[Freedombox-discuss] Unmet dependencies, "Applying updates failed".

[A. F. Cano]

On Wed, Dec 16, 2020 at 10:34:29AM +0100, Jonas Smedegaard wrote:
> Quoting James Valleroy via Freedombox-discuss (2020-12-16 03:50:50)
> > On 12/14/20 6:00 PM, A. F. Cano wrote:
> > > But the problem after all these packages got installed is that  there
> > > are still unmet dependencies.  From cockpit->software updates:
> > > 
> > > The following packages have unmet dependencies:
> > >   php-common: Breaks: php7.3-common but 7.3.15-3 is to be installed
> > >   libgc1: Conflicts: libgc1c2 but 1:7.6.4-0.4 is to be installed
> > >   fuse3: Breaks: fuse
> > >   libgcc1: Depends: gcc-10-base (= 10.1.0-1) but 10.2.0-19 is to be installed
> > >   python3-django: Breaks: python-django-common
> > >   libmailutils5: Depends: mailutils-common (= 1:3.5-3) but 1:3.10-3 is to be installed
> > >   libgc1c2: Conflicts: libgc1 but 1:8.0.4-3 is to be installed
> > > 
> > > What is the proper way to deal with this?  I've tried to keep the
> > > FreedomBox completely standard, not installing anything manually.
> > > Could this be related to backports?
> > 
> > This issue is common on testing/bullseye (until it is frozen for 
> > release).
> > 
> > The manual solution is to try upgrading just one of the listed 
> > packages (with "apt install <package>"), and see if that would lead to 
> > any important packages (freedombox, apps) being removed. If it would 
> > remove an important package, then you can cancel the upgrade. It may 
> > remove some non-important or obsolete packages, such as python2 
> > packages, and that is ok.
> 
> Sounds like the underlying issue for this is packages wrongly marked as 
> manually installed - check with this command:
> 
>   apt-mark showmanual

$ apt-mark showmanual | wc -l
217

> 
> If you find that packages you didn't explicitly install yourself gets 
> marked as manually installed, then see bug#742977 and consider 
> contributing to that bugreport.

I wouldn't know where to start since I really don't know how the apt
system works internally, but in the list of 217 packages (complete list
below) are what looks like all the Freedombox apps (including
freedombox) in addition to many standard linux/debian packages.
Is it possible that the apt system thinks that the packages installed or
modified by FreedomBox are manually installed?

I have done an occasional apt update/upgrade from the command line, via
ssh, in an attempt to see why the unattended upgrades got stuck and if I
could get them unstuck.  Not sure if that's the reason for the 217
supposedly manual packages.

$ apt-mark showmanual
adduser
apache2
apt
apt-utils
base-files
base-passwd
bash
borgbackup
bsdmainutils
bsdutils
btrfs-progs
cockpit-pcp
coreutils
cpio
cron
dash
debconf
debconf-i18n
debian-archive-keyring
debianutils
diffutils
dmidecode
dmsetup
dpkg
e2fsprogs
ejabberd
fdisk
findutils
firewalld
firmware-ath9k-htc
freedombox
gcc-9-base
gettext-base
gir1.2-udisks-2.0
gpgv
grep
grub-common
grub-pc
grub-pc-bin
grub2-common
gzip
hostname
i2p
ifupdown
ikiwiki
init
init-system-helpers
initramfs-tools
initramfs-tools-core
iproute2
iptables
iputils-ping
isc-dhcp-client
isc-dhcp-common
klibc-utils
kmod
ldap-utils
ldapscripts
less
libacl1
libapparmor1
libapt-inst2.0
libapt-pkg5.0
libargon2-1
libattr1
libaudit-common
libaudit1
libblkid1
libbsd0
libbz2-1.0
libc-bin
libc6
libcap-ng0
libcap2
libcap2-bin
libcom-err2
libcryptsetup12
libdb5.3
libdebconfclient0
libdevmapper1.02.1
libdigest-sha-perl
libdns-export1104
libefiboot1
libefivar1
libelf1
libestr0
libext2fs2
libfastjson4
libfdisk1
libffi6
libfreetype6
libfuse2
libgcc1
libgcrypt20
libgdbm-compat4
libgdbm6
libgmp10
libgnutls30
libgpg-error0
libhogweed4
libidn2-0
libimage-magick-perl
libip4tc2
libip6tc2
libiptc0
libisc-export1100
libjs-jsxc
libjson-c4
libklibc
libkmod2
liblocale-gettext-perl
liblognorm5
liblz4-1
liblzma5
liblzo2-2
libmnl0
libmount1
libncurses6
libncursesw6
libnetfilter-conntrack3
libnettle6
libnewt0.52
libnfnetlink0
libnftnl11
libnss-ldapd
libp11-kit0
libpam-ldapd
libpam-modules
libpam-modules-bin
libpam-runtime
libpam0g
libpcre2-8-0
libpcre3
libperl5.28
libpng16-16
libpopt0
libprocps7
libreadline8
libsearch-xapian-perl
libseccomp2
libselinux1
libsemanage-common
libsemanage1
libsepol1
libslang2
libsmartcols1
libss2
libssl1.1
libstdc++6
libsystemd0
libtasn1-6
libtext-charwidth-perl
libtext-iconv-perl
libtext-wrapi18n-perl
libtinfo6
libudev1
libunistring2
libuuid1
libxml-writer-perl
libxtables12
libzstd1
linux-base
linux-image-5.2.0-2-amd64
linux-image-amd64
login
logrotate
logsave
lsb-base
matrix-synapse
matrix-synapse-ldap3
mawk
mldonkey-server
mount
nano
ncurses-base
ncurses-bin
needrestart
netbase
nscd
nslcd
parted
passwd
perl
perl-base
perl-modules-5.28
php-fpm
privoxy
procps
radicale
readline-common
rsyslog
searx
sed
sensible-utils
slapd
sshfs
ssl-cert
syncthing
systemd
systemd-sysv
sysvinit-utils
tar
tasksel
tasksel-data
tzdata
ucf
udev
unattended-upgrades
util-linux
uwsgi
uwsgi-plugin-python3
vim-common
vim-tiny
whiptail
xapian-omega
xxd
zlib1g