apt wants to autoremove packages i explicitly installed

I've just reinstalled and have a similar situation. Basically I just came up from alternate and installed ubuntu-desktop

Same on edgy here.

Situation:

(1) Installed Ubuntu edgy.

(2) Installed kubuntu-desktop (3.5.6 from kubuntu.org).

(3) Installed OpenOffice 2.1 vanilla (which removed ubuntu-desktop meta package)

(4) Uninstalled kubuntu-desktop meta package (which survived OpenOffice-2.1-Install but can't be reinstalled without OpenOffice from edgy)

(5) Try to prevent apt from autoremoving kde-stuff:
sudo apt-get install kde-core
sudo apt-get --reinstall install acpi acpi-support acpid adept akregator amarok anacron ark arts avahi-daemon bc bogofilter cdparanoia cdrdao cdrecord cupsys cupsys-bsd cupsys-client cupsys-driver-gutenprint dbus dc digikam diveintopython doc-base dvd+rw-tools foo2zjs foomatic-db foomatic-db-engine foomatic-db-hpijs foomatic-filters fortune-mod gdb gs-esp gtk2-engines-gtk-qt gwenview hal hotkey-setup wdb-client-kde k3b kaddressbook kaffeine-xine kamera karm katapult kate kaudiocreator kcontrol kcron kde-guidance kde-guidance-powermanager kde-systemsettings kdeadmin-kfile-plugins kdebase-kio-plugins kdebluetooth kdegraphics-kfile-plugins kdemultimedia-kfile-plugins kdemultimedia-kio-plugins kdenetwork-filesharing kdenetwork-kfile-plugins kdepasswd kdepim-kio-plugins kdepim-wizards kdeprint kdesktop kdm kdnssd keep kfind kghostview khelpcenter kicker kio-apt kio-locate kipi-plugins klipper kmail kmailcvt kmenuedit kmilo kmix kmplayer-konq-plugins knetworkconf knotes konq-plugins konqueror konqueror-nsplugins konsole kontact konversation kooka kopete korganizer kpdf kpf kppp krdc krfb krita kscd ksmserver ksnapshot ksplash ksplash-engine-moodin ksvg ksysguard ksystemlog ktorrent kubuntu-artwork-usplash kubuntu-default-settings kubuntu-docs kubuntu-konqueror-shortcuts kwalletmanager kwin landscape-client language-selector-qt lftp libarts1-akode libgl1-mesa-glx libglut3 libnss-mdns libpam-foreground libsasl2-modules libstdc++5 libxp6 min12xxw mkisofs pmount pnm2ppa powermanagement-interface qca-tls readahead screen slocate smbclient speedcrunch ttf-bitstream-vera ttf-dejavu ttf-freefont unzip usplash vorbis-tools wlassistant wvdial x-ttcidfont-conf xkeyboard-config xorg xterm zip
(all Dependencies from kubuntu-desktop beside apmd)

(6) It didn't help:
LANG=C sudo apt-get --dry-run autoremove
...
The following packages will be REMOVED:
adept adept-batch adept-common adept-installer dept-manager adept-notifier adept-updater akregator apt-index-watcher ark bogofilter bogofilter-bdb bogofilter-common debtags digikam gimp-help-common gimp-help-de gstreamer0.10-gnonlin gwenview hwdb-client-kde k3b kaffeine kaffeine-xine karm katapult kaudiocreator kbstate kcron kde-guidance kde-guidance-powermanager kde-icons-mono kde-systemsettings kdeadmin-kfile-plugins kdebluetooth kdegraphics-kfile-plugins kdemultimedia-kfile-plugins kdenetwork-filesharing kdenetwork-kfile-plugins kdepim-kio-plugins kdepim-kresources kdepim-wizards kdnssd keep kio-apt kio-locate kipi-plugins kmag kmail kmailcvt kmilo kmix kmousetool kmplayer-base kmplayer-konq-plugins knetworkconf knotes koffice-data koffice-libs konq-plugins kontact konversation kooka kopete korganizer kpdf kpf kppp krdc krfb krita krita-data kscd ksnapshot ksplash-engine-moodin ksvg ksystemlog ktorre...

Sorry for the long post, but as you can see at the end it would even remove OpenOffice, which I installed manually as mentioned.

Thanks for your bugreport.

I prepared a new apt upload that will explicitly exclude all direct dependencies from meta-packages from being marked as automatic installs. This should fix a lot of the confusion seen here.

In addition to this I have attached a fixup script that will mark the current direct dependencies of installed meta-packages as manual installed. It will make a copy of your old state file in /var/lib/apt/extended_states.fixup-save so if anything goes wrong, you can still copy it back.

The script requires the latest python-apt to work.

Please test it and let me know if that fixes the issues at hand.

Thanks,
 Michael

This shell fragment should do the same job:

DEPS=""; for pkg in ubuntu-desktop kubuntu-desktop edubuntu-desktop xubuntu-desktop edubuntu-server ubuntu-minimal ubuntu-standard; do if dpkg -s $pkg >/dev/null 2>&1 ; then for dep in $(apt-cache depends $pkg --installed | awk '{print $2}'); do if [ ! -z $dep ]; then DEPS="$DEPS $dep"; fi; done; fi; done; apt-get install $DEPS

(also less elegant)

I'm sorry, but I dont know how to build python-apt 0.6.20ubuntu13 on feisty (upgraded meanwhile)
apt-get source does not work (seems to be not in the list file)
Did manual download of dsc and tgz, but it insists on 0.6.20ubuntu12
(and dpkg -b finds no DEBIAN/config)

I tried shell script to, replacing apt-get install by echo
Unfortunately result was not what would be expected :-(
echo $DEPS
ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: ab: apport-gtk bluez-cups bluez-pin bluez-utils ...

@Kurt: Thanks for testing the shell code. It works for me, but the python-apt code should be much more stable. So just wait a bit until the new python-apt hits the archive.

@Michael: OK, thank you for that work.

Upgraded feisty now and tested fixup.py and apt-get:

(1)
Uninstalled ubuntu-desktop and kubuntu-desktop (to get situation similar to edgy with OpenOffice 2.1)
Run fixup.py
Checked autoremove
Nothing did change (see below)

(2)
Installed ubuntu-desktop and kubuntu-desktop
Run fixup.py
Uninstalled ubuntu-desktop and kubuntu-desktop
Checked autoremove
Seems OK now :)

(3)
Reinstalled some other packages that apt-get wants to autoremove even when ubuntu-desktop and kubuntu-desktop are installed
Checked autoremove
Seems OK now too :)

Some Ideas about this:
Maybe posibility to give explicite [meta-]packages to fixup.py would be good in situation (1) ?
Otherwise someone may need to break his installation by installing gone meta-packages or do a reinstall on all depending packages manually which is not really easy to do.
Additionaly fixup.py could maybe give some warning in case no desktop meta package is installed ?

Apt is fixed in feisty to take the meta packages into account.

The release upgrader will take care of making sure that script I posed here is run during the upgrade to fix existing install.

Cheers,
 Michael

Thank you very much :)