Waited too long between updates, and now I'm stuck with conflicting packages...help?

Hey folks,

As the subject states, I just waited like, 3 months to fire up this little laptop I have garuda on. I always run update as soon as I log in anyway, so I expected this one to be a doozy. Well, it updated the script a few times, and I've run it about 5x now, and the last 2 times this has been the output:

❯ update
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 chaotic-aur is up to date

--> Refreshing mirrorlists using reflector, please be patient..
################################################################################
################# Arch Linux mirrorlist generated by Reflector #################
################################################################################

# With:       reflector --latest 5 --age 2 --fastest 5 --protocol https --sort rate --save /etc/pacman.d/mirrorlist
# When:       2022-08-30 23:58:02 UTC
# From:       https://archlinux.org/mirrors/status/json/
# Retrieved:  2022-08-30 23:57:43 UTC
# Last Check: 2022-08-30 23:44:00 UTC

Server = https://mirror.cyberbits.eu/archlinux/$repo/os/$arch
Server = https://mirror.chaoticum.net/arch/$repo/os/$arch
Server = https://mirror.telepoint.bg/archlinux/$repo/os/$arch
Server = https://archlinux-br.com.br/archlinux/$repo/os/$arch
Server = https://phinau.de/arch/$repo/os/$arch

:: Synchronizing package databases...
 garuda                                    87.1 KiB   167 KiB/s 00:01 [--------------------------------------] 100%
 core                                     157.3 KiB   133 KiB/s 00:01 [--------------------------------------] 100%
 extra                                   1844.9 KiB   720 KiB/s 00:03 [--------------------------------------] 100%
 community                                  6.9 MiB  1550 KiB/s 00:05 [--------------------------------------] 100%
 multilib                                 176.0 KiB   147 KiB/s 00:01 [--------------------------------------] 100%
 chaotic-aur                                2.1 MiB  2.83 MiB/s 00:01 [--------------------------------------] 100%
spawn pacman -Su sweet-theme-full-git --ignore sweet-kde-git,sweet-cursor-theme-git,kvantum-theme-sweet-git,sweet-gtk-theme-dark,plasma5-theme-sweet-git --asdeps
:: Starting full system upgrade...
warning: kvantum-theme-sweet-git: ignoring package upgrade (r256.866a934-1 => r269.6e058fc-1)
:: Replace kwayland-server with extra/kwin? [Y/n] y
:: Replace med with community/med-openmpi? [Y/n] y
:: Replace qemu with extra/qemu-desktop? [Y/n] y
:: Replace qemu-arch-extra with extra/qemu-emulators-full? [Y/n] y
:: Replace wxgtk-common with extra/wxwidgets-common? [Y/n] y
:: Replace wxgtk3 with extra/wxwidgets-gtk3? [Y/n] y
:: Replace zotero with chaotic-aur/zotero-bin? [Y/n] y
resolving dependencies...
looking for conflicting packages...
warning: removing 'hdf5' from target list because it conflicts with 'hdf5-openmpi'
:: sweet-theme-full-git and sweet-kde-git are in conflict (sweet-kde). Remove sweet-kde-git? [y/N] y
:: sweet-theme-full-git and sweet-cursor-theme-git are in conflict. Remove sweet-cursor-theme-git? [y/N] y
:: sweet-theme-full-git and kvantum-theme-sweet-git are in conflict. Remove kvantum-theme-sweet-git? [y/N] y
:: sweet-theme-full-git and sweet-gtk-theme-dark are in conflict. Remove sweet-gtk-theme-dark? [y/N] y
:: sweet-theme-full-git and plasma5-theme-sweet-git are in conflict. Remove plasma5-theme-sweet-git? [y/N] y
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] y
y
warning: dependency cycle detected:
warning: mesa will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: smbclient will be installed before its cifs-utils dependency
warning: dependency cycle detected:
warning: lib32-mesa will be installed before its lib32-libglvnd dependency

Packages (1215) 

