[SOLVED] messed up my packages with apt-mark -- a little help?

[chconnor]

Hi -- apt is showing a huge list of important-seeming packages that it wants to autoremove:

$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
acpi-support acpid alsa-base ark baloo-kf5 bluez-cups cryfs cups-pk-helper dc dolphin elisa encfs ffmpegthumbs fonts-kacst fonts-kacst-one fonts-khmeros-core fonts-lao
fonts-lklug-sinhala fonts-noto-color-emoji fonts-sil-abyssinica fonts-sil-padauk fonts-thai-tlwg fonts-tibetan-machine fonts-tlwg-garuda fonts-tlwg-garuda-ttf
fonts-tlwg-kinnari fonts-tlwg-kinnari-ttf fonts-tlwg-laksaman fonts-tlwg-laksaman-ttf fonts-tlwg-loma fonts-tlwg-loma-ttf fonts-tlwg-mono fonts-tlwg-mono-ttf
fonts-tlwg-norasi fonts-tlwg-norasi-ttf fonts-tlwg-purisa fonts-tlwg-purisa-ttf fonts-tlwg-sawasdee fonts-tlwg-sawasdee-ttf fonts-tlwg-typewriter fonts-tlwg-typewriter-ttf
fonts-tlwg-typist fonts-tlwg-typist-ttf fonts-tlwg-typo fonts-tlwg-typo-ttf fonts-tlwg-umpush fonts-tlwg-umpush-ttf fonts-tlwg-waree fonts-tlwg-waree-ttf gir1.2-notify-0.7
gnupg-agent go-mtpfs gstreamer-qapt gwenview haveged inputattach kaccounts-integration kamera kate kate5-data kcalc kde-config-tablet kde-config-whoopsie kde-spectacle
kdegames-card-data-kf5 kdegames-mahjongg-data-kf5 kdegraphics-thumbnailers kdenetwork-filesharing kerneloops kimageformat-plugins kio-audiocd kio-fuse kmahjongg kmines
konversation konversation-data kpat kross ksudoku ksystemlog kubuntu-desktop kubuntu-settings-desktop kubuntu-web-shortcuts language-selector-common laptop-detect libavif13
libcolamd2 libcupsimage2 libdolphinvcs5 libfreecell-solver0 libgav1-0 libhavege2 libkcolorpicker0 libkf5baloowidgets-bin libkf5baloowidgets-data libkf5baloowidgets5
libkf5compactdisc5 libkf5kdcraw5 libkf5kdegames-data libkf5kdegames7 libkf5kdegamesprivate7 libkf5kipi-data libkf5kipi32.0.0 libkf5kmahjongglib5 libkf5krosscore5
libkf5krossui5 libkf5modemmanagerqt6 libkf5sane-data libkf5sane5 libkf5unitconversion-data libkf5unitconversion5 libkimageannotator-common libkimageannotator0 libopenconnect5
libpskc0 libreoffice-calc libreoffice-draw libreoffice-impress libreoffice-kf5 libreoffice-plasma libreoffice-qt5 libsignon-extension1 libstoken1 libsuitesparseconfig5
libtomcrypt1 libtommath1 libtss2-tctildr0 libu2f-udev libwhoopsie-preferences0 libwhoopsie0 libxmlsec1-openssl libyuv0 linux-sound-base lp-solve memtest86+
mobile-broadband-provider-info mscompress muon pastebinit pavucontrol-qt pavucontrol-qt-l10n pcmciautils plasma-calendar-addons plasma-dataengines-addons
plasma-distro-release-notifier plasma-firewall plasma-nm plasma-runners-addons plasma-vault plasma-wallpapers-addons plasma-widgets-addons policykit-desktop-privileges
print-manager printer-driver-brlaser printer-driver-c2esp printer-driver-foo2zjs printer-driver-foo2zjs-common printer-driver-m2300w printer-driver-min12xxw
printer-driver-pnm2ppa printer-driver-ptouch printer-driver-pxljr printer-driver-sag-gdi printer-driver-splix python3-cups python3-cupshelpers python3-debconf
qapt-deb-installer qml-module-org-kde-kaccounts qml-module-qtquick-xmllistmodel rfkill sddm sddm-theme-breeze signon-kwallet-extension signon-plugin-password
signon-ui-service signon-ui-x11 signond skanlite spice-vdagent system-config-printer-common system-config-printer-udev ubuntu-drivers-common ubuntu-release-upgrader-qt
update-notifier-common whoopsie whoopsie-preferences x11-apps x11-session-utils xinit xorg
Use 'sudo apt autoremove' to remove them.
The following packages have been kept back:
initramfs-tools initramfs-tools-bin initramfs-tools-core python3-tz
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.​

