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#1 2025-09-19 18:40:14

Skeleton2323
Member
Registered: 2024-09-14
Posts: 72

[SOLVED]Conflicting files from virt-manager when trying to Syu

I decided to upgrade my system after last upgrading it about 3 months ago (kernel version 6.14.9)
Originally, I'd get the following output after the package integrity check

 error:libngtcp2: signature from "kpcyrd <git@rxv.cc>" is unknown trust
:: File /var/cache/pacman/pkg/libnqtcp2-1.15.1-1-x86_64.pkg.tar.zst is corrupted ( invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n] y
error: failed to commit transaction ( invalid or corrupted package)
Errors occured, no packages were upgraded.

I followed the instructions in the pacman troubleshooting page about the error which told me to erase .part files (which there were none as far as I could tell) and ran the command

 find /var/cache/pacman/pkg/ -iname "*.part" -delete

And I also reinstalled the arch keyring

 # pacman -Sy --needed archlinux-keyring && pacman -Su

This fixed the libnqtcp2 issues but the update still failed and is still failing with this output:

 [flan@yukarilinuxrog ~]$ sudo pacman -Syu
[sudo] password for flan: 
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace qgpgme-qt6 with extra/qgpgme? [Y/n] y
resolving dependencies...
looking for conflicting packages...
:: avogadrolibs-qt-1.101.0-1 and avogadrolibs-qt5-1.100.0-1 are in conflict. Remove avogadrolibs-qt5? [y/N] y
warning: dependency cycle detected:
warning: pam will be installed before its systemd-libs dependency
warning: dependency cycle detected:
warning: mesa will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: nvidia-utils will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: egl-wayland will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: qt6-multimedia-ffmpeg will be installed before its qt6-multimedia dependency
warning: dependency cycle detected:
warning: qt6-multimedia-gstreamer will be installed before its qt6-multimedia dependency
warning: dependency cycle detected:
warning: phonon-qt6-vlc will be installed before its phonon-qt6 dependency
warning: dependency cycle detected:
warning: xdg-desktop-portal-kde will be installed before its plasma-workspace dependency
warning: dependency cycle detected:
warning: libcamera-ipa will be installed before its libcamera dependency
warning: dependency cycle detected:
warning: python-soupsieve will be installed before its python-beautifulsoup4 dependency

Packages (1009) 7zip-25.01-1  aalib-1.4rc5-19  abseil-cpp-20250814.0-1  accessibility-inspector-25.08.1-1  adwaita-cursors-48.1-1
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                analitza-25.08.1-1  angelfish-25.08.1-1  aom-3.13.1-1  appstream-1.1.0-1  appstream-qt-1.1.0-1
                archlinux-appstream-data-20250825-1  arianna-25.08.1-1  ark-25.08.1-1  artikulate-25.08.1-1  at-spi2-core-2.56.4-1
                attica-6.18.0-1  audacity-1:3.7.5-1  audex-25.08.1-1  audiocd-kio-25.08.1-1  audiofile-0.3.6-11  audiotube-25.08.1-1
                audit-4.0.5-1  aurorae-6.4.5-1  automake-1.18.1-1  avahi-1:0.9rc2-1  avogadro-crystals-1.101.0-1  avogadro-fragments-1.101.0-1
                avogadro-molecules-1.101.0-1  avogadrolibs-1.101.0-1  avogadrolibs-qt-1.101.0-1  avogadrolibs-qt5-1.100.0-1 [removal]
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                webkit2gtk-4.1-2.48.6-1  wine-10.15-1  wireplumber-0.5.11-1  wolfssl-5.8.2-1  wxwidgets-common-3.2.8.1-2
                wxwidgets-gtk3-3.2.8.1-2  x264-3:0.164.r3108.31e19f9-3  x265-4.1-1  xapian-core-1:1.4.29-1  xapp-2.8.13-1
                xcb-util-cursor-0.1.6-1  xdg-desktop-portal-kde-6.4.5-1  xkeyboard-config-2.45-1  xorg-server-21.1.18-2
                xorg-server-common-21.1.18-2  xorg-xdpyinfo-1.4.0-1  xorg-xwayland-24.1.8-1  yakuake-25.08.1-1  yt-dlp-2025.09.05-1
                zanshin-25.08.1-1  zenity-4.1.99-2  zlib-ng-2.2.5-1