Total Installed Size:  19554.26 MiB
Net Upgrade Size:       1523.60 MiB

:: Proceed with installation? [Y/n] y
(1202/1202) checking keys in keyring                                  [--------------------------------------] 100%
(1202/1202) checking package integrity                                [--------------------------------------] 100%
(1202/1202) loading package files                                     [--------------------------------------] 100%
(1202/1202) checking for file conflicts                               [--------------------------------------] 100%
error: failed to commit transaction (conflicting files)
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/LICENSE exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/examples/normal-usage.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/examples/safe-string.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/index.d.ts exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/colors.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/custom/trap.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/custom/zalgo.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/extendStringPrototype.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/maps/america.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/maps/rainbow.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/maps/random.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/maps/zebra.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/styles.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/system/has-flag.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/lib/system/supports-colors.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/package.json exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/safe.d.ts exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/safe.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@colors/colors/themes/generic-logging.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@npmcli/disparity-colors/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@npmcli/fs/lib/common/owner-sync.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@npmcli/fs/lib/with-owner-sync.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@npmcli/fs/lib/with-owner.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@npmcli/move-file/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/@npmcli/promise-spawn/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/builtins/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/cli-table3/src/debug.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/cmd-shim/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/ignore-walk/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/ini/lib/ini.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/just-diff-apply/index.d.ts exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/just-diff-apply/index.tests.ts exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/make-fetch-happen/lib/dns.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/minimatch/lib/path.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/npm-install-checks/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/npm-registry-fetch/lib/clean-url.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/read-cmd-shim/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/brace-expansion/LICENSE exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/brace-expansion/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/brace-expansion/package.json exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/glob/LICENSE exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/glob/common.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/glob/glob.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/glob/package.json exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/glob/sync.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/minimatch/LICENSE exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/minimatch/minimatch.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/rimraf/node_modules/minimatch/package.json exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/ssri/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/treeverse/lib/index.js exists in filesystem
npm: /usr/lib/node_modules/npm/node_modules/validate-npm-package-name/lib/index.js exists in filesystem
Errors occurred, no packages were upgraded.

I'm at a loss for what could be at the root of this and how to fix it. Any advice or guidance would be appreciated. Here's my garuda-inxi:

