After large update today, vital packages are orphaned and pamac doesn't show text

heiko_s · 13 May 2024 23:51

I did the update today and it downloaded 3 GB. It ran a long time to build pyside2 (which I never saw before) and ended with some error.
It wanted to uninstall soonar (for my Logitech wireless stuff) to meet some conflict.

In the end, pamac stopped showing text. Actually text shows for a split second and disappears.

I checked for orphaned packages and got a list of critical packages that were orphaned. Below is the list:

sudo pacman -Rs $(pacman -Qdtq)
checking dependencies...
:: git optionally requires org.freedesktop.secrets: keyring credential helper
:: inxi optionally requires sudo: -Dx hddtemp-user; -o file-user
:: libgnome-keyring optionally requires org.freedesktop.secrets: secret storage backend
:: libisoburn optionally requires sudo: for use with xorriso-dd-target
:: libsecret optionally requires org.freedesktop.secrets: secret storage backend
:: pacman-contrib optionally requires fakeroot: for checkupdates
:: pacman-contrib optionally requires sudo: privilege elevation for several scripts
:: picard optionally requires qt5-multimedia: media player toolbar
:: pyside2 optionally requires qt5-speech: QtTextToSpeech bindings
:: python-pyqt5 optionally requires qt5-multimedia: QtMultimedia, QtMultimediaWidgets
:: python-pyqt5 optionally requires qt5-speech: QtTextToSpeech
:: python-shiboken2 optionally requires qt5-speech: QtTextToSpeech bindings
:: qt5-base optionally requires qt5-wayland: to run Qt applications in a Wayland session
:: qt5-tools optionally requires clang: for qdoc
:: qt6-tools optionally requires clang: for qdoc and lupdate
:: subversion optionally requires kwallet5: for KWallet for auth credentials
:: xorg-xrdb optionally requires gcc: for preprocessing
:: yay optionally requires sudo: privilege elevation

Packages (72) autoconf-2.72-1  bison-3.8.2-6  clang-17.0.6-2  compiler-rt-17.0.6-2  cppdap-1.58.0-1
              debugedit-5.0-5  dnssec-anchors-20190629-3  fakeroot-1.34-1  gcc-13.2.1-6
              jsoncpp-1.9.5-2  kbookmarks5-5.115.0-1  kcodecs5-5.115.0-1  kcompletion5-5.115.0-1
              kconfig5-5.115.0-1  kconfigwidgets5-5.115.0-1  kcrash5-5.115.0-1
              kdbusaddons5-5.115.0-1  kded5-5.115.0-1  kglobalaccel5-5.115.0-3
              kguiaddons5-5.115.0-2  ki18n5-5.115.1-1  kiconthemes5-5.115.0-1
              kitemviews5-5.115.0-1  kjobwidgets5-5.115.0-1  knotifications5-5.115.0-1
              kservice5-5.115.0-2  ktextwidgets5-5.115.0-1  kwallet5-5.115.0-2
              kwidgetsaddons5-5.115.0-1  kwindowsystem5-5.115.0-1  kxmlgui5-5.115.0-1
              libdbusmenu-qt5-0.9.3+16.04.20160218-7  libisl-0.26-2  libmpc-1.3.1-1  llvm-17.0.6-4
              patch-2.7.6-10  pkgconf-2.1.1-1  pyside6-6.7.0-5  python-annotated-types-0.6.0-3
              python-manjaro-sdk-1:0.1.1-1  python-pydantic-core-1:2.18.2-2
              python-pyproject-hooks-1.1.0-1  python-systemd-235-3  qca-qt5-2.3.8-3
              qt5-multimedia-5.15.13+kde+r2-1  qt5-speech-5.15.13+kde+r1-1
              qt5-wayland-5.15.13+kde+r60-1  rhash-1.4.4-1  shiboken6-6.7.0-5  solid5-5.115.0-1
              sonnet5-5.115.0-1  sudo-1.9.15.p5-1  base-devel-1-2  cmake-3.29.2-1  gcab-1.6-1
              gendesk-1.0.9-4  kio5-5.115.0-3  ldns-1.8.3-2  lib32-libunwind-1.8.1-1
              libsmbios-2.4.3-7  poppler-qt6-24.03.0-1  python-build-1.2.1-3  python-evdev-1.7.0-3
              python-hid-parser-0.0.3-6  python-installer-0.7.0-8  python-ply-3.11-13
              python-pycurl-7.45.2-4  python-pydantic-2.7.1-2  python-xlib-0.33-3
              ttf-opensans-1.101-2  web-installer-url-handler-2.3-1
              webrtc-audio-processing-0.3.1-4

