Debian APT dependency resolver

Debian’s package manager APT is famous for its inter-package dependency resolving mechanism: Long before rpm based distributions learned how to install dependant packages automatically Debian did do this for many years. You simply can install a high-level package using apt-get install $pkg, which will then automatically resolve all dependencies: Dependant packages are downloaded and install along automatically.

This works very well when you just use packages from a single consistent source like the stable Debian repository. It mostly also works with multiple repositories, but from time to time the resolver does strange things.

Here at Univention GmbH we build our own packages. Therefore it is essential for our customers that we get the dependencies right. Today we had the strange behavior, where one of our packages could not be upgraded: APT decided to refuse the package from getting installed. Simplify specifying one additional dependency on the command line made it work.

So what happened and why did APT refuse the initial command?

Resolver

Dependency resolution has some very useful information on how the resolver works:

APT works in its internal resolver in two stages: First all packages are visited and marked for installation, keep back or removal. Option Debug::pkgDepCache::Marker shows this. This also decides which packages are to be installed to satisfy dependencies, which can be seen by Debug::pkgDepCache::AutoInstall. After this is done, we might be in a situation in which two packages want to be installed, but only one of them can be. It is the job of the pkgProblemResolver to decide which of two packages ‘wins’ and can therefore decide what has to happen. You can see the contenders as well as their fight and the resulting resolution with Debug::pkgProblemResolver.

There are some options, which can be set to have a look at the internal working of the APT conflict resolver:

LC_ALL=C apt-get install \
  -t apt \
  -s \
  -o Debug::pkgDepCache::Marker=yes \
  -o Debug::pkgDepCache::AutoInstall=yes \
  -o Debug::pkgProblemResolver=yes \
  -o Debug::pkgProblemResolver::ShowScores=yes \
  univention-s4-connector 2>&1 | less
  • -t apt boosts all packages from my repository named Suite: apt in its Release file.
  • -s does a simulated install: it only shows what would be done but does not modify the actual state of the system.
  • -o Debug::pkgDepCache::Marker=yes shows the initial package marking for installation, keep or removal.
  • -o Debug::pkgDepCache::AutoInstall=yes shows installation of additional dependencies.
  • -o Debug::pkgProblemResolver=yes enables debug output.
  • -o Debug::pkgProblemResolver::ShowScores=yes shows the calculated importance score of all packages.
  • univention-s4-connector is the package to install.

Explanation

Reading package lists...
Building dependency tree...
Reading state information...

Some progress information.