garuda-inxi
❯ garuda-inxi
System:
  Kernel: 5.15.37-1-lts arch: x86_64 bits: 64 compiler: gcc v: 11.2.0
    parameters: BOOT_IMAGE=/@/boot/vmlinuz-linux-lts
    root=UUID=12979374-b0c5-4bc8-8f21-3b53bd02741b rw [email protected]
    quiet splash rd.udev.log_priority=3 vt.global_cursor_default=0
    systemd.unified_cgroup_hierarchy=1 loglevel=3 sysrq_always_enabled=1
    intel_iommu=on iommu=pt acpi_backlight=vendor delayacct
    intel_pstate=passive
  Desktop: KDE Plasma v: 5.24.5 tk: Qt v: 5.15.3 info: latte-dock
    wm: kwin_x11 vt: 1 dm: SDDM Distro: Garuda Linux base: Arch Linux
Machine:
  Type: Laptop System: LENOVO product: 20175 v: Lenovo IdeaPad Yoga 13
    serial: <superuser required> Chassis: type: 10 v: Lenovo IdeaPad Yoga 13
    serial: <superuser required>
  Mobo: LENOVO model: INVALID v: 31900003WIN8 STD MLT
    serial: <superuser required> UEFI: LENOVO v: 66CN55WW date: 02/28/2013
Battery:
  ID-1: BAT1 charge: 38.4 Wh (100.0%) condition: 38.4/49.3 Wh (78.0%)
    volts: 16.2 min: 14.8 model: Lenovo IdeaPad Mocca2 type: Unknown
    serial: <filter> status: full
CPU:
  Info: model: Intel Core i7-3537U bits: 64 type: MT MCP arch: Ivy Bridge
    family: 6 model-id: 0x3A (58) stepping: 9 microcode: 0x21
  Topology: cpus: 1x cores: 2 tpc: 2 threads: 4 smt: enabled cache:
    L1: 128 KiB desc: d-2x32 KiB; i-2x8888832 KiB L2: 512 KiB desc: 2x256 KiB
    L3: 4 MiB desc: 1x4 MiB
  Speed (MHz): avg: 2013 high: 2844 min/max: 800/3100 scaling:
    driver: intel_cpufreq governor: performance cores: 1: 2117 2: 2844 3: 1171
    4: 1920 bogomips: 19953
  Flags: avx ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Vulnerabilities:
  Type: itlb_multihit status: KVM: VMX disabled
  Type: l1tf
    mitigation: PTE Inversion; VMX: conditional cache flushes, SMT vulnerable
  Type: mds mitigation: Clear CPU buffers; SMT vulnerable
  Type: meltdown mitigation: PTI
  Type: spec_store_bypass
    mitigation: Speculative Store Bypass disabled via prctl and seccomp
  Type: spectre_v1
    mitigation: usercopy/swapgs barriers and __user pointer sanitization
  Type: spectre_v2 mitigation: Retpolines, IBPB: conditional, IBRS_FW,
    STIBP: conditional, RSB filling
  Type: srbds status: Vulnerable: No microcode
  Type: tsx_async_abort status: Not affected
Graphics:
  Device-1: Intel 3rd Gen Core processor Graphics vendor: Lenovo driver: i915
    v: kernel ports: active: LVDS-1 empty: DP-1,HDMI-A-1,VGA-1 bus-ID: 00:02.0
    chip-ID: 8086:0166 class-ID: 0300
  Device-2: Chicony Lenovo EasyCamera type: USB driver: uvcvideo
    bus-ID: 2-1.7:4 chip-ID: 04f2:b322 class-ID: 0e02
  Display: x11 server: X.Org v: 21.1.3 with: Xwayland v: 22.1.1
    compositor: kwin_x11 driver: X: loaded: intel unloaded: modesetting
    alternate: fbdev,vesa gpu: i915 display-ID: :0 screens: 1
  Screen-1: 0 s-res: 1600x900 s-dpi: 96 s-size: 423x238mm (16.65x9.37")
    s-diag: 485mm (19.11")
  Monitor-1: LVDS-1 mapped: LVDS1 model: LG Display 0x0360 built: 2011
    res: 1600x900 hz: 60 dpi: 140 gamma: 1.2 size: 290x170mm (11.42x6.69")
    diag: 338mm (13.3") ratio: 16:9 modes: 1600x900
  OpenGL: renderer: Mesa Intel HD Graphics 4000 (IVB GT2)
    v: 4.2 Mesa 22.0.3 compat-v: 3.1 direct render: Yes
Audio:
  Device-1: Intel 7 Series/C216 Family High Definition Audio vendor: Lenovo
    driver: snd_hda_intel v: kernel bus-ID: 00:1b.0 chip-ID: 8086:1e20
    class-ID: 0403
  Sound Server-1: ALSA v: k5.15.37-1-lts running: yes
  Sound Server-2: PulseAudio v: 15.0 running: no
  Sound Server-3: PipeWire v: 0.3.51 running: yes
Network:
  Message: No device data found.
  IF-ID-1: virbr0 state: down mac: <filter>
  IF-ID-2: virbr1 state: down mac: <filter>
  IF-ID-3: vmnet1 state: unknown speed: N/A duplex: N/A mac: <filter>
  IF-ID-4: vmnet8 state: unknown speed: N/A duplex: N/A mac: <filter>
  IF-ID-5: wlan0 state: up mac: <filter>
Bluetooth:
  Device-1: Realtek RTL8723AU 802.11n WLAN Adapter type: USB
    driver: btusb,rtl8723au bus-ID: 1-1.4:5 chip-ID: 0bda:1724 class-ID: e001
    serial: <filter>
  Report: bt-adapter ID: hci0 rfk-id: 0 state: down
    bt-service: enabled,running rfk-block: hardware: no software: yes
    address: <filter>
Drives:
  Local Storage: total: 1.14 TiB used: 587.76 GiB (50.2%)
  SMART Message: Unable to run smartctl. Root privileges required.
  ID-1: /dev/sda maj-min: 8:0 vendor: Samsung model: MZMTD256HAGM-000L1
    size: 238.47 GiB block-size: physical: 512 B logical: 512 B speed: 3.0 Gb/s
    type: SSD serial: <filter> rev: 2L0Q scheme: GPT
  ID-2: /dev/sdb maj-min: 8:16 type: USB vendor: Western Digital
    model: WD My Passport 0820 size: 931.48 GiB block-size: physical: 512 B
    logical: 512 B type: N/A serial: <filter> rev: 1007 scheme: GPT
Partition:
  ID-1: / raw-size: 931.22 GiB size: 931.22 GiB (100.00%)
    used: 397.72 GiB (42.7%) fs: btrfs dev: /dev/sdb2 maj-min: 8:18
  ID-2: /boot/efi raw-size: 260 MiB size: 256 MiB (98.45%)
    used: 562 KiB (0.2%) fs: vfat dev: /dev/sdb1 maj-min: 8:17
  ID-3: /home raw-size: 931.22 GiB size: 931.22 GiB (100.00%)
    used: 397.72 GiB (42.7%) fs: btrfs dev: /dev/sdb2 maj-min: 8:18
  ID-4: /var/log raw-size: 931.22 GiB size: 931.22 GiB (100.00%)
    used: 397.72 GiB (42.7%) fs: btrfs dev: /dev/sdb2 maj-min: 8:18
  ID-5: /var/tmp raw-size: 931.22 GiB size: 931.22 GiB (100.00%)
    used: 397.72 GiB (42.7%) fs: btrfs dev: /dev/sdb2 maj-min: 8:18
Swap:
  Alert: No swap data was found.
Sensors:
  System Temperatures: cpu: 65.0 C mobo: N/A
  Fan Speeds (RPM): N/A
Info:
  Processes: 277 Uptime: 3h 18m wakeups: 1 Memory: 7.65 GiB
  used: 3.85 GiB (50.4%) Init: systemd v: 250 tool: systemctl Compilers:
  gcc: 11.2.0 clang: 13.0.1 Packages: 2023 pacman: 2009 lib: 507 flatpak: 14
  Shell: Zsh v: 5.8.1 running-in: alacritty inxi: 3.3.15
Garuda (2.6.2-1):
  System install date:     2021-08-19
  Last full system update: 2022-05-07
  Is partially upgraded:   No
  Relevant software:       NetworkManager
  Windows dual boot:       Probably (Run as root to verify)
  Snapshots:               Snapper
  Failed units:            home-Network-desktop.mount systemd-networkd-wait-online.service

Thanks, y'all!