Total Removed Size:  816.60 MiB

:: Do you want to remove these packages? [Y/n] n

Below is the end of the pacman.log, the full log of this update is much much longer:

[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] e[1;1me[1;32m==>e[1;0me[1;1m Warning:
[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] 	 -> Kernel has been updated. Modules of the current kernel
[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] 	 -> have been backed up so you can continue to use your
[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] 	 -> computer. However, the new kernel will only work
[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] 	 -> at next boot.
[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] 	e[1;0m
[2024-05-14T01:04:01+0300] [ALPM-SCRIPTLET] 	e[1;0m
[2024-05-14T01:04:01+0300] [ALPM] running 'manjaro-printer.hook'...
[2024-05-14T01:04:01+0300] [ALPM] running 'pacman-mirrors-upgrade.hook'...
[2024-05-14T01:04:03+0300] [ALPM-SCRIPTLET] ::e[1;37mINFOe[1;m Downloading mirrors from Manjaro
[2024-05-14T01:04:03+0300] [ALPM-SCRIPTLET] ::e[1;37mINFOe[1;m => Mirror pool: https://repo.manjaro.org/mirrors.json
[2024-05-14T01:04:03+0300] [ALPM-SCRIPTLET] ::e[1;37mINFOe[1;m => Mirror status: https://repo.manjaro.org/status.json
[2024-05-14T01:04:03+0300] [ALPM-SCRIPTLET] hint: use `pacman-mirrors` to generate and update your pacman mirrorlist.
[2024-05-14T01:04:03+0300] [ALPM] running 'texinfo-install.hook'...
[2024-05-14T01:04:04+0300] [ALPM] running 'thunderbird-post.hook'...
[2024-05-14T01:04:04+0300] [ALPM] running 'update-desktop-database.hook'...
[2024-05-14T01:04:04+0300] [ALPM] running 'update-vlc-plugin-cache.hook'...
[2024-05-14T01:04:05+0300] [ALPM] running 'vimdoc.hook'...
[2024-05-14T01:35:29+0300] [ALPM] transaction started
[2024-05-14T01:35:29+0300] [ALPM] upgraded python-shiboken2 (5.15.12-1 -> 5.15.13-2)
[2024-05-14T01:35:29+0300] [ALPM] upgraded pyside2 (5.15.12-1 -> 5.15.13-2)
[2024-05-14T01:35:29+0300] [ALPM] transaction completed
[2024-05-14T01:35:29+0300] [ALPM] running '30-systemd-update.hook'...
[2024-05-14T01:35:45+0300] [PAMAC] synchronizing package lists
[2024-05-14T01:36:43+0300] [PAMAC] synchronizing package lists
[2024-05-14T01:37:49+0300] [PAMAC] synchronizing package lists
[2024-05-14T01:41:28+0300] [PAMAC] synchronizing package lists
[2024-05-14T01:41:57+0300] [ALPM] transaction started
[2024-05-14T01:41:57+0300] [ALPM] installed pkgconf (2.1.1-1)
[2024-05-14T01:41:57+0300] [ALPM] installed debugedit (5.0-5)
[2024-05-14T01:41:57+0300] [ALPM] installed autoconf (2.72-1)
[2024-05-14T01:41:57+0300] [ALPM] installed bison (3.8.2-6)
[2024-05-14T01:41:57+0300] [ALPM] installed patch (2.7.6-10)
[2024-05-14T01:41:57+0300] [ALPM] installed base-devel (1-2)
[2024-05-14T01:41:57+0300] [ALPM] transaction completed
[2024-05-14T01:41:57+0300] [ALPM] running '30-systemd-update.hook'...
[2024-05-14T01:41:57+0300] [ALPM] running 'texinfo-install.hook'...
[2024-05-14T01:42:02+0300] [ALPM] transaction started
[2024-05-14T01:42:02+0300] [ALPM] removed solaar (1.1.12-1)
[2024-05-14T01:42:02+0300] [ALPM] upgraded python-hid-parser (0.0.3-2 -> 0.0.3-6)
[2024-05-14T01:42:02+0300] [ALPM] transaction completed
[2024-05-14T01:42:02+0300] [ALPM] running '30-systemd-udev-reload.hook'...
[2024-05-14T01:42:04+0300] [ALPM] running '30-systemd-update.hook'...
[2024-05-14T01:42:04+0300] [ALPM] running 'gtk-update-icon-cache.hook'...
[2024-05-14T01:42:04+0300] [ALPM] running 'update-desktop-database.hook'...