Total Installed Size:  12486,63 MiB
Net Upgrade Size:        197,92 MiB

:: Proceed with installation? [Y/n] y
(1007/1007) checking keys in keyring                                                   [##################################################] 100%
(1007/1007) checking package integrity                                                 [##################################################] 100%
(1007/1007) loading package files                                                      [##################################################] 100%
(1007/1007) checking for file conflicts                                                [##################################################] 100%
error: failed to commit transaction (conflicting files)
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virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/panic.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/redirdev.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/rng.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/shmem.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/smartcard.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/sound.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/tpm.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/video.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/vsock.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/devices/__pycache__/watchdog.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/blkiotune.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/clock.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/cpu.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/cputune.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/features.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/idmap.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/keywrap.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/launch_security.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/memorybacking.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/memtune.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/metadata.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/numatune.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/os.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/pm.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/resource.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/seclabel.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/sysinfo.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/vcpus.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/domain/__pycache__/xmlnsqemu.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/cloudinit.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/installer.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/installerinject.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/installertreemedia.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/unattended.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/urldetect.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/urlfetcher.cpython-313.pyc exists in filesystem
virt-install: /usr/share/virt-manager/virtinst/install/__pycache__/volumeupload.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/addhardware.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/asyncjob.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/baseclass.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/config.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/connection.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/connmanager.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/createconn.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/createpool.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/createvm.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/createvol.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/delete.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/engine.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/hoststorage.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/manager.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/oslist.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/storagebrowse.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/systray.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/virtmanager.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/vmmenu.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/vmwindow.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/__pycache__/xmleditor.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/console.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/details.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/serialcon.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/snapshots.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/sshtunnels.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/details/__pycache__/viewers.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/addstorage.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/fsdetails.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/gfxdetails.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/mediacombo.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/netlist.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/tpmdetails.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/device/__pycache__/vsockdetails.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/connectauth.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/graphwidgets.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/inspection.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/keyring.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/libvirtenummap.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/statsmanager.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/testmock.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/lib/__pycache__/uiutil.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/object/__pycache__/__init__.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/object/__pycache__/domain.cpyth
on-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/object/__pycache__/libvirtobject.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/object/__pycache__/network.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/object/__pycache__/nodedev.cpython-313.pyc exists in filesystem
virt-manager: /usr/share/virt-manager/virtManager/object/__pycache__/storagepool.cpython-313.pyc exists in filesystem
Errors occurred, no packages were upgraded.
[flan@yukarilinuxrog ~]$

also originally on top of the virt-manager errors, I'd get the ad107 exists in filesystem error from the news article but removing linux-firmware seemed to get rid of it.

What should I do? I'd like to keep virt-manager or its configuration if possible. Any help is appreciated!

Last edited by Skeleton2323 (2025-09-20 03:21:10)

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#2 2025-09-20 00:34:53

twelveeighty
Member
Registered: 2011-09-04
Posts: 1,448

Re: [SOLVED]Conflicting files from virt-manager when trying to Syu

Post the output of `pacman -Qo /usr/share/virt-manager/virtinst/__pycache__/__init__.cpython-313.pyc`.

These issues are *typically* encountered when you've used something other than pacman to install Python modules as root, or with root access, but this command will tell us more.

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#3 2025-09-20 01:33:12

Scimmia
Fellow
Registered: 2012-09-01
Posts: 13,724

Re: [SOLVED]Conflicting files from virt-manager when trying to Syu

It's only .pyc files, so this isn't a matter of using pip or anything. When you run a python script, they get byte-compiled, and if it has permissions, it writes that out as a .pyc file. Typically, these files are packaged, but they appear to have been missing so were generated at runtime. Just overwrite them.

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#4 2025-09-20 03:06:13

Skeleton2323
Member
Registered: 2024-09-14
Posts: 72

Re: [SOLVED]Conflicting files from virt-manager when trying to Syu

twelveeighty wrote:

Post the output of `pacman -Qo /usr/share/virt-manager/virtinst/__pycache__/__init__.cpython-313.pyc`.

These issues are *typically* encountered when you've used something other than pacman to install Python modules as root, or with root access, but this command will tell us more.

error: No package owns /usr/share/virt-manager/virtinst/__pycache__/__init__.cpython-313.pyc

now, I do have yay installed on the system but virt-manager is an official arch package. I haven't used yay for 6 months more or less

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#5 2025-09-20 03:20:51

Skeleton2323
Member
Registered: 2024-09-14
Posts: 72

Re: [SOLVED]Conflicting files from virt-manager when trying to Syu

Scimmia wrote:

It's only .pyc files, so this isn't a matter of using pip or anything. When you run a python script, they get byte-compiled, and if it has permissions, it writes that out as a .pyc file. Typically, these files are packaged, but they appear to have been missing so were generated at runtime. Just overwrite them.

sudo pacman -Syu --overwrite '*' virt-manager

Overwriting them fixed it. Thanks!

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