Mark phase

  MarkInstall univention-s4-connector:amd64 < none -> 14.0.10-2A~5.0.0.202207141231 @un puN Ib > FU=1
  Installing attr as Depends of univention-s4-connector
    MarkInstall attr:amd64 < none -> 1:2.4.48-4 @un uN > FU=0
  Installing python3-univention-connector-s4 as Depends of univention-s4-connector
    MarkInstall python3-univention-connector-s4:amd64 < none -> 14.0.10-2A~5.0.0.202207141231 @un uN > FU=0
  Installing univention-samba4 as Depends of univention-s4-connector
    MarkInstall univention-samba4:amd64 < none -> 9.0.8-2A~5.0.0.202207141233 @un uN Ib > FU=0
    Installing ldb-tools as Depends of univention-samba4
      MarkInstall ldb-tools:amd64 < none -> 2:2.5.2-1A~5.0.0.202207191717 @un uN > FU=0
    Installing libunivention-ldb-modules as Depends of univention-samba4
      MarkInstall libunivention-ldb-modules:amd64 < none -> 8.0.0-7A~5.0.0.202207191820 @un uN > FU=0
    Installing samba as Depends of univention-samba4
      MarkInstall samba:amd64 < none -> 2:4.16.2-1A~5.0.0.202207191731 @un uN Ib > FU=0
      Installing samba-common as Depends of samba
        MarkInstall samba-common:amd64 < 2:4.16.2-1A~5.0.0.202206271026 -> 2:4.16.2-1A~5.0.0.202207191731 @ii umU > FU=0
      Installing samba-common-bin as Depends of samba
        MarkInstall samba-common-bin:amd64 < 2:4.16.2-1A~5.0.0.202206271026 -> 2:4.16.2-1A~5.0.0.202207191731 @ii umU Ib > FU=0
        Installing samba-libs as Depends of samba-common-bin
          MarkInstall samba-libs:amd64 < 2:4.16.2-1A~5.0.0.202206271026 -> 2:4.16.2-1A~5.0.0.202207191731 @ii umU > FU=0
      Installing tdb-tools as Depends of samba
        MarkInstall tdb-tools:amd64 < none -> 1.4.7-1A~5.0.0.202206171840 @un uN > FU=0
      Installing python3-markdown as Recommends of samba
        MarkInstall python3-markdown:amd64 < none -> 3.0.1-3 @un uN > FU=0
      Installing samba-vfs-modules as Recommends of samba
        MarkInstall samba-vfs-modules:amd64 < none -> 2:4.16.2-1A~5.0.0.202207191731 @un uN IPb > FU=0
        Installing libcephfs2 as Recommends of samba-vfs-modules
          MarkInstall libcephfs2:amd64 < none -> 12.2.11+dfsg1-2.1+b1 @un uN Ib > FU=0
          Installing libboost-thread1.67.0 as Depends of libcephfs2
            MarkInstall libboost-thread1.67.0:amd64 < none -> 1.67.0-13+deb10u1 @un uN Ib > FU=0
            Installing libboost-atomic1.67.0 as Depends of libboost-thread1.67.0
              MarkInstall libboost-atomic1.67.0:amd64 < none -> 1.67.0-13+deb10u1 @un uN > FU=0
          Installing librados2 as Depends of libcephfs2
            MarkInstall librados2:amd64 < none -> 12.2.11+dfsg1-2.1+b1 @un uN Ib > FU=0
            Installing libboost-regex1.67.0 as Depends of librados2
              MarkInstall libboost-regex1.67.0:amd64 < none -> 1.67.0-13+deb10u1 @un uN > FU=0
            Installing libibverbs1 as Depends of librados2
              MarkInstall libibverbs1:amd64 < none -> 22.1-1 @un uN Ib > FU=0
              Installing libnl-route-3-200 as Depends of libibverbs1
                MarkInstall libnl-route-3-200:amd64 < none -> 3.4.0-1 @un uN > FU=0
              Installing ibverbs-providers as Recommends of libibverbs1
                MarkInstall ibverbs-providers:amd64 < none -> 22.1-1 @un uN > FU=0
            Installing libnspr4 as Depends of librados2
              MarkInstall libnspr4:amd64 < none -> 2:4.20-1 @un uN > FU=0
            Installing libnss3 as Depends of librados2
              MarkInstall libnss3:amd64 < none -> 2:3.42.1-1+deb10u5 @un uN > FU=0
        Installing libgfapi0 as Recommends of samba-vfs-modules
          MarkInstall libgfapi0:amd64 < none -> 5.5-3 @un uN Ib > FU=0
          Installing libgfrpc0 as Depends of libgfapi0
            MarkInstall libgfrpc0:amd64 < none -> 5.5-3 @un uN Ib > FU=0
            Installing libgfxdr0 as Depends of libgfrpc0
              MarkInstall libgfxdr0:amd64 < none -> 5.5-3 @un uN Ib > FU=0
              Installing libglusterfs0 as Depends of libgfxdr0
                MarkInstall libglusterfs0:amd64 < none -> 5.5-3 @un uN > FU=0
    Installing univention-samba-local-config as Depends of univention-samba4
      MarkInstall univention-samba-local-config:amd64 < none -> 14.0.5-6A~5.0.0.202204260244 @un uN > FU=0
    Installing univention-samba4-sysvol-sync as Depends of univention-samba4
      MarkInstall univention-samba4-sysvol-sync:amd64 < none -> 9.0.8-2A~5.0.0.202207141233 @un uN > FU=0
    Installing winbind as Depends of univention-samba4
      MarkInstall winbind:amd64 < none -> 2:4.16.2-1A~5.0.0.202207191731 @un uN > FU=0
    Installing univention-monitoring-samba as Recommends of univention-samba4
      MarkInstall univention-monitoring-samba:amd64 < none -> 1.0.0-6A~5.0.0.202207221052 @un uN > FU=0
    Installing univention-nagios-samba as Recommends of univention-samba4
      MarkInstall univention-nagios-samba:amd64 < none -> 5.0.1-1A~5.0.0.202206231931 @un uN > FU=0
  Installing sqlite3 as Recommends of univention-s4-connector
    MarkInstall sqlite3:amd64 < none -> 3.27.2-3+deb10u1 @un uN > FU=0
  Installing univention-monitoring-s4-connector as Recommends of univention-s4-connector
    MarkInstall univention-monitoring-s4-connector:amd64 < none -> 1.0.0-6A~5.0.0.202207221052 @un uN > FU=0
  Installing univention-nagios-s4-connector as Recommends of univention-s4-connector
    MarkInstall univention-nagios-s4-connector:amd64 < none -> 5.0.1-1A~5.0.0.202206231929 @un uN > FU=0