When running pacman -Syu it tells me there is nothing to update.

The Pamac GUI is unusable now. Can anyone point toward a solution?

Strangely, the system still boots.
Here a screenshot of Pamac:

cscs · 14 May 2024 00:03

Unsupported package(s).
pyside2 is an AUR package that you were compiling yourself. (hence the time).
This could go part ways to explaining your tweaked situation.

Heres another one.

But you skipped all the information that went on before it.

Sure.
The mapare script can try to make sure you have the default packages.
This may install a few things that come default that you dont want. But you can remove them after the fact.

bash <(curl -s https://gitlab.com/cscs/mapare/-/raw/main/mapare) -IA

Input kde at the prompt.

Yochanan · 14 May 2024 00:21

You might have done an update once while attempting to install a package as a dependency:

sudo pacman -Syu --asdeps <package-name>  ## never do this

Dong so would install said package as a dependency, but also all updated packages would also be installed as dependencies.

To resolve the issue, mark the packages that should be installed explicitly as such:

sudo pacman -D --asexplicit <list of package names>

Both pyside2 and python-shiboken2 were dropped from the repos to the AUR. See what depends on them, you may not need them anymore.

pacman -Qi <package-name> | grep 'Required By\|Optional For'

heiko_s · 14 May 2024 01:31

I checked the need for the pyside2 etc. packages and no, I don’t need them. I had removed Windscribe VPN utility earlier that might have used these packages.

Then I followed @cscs advice and used the script:

It installed quite a lot of stuff (~200 MB compressed) and asked to me remove conflicting packages. I was skeptical regarding removal of some audio utils to be replaced by pipewire, but it seemed to have worked well.

The Pamac GUI is fine now. Rebooted the PC, all is working. I tested my Windows VM and it also booted fine.

Only thing is that it notified me of a kernel update, which has already been applied and I’m running the kernel. Manjaro Settings Manager shows me that I use the latest LTS kernel (6.6.30-2). Any idea how to get rid of the “fake news”?

Thanks to both of you for your quick and very helpful response!

Unfortunately I use quite a number of AUR packages that I need, like Zoom, Dropbox, and apfs-fuse-git, among others. I don’t use flatpacks though. Would flatpacks make life easier?

In the end I also removed all orphaned packages. Hope it won’t cause issues.

Again thanks for everything - you saved my day (actually night)!

cscs · 14 May 2024 01:39

Pipewire is default now.
If you want to return to pulseadio for some reason it should be

sudo pacman -Syu manjaro-pulse pulseaudio-bluetooth

But if pipewire works for you, I would suggest sticking with that.

In general the replacements/reinstalls were the intention.

This is a longstanding gripe with that notifier.
You can augment the settings, disable it, or remove it entirely.
Its simply informing you that a new kernel series (6.9, not an LTS) is available.
With a poor choice of words.
Not that yours is ‘bad’.

manjaro-settings-manager-notifier
(and/or manjaro-settings-manager-knotifier, but that is for plasma5)

Huzzah.
Happy penguins.

heiko_s · 14 May 2024 01:49

Thanks for the clarifications, @cscs . I just noticed that gksu seems to be replaced by zensu. I use gksu in launchers that run scripts. I have a script to mount NTFS partitions residing on LVM (thus a script) that uses notify-send to display messages on screen.
Here is what I get when using gksu or zensu:
Screenshot_2024-05-14_04-47-54

Looks like I have to rewrite some scripts, or install the gksu dependencies again. What’s the best option here - stick with gksu and notify-send or switch to zensu and zenity?

Note that the gksu dependencies were listed as “orphans”.

cscs · 14 May 2024 01:59

gksu is very old and not really advisable.

Are you sure they need to be run this way?

In any case gksu still exists in the AUR if you need it.

Maybe you would like to start another thread about your situation and what you want to accomplish.

I have a feeling that what you are doing has other approaches.

system · 15 May 2024 14:00

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