Bug#1104141: apt autoremove marks some packages as manual

Control: tag -1 wontfix

On Fri, Apr 25, 2025 at 11:37:33PM +0200, inasprecali wrote:
> Package: apt
> Version: 2.6.1
> Severity: normal
> X-Debbugs-Cc: [email protected]
> 
> Dear Maintainer,
> 
> Running apt autoremove (or autopurge) resulted in some packages being
> marked as manual afterwards, as shown by the output of apt-mark
> showmanual.
> 
> Here is what happened in my particular situation.
> 
> I run the full GNOME desktop environment, obtained by installing the
> "gnome" metapackage (not gnome-core).  Some time later, I also
> installed the "libreoffice" metapackage.
> 
> Afterwards, I noticed that the libreoffice metapackage also pulls in
> libreoffice-base and libreoffice-draw, which I am not using.  Since I
> noticed that the gnome metapackage depends on the following packages:
> 
> - libreoffice-writer
> - libreoffice-impress
> - libreoffice-draw
> - libreoffice-calc
> 
> which are the only parts of the LibreOffice suite I use regularly, I
> decided to remove the libreoffice metapackage to tidy things up.
> 
> To do so, I marked it as "automatically installed" by running
> "apt-mark auto libreoffice", then running "apt autoremove"
> 
> As expected, packages that were now no longer required, including the
> libreoffice metapackage itself, were removed.  To my surprise, the
> following packages were later marked as manual according to apt-mark.
> Here is the output of apt-mark showmanual | grep libreoffice right
> after autoremoval:
> 
> libreoffice-calc
> libreoffice-core
> libreoffice-draw
> libreoffice-gtk3
> libreoffice-impress
> libreoffice-writer
> 
> Before autoremoval, only libreoffice-gtk3 was listed, which was
> expected since I did install that package manually.
> 
> Using autopurge instead of autoremove produces the same result.
> Interestingly enough, if I just run "apt autoremove libreoffice"
> directly instead of using apt-mark auto and _then_ running apt
> atoremove, the issue does not occur: autoremove does not mark any
> additional packages as manual.
> 
> To summarize, the following commands should be sufficient to reproduce
> the issue:
> 
> apt install gnome && apt install libreoffice && apt-mark auto libreoffice && apt autoremove
> 
> After a brief interaction on the #debian channel on the IRC server
> irc.debian.org, another user was able to reproduce the issue on
> Trixie.  This bug report specifically refers to Bookworm.
> 
> The main question is: is this the expected behavior?

Yes.

> 
> If so, this should be described in detail in the official
> documentation, preferably in the manpage.  I couldn't find anything
> about this anywhere in the documentation or the internet.

This is an implementation detail of the solver to not remove entire
desktops and cause systems to become inoperable when a metapackage is
being removed.

i.e. if you just run apt remove libreoffice-writer, it should not remove
your entire gnome desktop, only the metapackage that pulls in
libreoffice-writer and preserve the rest.

I do not think we should be committing to this behavior to the extent
of documenting it, it's a last resort safe guard and not a particularly
good one at that, and we might want to improve on it.

-- 
debian developer - deb.li/jak | jak-linux.org - free software dev
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