For each package a line consisting of multiple fields is printed by apt-pkg/prettyprinters.cc:

  • the package name
  • <: start of package details
  • the version of the currently installed package version or none.
  • -> Optional to-be-installed package version.
  • | Optional candidate package version if different then installed to to-be-installed version.
  • @ the short status of the package, consisting of 2-3 characters describing the current and desired state:
    • Selected state:
      • u: unknown
      • i: install
      • h: hold
      • r: remove
      • p: purge
      • X: other
    • Installation state:
      • R: re-installation required
      • H: hold
      • HR: hold and re-installation required
      • X: other
    • Current state:
      • `n’: not installed.
      • c: configuration files
      • `H’: half installed
      • U: unpacked
      • F: half configured
      • W: triggers awaited
      • T: triggers pending
      • i: installed
      • X: other
  • p: Protected
  • r: re-install
  • u: Upgradable
  • m: Marked
  • g: Garbage
  • State:
    • N: new installation
    • U: upgrade
    • D: downgrade
    • I: install
    • P: purge
    • R: remove
    • H: held
    • K: keep
  • Now Broken state:
    • Nb: now broken
    • `NPb’: now policy broken
  • Install broken state:
    • Ib: installation broken
    • IPb: installation policy broken
  • > end of package details
  • FU=1 for packages named on the command line, otherwise FU=0.

Conflict resolution phase

Starting pkgProblemResolver with broken count: 1

By just marking the given package as to be installed, the dependencies are then broken as not all dependencies are satisfied. Here one package is broken, which the resolver must now fix.

Settings used to calculate pkgProblemResolver::Scores::
  Required => 3
  Important => 2
  Standard => 1
  Optional => -1
  Extra => -2
  Essentials => 100
  InstalledAndNotObsolete => 1
  Pre-Depends => 1
  Depends => 1
  Recommends => 1
  Suggests => 0
  Conflicts => -1
  Breaks => -1
  Replaces => 0
  Obsoletes => 0
  Enhances => 0
  AddProtected => 10000
  AddEssential => 5000

All packages get a score, which matches how important they are: The more packages depends on it, the higher their score is. Packages are also boosted by their Importance and Essential status. As one package is to be installed via the command line they get the AddProtected boost; otherwise the resolver would resolve the conflict by not installing them in the first place.

Show Scores
9999 univention-s4-connector:amd64 < none -> 14.0.10-2A~5.0.0.202207141231 @un puN >
...
35 python3-ldb:amd64 < 2:2.5.1-1A~5.0.0.202206171844 | 2:2.5.2-1A~5.0.0.202207191717 @ii umH >
...
30 libldb2:amd64 < 2:2.5.1-1A~5.0.0.202206171844 | 2:2.5.2-1A~5.0.0.202207191717 @ii umH >
...
8 samba-dsdb-modules:amd64 < 2:4.16.2-1A~5.0.0.202206271026 -> 2:4.16.2-1A~5.0.0.202207191731 @ii umU Ib >
...

All installed and to-be-installed packages are listed here. Each line starts with the calculated score for the package.

Starting 2 pkgProblemResolver with broken count: 1

This is the same line as above, with just the 2 inserted to disginguish those two copy and pasted lines.