Sorry :wink:
I fix a little you're post, in "hide details" you can't use the "full view" with arrows in the upper right corner.

2 Likes

Thank you for the suggestion. Tried it, and it didn't look like it worked:

❯ LANG=C sudo pacman -Syu --overwrite "*"
[sudo] password for shaya:
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community                                                  6.9 MiB  1265 KiB/s 00:06 [--------------------------------------------------] 100%
 multilib is up to date
 chaotic-aur                                                2.1 MiB  2.36 MiB/s 00:01 [--------------------------------------------------] 100%
:: Starting full system upgrade...
:: Replace kwayland-server with extra/kwin? [Y/n]
:: Replace med with community/med-openmpi? [Y/n]
:: Replace qemu with extra/qemu-desktop? [Y/n]
:: Replace qemu-arch-extra with extra/qemu-emulators-full? [Y/n]
:: Replace wxgtk-common with extra/wxwidgets-common? [Y/n]
:: Replace wxgtk3 with extra/wxwidgets-gtk3? [Y/n]
:: Replace zotero with chaotic-aur/zotero-bin? [Y/n]
resolving dependencies...
looking for conflicting packages...
warning: removing 'hdf5' from target list because it conflicts with 'hdf5-openmpi'
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: sweet-theme-full-git and kvantum-theme-sweet-git are in conflict

I entered y for all the replace prompts.

Please, use search function

I tried this as well...

sudo pacman -Syu python-h5py-openmpi med-openmpi
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 chaotic-aur                                                2.1 MiB  3.09 MiB/s 00:01 [--------------------------------------------------] 100%
:: Starting full system upgrade...
:: Replace kwayland-server with extra/kwin? [Y/n] y
:: Replace med with community/med-openmpi? [Y/n] y
:: Replace qemu with extra/qemu-desktop? [Y/n] y
:: Replace qemu-arch-extra with extra/qemu-emulators-full? [Y/n] y
:: Replace wxgtk-common with extra/wxwidgets-common? [Y/n] y
:: Replace wxgtk3 with extra/wxwidgets-gtk3? [Y/n] y
:: Replace zotero with chaotic-aur/zotero-bin? [Y/n] y
resolving dependencies...
looking for conflicting packages...
warning: removing 'hdf5' from target list because it conflicts with 'hdf5-openmpi'
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: sweet-theme-full-git and kvantum-theme-sweet-git are in conflict

Still didn't work :confused:

Next one, did you search in forum?

No

image
its solved.

1 Like

Actually, this was the first thing I did, and it still didn't work. In fact, if you look a few lines down in the output from my OP, you'll see that it's running the same command that I ran manually as well, and pressed y for all the prompts, then proceeded to download all 1215 packages, and then fails out at the very last step with:

error: failed to commit transaction (conflicting files)

You have now the third conflict, now you must fix them.

Maybe after that you got the next conflict, search in forum and web and fix it.

Do you think I will search for you again?

You know the way, copy the conflict and put in search bar.

2 Likes

That's what I'm saying, I'm now going in a loop. It's the same 2 conflicts that keep looping, I cannot resolve one without the other. It keeps conflicting between the hdf5 conflict, and the sweet-theme conflict....

Ok, I think I fixed it....found a whole bunch of errors related to npm...
pacman -S npm --overwrite '/usr/lib/node_modules/npm/*' seemed to resolve those conflicts, and then update was able to complete properly.

Thanks, as always!

Me still waiting for @edu4rdshl to add the pacman parameter feature to garuda-update ;-;
You said you would, that means I legally and morally can't!

1 Like

Please don't install packages using npm.

It leads to problems exactly like yours.

regards

I don't recall ever installing packages with npm, it must have been something else I installed that needed it.... after it successfully ran update, a reboot is now throwing me into emergency mode, so I'm booting off a live usb of the latest dragonized iso, and attempting to chroot and see if I can fix it....

1 Like

Restore a snapshot, that's probably easier.

Nah, I figured it out. I have an NTFS volume that I was automounting in /etc/fstab with the kernel's built-in ntfs3 support, that had the "dirty" bit flagged on it, and for some reason, it caused the whole system to go into emergency mode. Once I commented that entry out, rebooted, all was well. Ran ntfsfix -d on it, restored the fstab entry, rebooted, and all was well.

2 Likes

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