Looking through my bash history, I suspect the reason is that I saw some "kept back" packages and manually installed them, then marked them as "auto":

$ sudo apt-get install kubuntu-desktop libsmbclient libwbclient0 python3-distupgrade python3-samba samba-common samba-common-bin samba-dsdb-modules samba-libs smbclient ubuntu-release-upgrader-core ubuntu-release-upgrader-qt xserver-common xserver-xorg-core xserver-xorg-legacy
$ sudo apt-mark auto kubuntu-desktop libsmbclient libwbclient0 python3-distupgrade python3-samba samba-common samba-common-bin samba-dsdb-modules samba-libs smbclient ubuntu-release-upgrader-core ubuntu-release-upgrader-qt xserver-common xserver-xorg-core xserver-xorg-legacy​

...I did that not knowing about the "phased" release thing that's apparently happening now, and because some advice online was that if you manually install kept back packages you should mark them as auto... but now I'm wondering if one (or many) of those (e.g. kubuntu-desktop?) maybe should not be marked as "auto" if they are top-level packages?

Any advice on how to fix this? Thanks!

[Schwarzer Kater]

tl;dr: The meta-package kubuntu-desktop has the "manual" flag in my standard Kubuntu 22.04 installation. So I would go from there:

sudo apt-mark manual kubuntu-desktop and see if the output of sudo apt update && sudo apt -s full-upgrade is any different.



To be more thorough here is a full list of all the packages' state in my system which you marked as "auto":

~$ apt-mark showmanual kubuntu-desktop libsmbclient libwbclient0 python3-distupgrade python3-samba
samba-common samba-common-bin samba-dsdb-modules samba-libs smbclient ubuntu-release-upgrader-core
ubuntu-release-upgrader-qt xserver-common xserver-xorg-core xserver-xorg-legacy​

kubuntu-desktop​​

and

~$ apt-mark showauto kubuntu-desktop libsmbclient libwbclient0 python3-distupgrade python3-samba
samba-common samba-common-bin samba-dsdb-modules samba-libs smbclient ubuntu-release-upgrader-core
ubuntu-release-upgrader-qt xserver-common xserver-xorg-core xserver-xorg-legacy​

libsmbclient
libwbclient0
python3-distupgrade
python3-samba
samba-common
samba-common-bin
samba-dsdb-modules
samba-libs
smbclient
ubuntu-release-upgrader-core
ubuntu-release-upgrader-qt
xserver-common
xserver-xorg-core​

And to verify this:

~$ apt show kubuntu-desktop libsmbclient libwbclient0 python3-distupgrade python3-samba
samba-common samba-common-bin samba-dsdb-modules samba-libs smbclient ubuntu-release-upgrader-core
ubuntu-release-upgrader-qt xserver-common xserver-xorg-core xserver-xorg-legacy​ | grep -i manual

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

APT-Manual-Installed: yes
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no
APT-Manual-Installed: no​

I don't know why xserver-xorg-legacy doesn't show up with apt-mark showauto or apt show | grep -i manual, but is is marked as "auto" in my system, too.

Hope this helps.

[chconnor]

That fixed it! Thank you so much for the detailed response.

Mine does the same odd thing with xserver-xorg-legacy. Wonder what that's about.