Help with 'dreaded' exists in filesystem upgrade issue required please

General system
#1

Hi

Running pacman -Syu to do full system upgrade and getting lots of ‘exists in filesystem’ errors (see below)

They appear to be caused by flatpak and xdg-desktop-portal

I’m out of my depth on this one. would it be safe to overwrite? and if so what is the command to do that??

‘flatpak list’ doesn’t show anything installed!?

Apologies for being clueless

Thanks

Keith

error: failed to commit transaction (conflicting files)
xdg-desktop-portal: /usr/lib/systemd/user/xdg-desktop-portal.service exists in filesystem
xdg-desktop-portal: /usr/lib/systemd/user/xdg-document-portal.service exists in filesystem
xdg-desktop-portal: /usr/lib/systemd/user/xdg-permission-store.service exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Access.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Account.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.AppChooser.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Email.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.FileChooser.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Inhibit.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Lockdown.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Notification.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.PermissionStore.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Print.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.RemoteDesktop.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Request.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.ScreenCast.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Screenshot.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Session.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.impl.portal.Settings.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Account.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Device.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Documents.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Email.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.FileChooser.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Inhibit.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Location.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.NetworkMonitor.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Notification.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.OpenURI.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Print.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.ProxyResolver.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.RemoteDesktop.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Request.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.ScreenCast.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Screenshot.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Session.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Settings.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Trash.xml exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/services/org.freedesktop.impl.portal.PermissionStore.service exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/services/org.freedesktop.portal.Desktop.service exists in filesystem
xdg-desktop-portal: /usr/share/dbus-1/services/org.freedesktop.portal.Documents.service exists in filesystem
xdg-desktop-portal: /usr/share/doc/xdg-desktop-portal/docbook.css exists in filesystem
xdg-desktop-portal: /usr/share/doc/xdg-desktop-portal/portal-docs.html exists in filesystem
xdg-desktop-portal: /usr/share/pkgconfig/xdg-desktop-portal.pc exists in filesystem
flatpak: /etc/profile.d/flatpak-bindir.sh exists in filesystem
flatpak: /etc/profile.d/flatpak.sh exists in filesystem
flatpak: /usr/bin/flatpak exists in filesystem
flatpak: /usr/bin/flatpak-bisect exists in filesystem
flatpak: /usr/bin/flatpak-coredumpctl exists in filesystem
flatpak: /usr/include/flatpak/flatpak-bundle-ref.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-enum-types.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-error.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-installation.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-installed-ref.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-instance.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-portal-error.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-ref.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-related-ref.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-remote-ref.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-remote.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-transaction.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak-version-macros.h exists in filesystem
flatpak: /usr/include/flatpak/flatpak.h exists in filesystem
flatpak: /usr/lib/girepository-1.0/Flatpak-1.0.typelib exists in filesystem
flatpak: /usr/lib/libflatpak.so exists in filesystem
flatpak: /usr/lib/pkgconfig/flatpak.pc exists in filesystem
flatpak: /usr/lib/systemd/system/flatpak-system-helper.service exists in filesystem
flatpak: /usr/lib/systemd/user-environment-generators/60-flatpak exists in filesystem
flatpak: /usr/lib/systemd/user/flatpak-portal.service exists in filesystem
flatpak: /usr/lib/systemd/user/flatpak-session-helper.service exists in filesystem
flatpak: /usr/share/bash-completion/completions/flatpak exists in filesystem
flatpak: /usr/share/dbus-1/interfaces/org.freedesktop.Flatpak.xml exists in filesystem
flatpak: /usr/share/dbus-1/interfaces/org.freedesktop.portal.Flatpak.xml exists in filesystem
flatpak: /usr/share/dbus-1/services/org.freedesktop.Flatpak.service exists in filesystem
flatpak: /usr/share/dbus-1/services/org.freedesktop.portal.Flatpak.service exists in filesystem
flatpak: /usr/share/dbus-1/system-services/org.freedesktop.Flatpak.SystemHelper.service exists in filesystem
flatpak: /usr/share/dbus-1/system.d/org.freedesktop.Flatpak.SystemHelper.conf exists in filesystem
flatpak: /usr/share/doc/flatpak/docbook.css exists in filesystem
flatpak: /usr/share/doc/flatpak/flatpak-docs.html exists in filesystem
flatpak: /usr/share/flatpak/triggers/desktop-database.trigger exists in filesystem
flatpak: /usr/share/flatpak/triggers/gtk-icon-cache.trigger exists in filesystem
flatpak: /usr/share/flatpak/triggers/mime-database.trigger exists in filesystem
flatpak: /usr/share/gdm/env.d/flatpak.env exists in filesystem
flatpak: /usr/share/gir-1.0/Flatpak-1.0.gir exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakBundleRef.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakInstallation.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakInstalledRef.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakInstance.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakRef.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakRelatedRef.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakRemote.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakRemoteRef.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakTransaction.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakTransactionOperation.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/FlatpakTransactionProgress.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/annotation-glossary.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/ch01.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/flatpak-Error-codes.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/flatpak-Version-information.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/flatpak.devhelp2 exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/home.png exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/index.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/left-insensitive.png exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/left.png exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/object-tree.html exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/right-insensitive.png exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/right.png exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/style.css exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/up-insensitive.png exists in filesystem
flatpak: /usr/share/gtk-doc/html/flatpak/up.png exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-bundle.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-commit-from.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-export.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-finish.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-import-bundle.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-init.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-sign.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build-update-repo.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-build.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-config.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-create-usb.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-document-export.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-document-info.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-document-unexport.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-documents.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-enter.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-history.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-info.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-install.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-kill.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-list.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-make-current.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-override.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-permission-remove.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-permission-reset.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-permission-show.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-permissions.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-ps.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-remote-add.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-remote-delete.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-remote-info.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-remote-ls.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-remote-modify.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-remotes.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-repair.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-repo.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-run.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-search.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-spawn.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-uninstall.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak-update.1.gz exists in filesystem
flatpak: /usr/share/man/man1/flatpak.1.gz exists in filesystem
flatpak: /usr/share/man/man5/flatpak-flatpakref.5.gz exists in filesystem
flatpak: /usr/share/man/man5/flatpak-flatpakrepo.5.gz exists in filesystem
flatpak: /usr/share/man/man5/flatpak-installation.5.gz exists in filesystem
flatpak: /usr/share/man/man5/flatpak-metadata.5.gz exists in filesystem
flatpak: /usr/share/man/man5/flatpak-remote.5.gz exists in filesystem
flatpak: /usr/share/polkit-1/actions/org.freedesktop.Flatpak.policy exists in filesystem
flatpak: /usr/share/polkit-1/rules.d/org.freedesktop.Flatpak.rules exists in filesystem
flatpak: /usr/share/zsh/site-functions/_flatpak exists in filesystem
Errors occurred, no packages were upgraded.
Pacman error : file exists in filesystem (python-evdev)
#2