Investigating (0) samba-dsdb-modules:amd64 < 2:4.16.2-1A~5.0.0.202206271026 -> 2:4.16.2-1A~5.0.0.202207191731 @ii umU Ib >
  • The package univention-samba4 depends on samba-dsdb-modules, which APT claims to be unresolved.
  • Actually version 2:4.16.2-1A~5.0.0.202206271026 is installed but 2:4.16.2-1A~5.0.0.202207191731 is to be installed. the -> indicates a schedules action to update it; | would be used to inform you instead that the package is eithe currently already installed or to be installed.
  • The package should be installed and actually is installed (@ii).
  • The package is upgradable u, marked m and currently scheduled for upgrade U.
  • The installation status us currently borken Ib.
Broken samba-dsdb-modules:amd64 Depends on libldb2:amd64 < 2:2.5.1-1A~5.0.0.202206171844 | 2:2.5.2-1A~5.0.0.202207191717 @ii umH > (> 2:2.5.2~)
  • The package samba-dsdb-modules itself depends on a newer version of libldb2 (> 2:2.5.2~).
  • Currently version 2:2.5.1-1A~5.0.0.202206171844 is installed.
  • But a candidate 2:2.5.2-1A~5.0.0.202207191717 is available.
  • The package is upgradable u, marked m but currently held H.
  Considering libldb2:amd64 30 as a solution to samba-dsdb-modules:amd64 8

As the package libldb2 has a higher priority 30 over the more low-level package samba-dsdb-modules with only priority 8 the resolver decides to upgrade that dependency.

  Re-Instated libldb2:amd64
  Re-Instated samba-dsdb-modules:amd64

The resolver decides to schedule upgrades for these two packages as it delcares Breaks: on them.

Investigating (1) python3-ldb:amd64 < 2:2.5.1-1A~5.0.0.202206171844 | 2:2.5.2-1A~5.0.0.202207191717 @ii umH Ib >

Upgrading libdb2 alone violates the containt of python3-ldb, which depends on the exact same version: python3-ldb: Depends: libdb2 (= ${binary:Version}).

  • Currently version 2:2.5.1-1A~5.0.0.202206171844 is installed.
  • Version 2:2.5.2-1A~5.0.0.202207191717 is available, but (currently) not scheduled for installation: notice the | here instead of ->!
  • The package should be installed and actually is installed (@ii).
  • The package is upgradable u, marked m but currently held H.
  • The package is in the install broken state, which needs fixing next.
Broken python3-ldb:amd64 Depends on libldb2:amd64 < 2:2.5.1-1A~5.0.0.202206171844 -> 2:2.5.2-1A~5.0.0.202207191717 @ii umU > (= 2:2.5.1-1A~5.0.0.202206171844)

Due to the pending upgrade of libdb2 package python3-ldb is now broken.

  Considering libldb2:amd64 30 as a solution to python3-ldb:amd64 35

Because the priority of python3-ldb with 35 is higher than priority 30 for libldb2, the resolver decides to keep python3-ldb in the current state. For that it cancels the upgrade of libldb2, which re-established the contraint on the same version match.

  Added libldb2:amd64 to the remove list
  Fixing python3-ldb:amd64 via keep of libldb2:amd64

The canceled upgrade of libdb2 bubbles up the chain and the installation command aborts with an error.

Fixes

There are multiple fixes, to get the installation working.

  1. It can be fixed by adding libdb2 manually to the apt-get install command. The will add libdb2 with score 10000-2 = 9998 to the list, foring an update.

  2. univention-samba4 can add a dependency on samba-dsdb-modules (>= 2:4.16.2-1A~5.0.0.202207191731),. This explicitly pulls in the newer version, which then also pulls in newer versions of libldb2 and python3-ldb.

  3. Add a libldb2: Breaks: python3-ldb (<< ${binary:Version}). When upgrading libldb2 is considerd, this will also schedule an upgrade of python3-ldb, which will then will be in lock-step again.

According to my gut feeling I think 3 is the most correct one, but if you know better: please mail me.

Post Script

After publishing this and also asking the APT Team Andre Wagner mailed me this link: An Ubuntu 22.04 LTS Fix Is Coming For A Very Annoying & Serious APT Problem It points to an Ubuntu bug report and includes a patch, which was merged 2 weeks ago into apt.

Disclaimer

Please note that there are different tools, which might use different resolvers:

  • apt-get is the stable command line tool, which should be used from scripts.
  • aptitude provides an interactive text user interface, but can also be used from scripts. It can be used interactively to resolve conflicts, but requires some extra knowledge.
  • apt is a new tool for interactive usage: It combines functions from other tools like apt-cache and apt-mark, but is not yet considered stable and should not be used in scripts.
Written on July 25, 2022