info:
  Processes: 469 Power: uptime: 6h 42m states: freeze,mem,disk suspend: deep
    avail: s2idle wakeups: 0 hibernate: platform avail: shutdown, reboot,
    suspend, test_resume image: 6.21 GiB services: upowerd,xfce4-power-manager
    Init: systemd v: 255 default: graphical tool: systemctl
  Compilers: clang: 16.0.6 gcc: 13.2.1 Shell: Bash v: 5.2.26
    running-in: xfce4-terminal inxi: 3.3.34
[ultra@ultra-ms7b86 ~]$

What do I do next?

Mod edit: See [HowTo] Post command output and file content as formatted text

shiboken2 was dropped from the repos to the AUR.

Always update repo packages first, then deal with AUR packages later.

pamac update --no-aur

or

sudo pacman -Syu
3 Likes

Thanks for responding Yochanan
This is what happens when I execute pamac updae --no-aur

[ultra@ultra-ms7b86 ~]$ pamac update --no-aur
Preparing...
Synchronizing package databases...
Choose a provider for qt6-multimedia-backend:
1:  qt6-multimedia-ffmpeg     6.7.0-1  extra
2:  qt6-multimedia-gstreamer  6.7.0-1  extra

Enter a number (default=1): 1

Warning: installing clang (17.0.6-2) breaks dependency 'clang=16.0.6' required by shiboken2
Add shiboken2 to remove
Error: Failed to prepare transaction:
could not satisfy dependencies:
- removing shiboken2 breaks dependency 'shiboken2' required by freecad-linkstage3-bin
Resolving dependencies...
Choose a provider for qt6-multimedia-backend:
1:  qt6-multimedia-ffmpeg     6.7.0-1  extra
2:  qt6-multimedia-gstreamer  6.7.0-1  extra

Enter a number (default=1): 1

Checking inter-conflicts...
Error: Failed to prepare transaction:
could not satisfy dependencies:
- removing shiboken2 breaks dependency 'shiboken2' required by freecad-linkstage3-bin
[ultra@ultra-ms7b86 ~]$

This is what happens when I execute sudo pacman -Syu

[ultra@ultra-ms7b86 ~]$ sudo pacman -syu
[sudo] password for ultra: 
error: invalid option '-s'
[ultra@ultra-ms7b86 ~]$ sudo pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace breeze with extra/breeze5? [Y/n] y
resolving dependencies...
:: There are 2 providers available for qt6-multimedia-backend:
:: Repository extra
   1) qt6-multimedia-ffmpeg  2) qt6-multimedia-gstreamer

Enter a number (default=1): 1
looking for conflicting packages...
error: failed to prepare transaction (could not satisfy dependencies)
:: installing clang (17.0.6-2) breaks dependency 'clang=16.0.6' required by shiboken2

What depends on shiboken2?

pamac info shiboken2 | grep 'Required By\|Optional For'

or

pacman -Qi shiboken2 | grep 'Required By\|Optional For'

Whatever it is, at least temporarily remove it, update then reinstall if desired.

It looks like you need to lose freecad-linkstage3-bin first; then likely shiboken2.

Yochanan, when I executed the commands you suggested, they came up with the freecad-linkstage3-bin, which I uninstalled.
I was then able to complete the update without any more problems.

I Thank everyone for helping. My God Bless you all.

…did you also remove the unnecessary shiboken2?

No - should I, will it cause problems later?

Well, since you removed the only package depending on it, then yes. :wink:

After CSCS asked me if I removed shiboken2, I remembered that I did not remove it and the update transactions did not ask me to remove it.

So I checked pamac and see if it was still there. So I saw that the update transactions removed shiboken2 and replaced it with shiboken6 without my intervention.

After the successful completed update, I rebooted and the machine is working fine. I’ll re-install freecad-linkstage3-bin later if I need it.

Thanks again for the responses.

1 Like

Hi @Rod , please consider to install another kernel because the one you are using has reached EOL.

Regards,

1 Like

Oh missed that.
Beyond consider. Do. Install 6.6 (or 6.1) LTS, boot into it, and remove 6.5.

1 Like

What? Oh, yes, sure… You’re welcome.

Thank you for the kernel advice, will do.

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