Before you overwrite them should check to ensure another package doesn’t own them.

What does this return:

pacman -Qo /usr/bin/flatpak
pacman -Qo /usr/share/pkgconfig/xdg-desktop-portal.pc

Also, what does this return:

pacman -Qs flatpak
1 Like
#3

Dalto,

Many thanks for taking an interest :slight_smile:

pacman -Qo /usr/bin/flatpak
error: No package owns /usr/bin/flatpak

pacman -Qo /usr/share/pkgconfig/xdg-desktop-portal.pc
error: No package owns /usr/share/pkgconfig/xdg-desktop-portal.pc

pacman -Qs flatpak - this doesn't return anything!
#4

So…that means that pacman doesn’t know you have flatpak installed. However, pacman -Syu is trying to install it, so it must be a dependency for something else you have installed?

How did you install flatpak initially?

#5

Ah, I had a suspicion that question might come up. I’m afraid I have no idea!

This installation started as Antergos and I converted to Endeavouros FWIW

Where do I go from here?

Thanks again

#6

are two things remove manually that files or must use overwrite option

pacman -S --overwrite glob package

that case flatpak package , dont use it with -Syu

#7

if a install breakoff in a way files get without owner then you get things like this, also , if a package is splitted it can accure same thing as this.

#8

In that case, your only choice is likely to overwrite. It is a little dangerous so I wouldn’t recommend it as a general practice.

sudo pacman -S flatpak xdg-desktop-portal --overwrite "*"
sudo pacman -Syu
4 Likes
#9

Thanks,

the overwrite doesn’t appear to have broken anything.

I appreciate you both providing assistance

Take care

Keith