Fail to upgrade due to file conflict between libtsk and sleuthkit-java

[hawko2600]

Nov 26 11:08:39 pop-os pop-upgrade[18772]: Selecting previously unselected package libtsk19:amd64.
Nov 26 11:08:39 pop-os pop-upgrade[18772]: Preparing to unpack .../029-libtsk19_4.11.1+dfsg-1_amd64.deb ...
Nov 26 11:08:39 pop-os pop-upgrade[18772]: Unpacking libtsk19:amd64 (4.11.1+dfsg-1) ...
Nov 26 11:08:39 pop-os pop-upgrade[18772]: dpkg: error processing archive /tmp/apt-dpkg-install-2SGsJt/029-libtsk19_4.11.1+dfsg-1_amd64.deb (--unpack):
Nov 26 11:08:39 pop-os pop-upgrade[18772]: trying to overwrite '/usr/lib/x86_64-linux-gnu/libtsk.so.19.1.7', which is also in package sleuthkit-java 4.11.1-1
Nov 26 11:08:40 pop-os pop-upgrade[18772]: dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)

root@pop-os:~# apt show sleuthkit-java
Package: sleuthkit-java
Version: 4.11.1-1
Status: install ok installed
Priority: optional
Section: contrib
Maintainer: Rishwanth Senthilkumar rishwanth@basistech.com
Installed-Size: 13.8 MB
Depends: libafflib0v5 (>= 3.7.6), libc6 (>= 2.14), libewf2 (>= 20121209), libgcc1 (>= 1:4.2), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5.2), libvhdi1 (>= 20150110), libvmdk1 (>= 20150516), zlib1g (>= 1:1.1.4), libewf-dev (>= 20130416), libafflib-dev (>= 3.6.6), libsqlite3-dev, libc3p0-java, libvmdk-dev, libvhdi-dev
Conflicts: libtsk13
Replaces: libtsk13
Homepage: http://www.sleuthkit.org/sleuthkit
Download-Size: unknown
APT-Manual-Installed: yes
APT-Sources: /var/lib/dpkg/status
Description: tools for forensics analysis on volume and filesystem data

root@pop-os:~# apt show libtsk19
Package: libtsk19
Version: 4.11.1+dfsg-1
Priority: optional
Section: universe/libs
Source: sleuthkit
Origin: Ubuntu
Maintainer: Ubuntu Developers ubuntu-devel-discuss@lists.ubuntu.com
Original-Maintainer: Debian Security Tools team+pkg-security@tracker.debian.org
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 1,200 kB
Depends: libafflib0v5 (>= 3.7.6), libc6 (>= 2.34), libewf2 (>= 20130416), libgcc-s1 (>= 4.2), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 11), libvhdi1 (>= 20150110), libvmdk1 (>= 20150516), zlib1g (>= 1:1.1.4)
Conflicts: libtsk10v5
Replaces: libtsk10v5
Homepage: http://www.sleuthkit.org/sleuthkit
Download-Size: 447 kB
APT-Sources: http://apt.pop-os.org/ubuntu jammy/universe amd64 Packages
Description: library for forensics analysis on volume and filesystem data

I'm going to uninstall sleuthkit-java in the hope it'll move to the next weirdo package I have installed.

[hawko2600]

I ended up having to do this to correct the error:

root@pop-os:/etc/apt/sources.list.d# apt purge guestfish guestfs-tools guestmount libguestfs-hfsplus libguestfs-perl libguestfs-reiserfs libguestfs-tools libguestfs-xfs sleuthkit sleuthkit-java libguestfs0 virt-p2v

[jacobgkau]

The sleuthkit-java package is not available in the Ubuntu repositories and is orphaned in your output, so it must have been installed as a .deb file from somewhere else.

libtsk19 does exist in Ubuntu. Seeing as Ubuntu can't reasonably be expected to be aware of packages not in their repositories, the correct solution here would be for the creators of sleuthkit-java to mark it as conflicting with libtsk19 if it has a file conflict with that package. However, as we don't control sleuthkit-java, we'll likely need to add that to the list of packages to be removed on upgrade (especially since it would be removed anyway as an orphaned package if this error hadn't occurred).

[jacobgkau]

Selecting previously unselected package libtsk19:amd64.

More background to know why this package was selected would've been good. However, I'm assuming you may not have the full log anymore since it's been some time.

[jacobgkau]

I see that sleuthkit, which does exist in Ubuntu (unlike sleuthkit-java), depends on libtsk19. I'll check to see if simply having sleuthkit-java installed leads to this error occurring when pop-upgrade tries to downgrade sleuthkit to the version included in Ubuntu.

[jacobgkau]

This Sleuthkit issue looks relevant: sleuthkit/sleuthkit#2822

[jacobgkau]

Just having sleuthkit-java installed before attempting to upgrade wasn't enough to replicate the issue.

[jacobgkau]

I do hit the file conflict issue if I just install sleuthkit while sleuthkit-java is installed. However, that doesn't have anything to do with pop-upgrade/the release upgrade.

[jacobgkau]

@hawko2600 Can you please tell me how you installed Sleuthkit to begin with before the upgrade? That is the only way we can determine how to replicate this issue. Sleuthkit doesn't publish their own non-Java .deb file, so I don't understand how you had both sleuthkit and sleuthkit-java installed in the first place.

[hawko2600]

@hawko2600 Can you please tell me how you installed Sleuthkit to begin with before the upgrade? That is the only way we can determine how to replicate this issue. Sleuthkit doesn't publish their own non-Java .deb file, so I don't understand how you had both sleuthkit and sleuthkit-java installed in the first place.

Hi @jacobgkau - I suspect I pulled it off autopsy.com either before it was packaged or just because.

Do you think it's fair we close this as out of scope? I don't think you should have to deal with 3rd party packages in pop-upgrade, even if they're from the upstream vendor. You could use the contents (or missing) Origin header in the package to easily weed them all out and warn the user though that they'll need to manually resolve this issue before doing the pop-upgrade.

[jacobgkau]

I think I missed your last reply since it was over a month later.

I don't think you should have to deal with 3rd party packages in pop-upgrade, even if they're from the upstream vendor. You could use the contents (or missing) Origin header in the package to easily weed them all out and warn the user though that they'll need to manually resolve this issue before doing the pop-upgrade.

We already do this to remove third-party (orphaned after resetting apt sources) packages. It just happens slightly later in the process.

What's confusing about this case isn't that there was package breakage, but that it should've already happened when you first installed one or the other of those packages, not when you were running pop-upgrade. It may've been more clear what was going on if we had the entire journalctl and or /var/log/apt/history.log at the time of attempting the upgrade, but I assume those are long-gone by now.