Conflict hell after freebsd-update

V

Vladimir1922

Hello there. I am writing because I did a cock-up and I have no idea how to untangle it:

I upgraded from 14.2 to 15 a few days ago, it screwed up and managed to fix it with an pkg update -f
-Then I decided to try fixing up my Bluetooth, which It never worked on any FreeBSD I installed, and stupidly followed this guide: https://www.siberoloji.com/how-to-set-up-bluetooth-support-on-freebsd-operating-system/ (I know, there is no bluez on freeBSD, so this is fake/guy must have been drunk but at the time I was desperate, as I have been trying to have Bluetooth working for the last 4 months)

In one of the steps, it recommends making an upgrade again, so a freebsd-fetch and freebsd-update, it actually wanted to move into FREEBSD-15-RELEASE-p1.

but now, when I try to do a pkg update / pkg upgrade I get this

Checking integrity... done (11 conflicting)
- mozjpeg-4.1.5 [FreeBSD-ports] conflicts with jpeg-turbo-3.1.2 [installed] on /usr/local/bin/cjpeg
- mozjpeg-4.1.5 [FreeBSD-ports] conflicts with jpeg-turbo-3.1.2 [FreeBSD] on /usr/local/bin/cjpeg
- mozjpeg-4.1.5 [FreeBSD-ports] conflicts with jpeg-turbo-3.1.2 [FreeBSD-ports] on /usr/local/bin/cjpeg
- svt-av1-hdr-3.1.3 [FreeBSD-ports] conflicts with svt-av1-3.1.2 [installed] on /usr/local/bin/SvtAv1EncApp
- svt-av1-hdr-3.1.3 [FreeBSD-ports] conflicts with svt-av1-3.1.2 [FreeBSD] on /usr/local/bin/SvtAv1EncApp
- libebur128-1.2.6 [FreeBSD-ports] conflicts with ebur128-0.1.10_9 [installed] on /usr/local/include/ebur128.h
- libebur128-1.2.6 [FreeBSD-ports] conflicts with ebur128-0.1.10_9 [FreeBSD] on /usr/local/include/ebur128.h
- ja-libslang-1.4.5.j2_1 [FreeBSD-ports] conflicts with libslang2-2.3.3_2 [installed] on /usr/local/lib/libslang.a
- ja-libslang-1.4.5.j2_1 [FreeBSD-ports] conflicts with libslang2-2.3.3_2 [FreeBSD] on /usr/local/lib/libslang.a
- llvm19-lite-19.1.7_1 [FreeBSD-ports] conflicts with llvm19-19.1.7_1 [installed] on /usr/local/llvm19/lib/clang/19/include/arm_bf16.h
- llvm19-lite-19.1.7_1 [FreeBSD-ports] conflicts with llvm19-19.1.7_1 [FreeBSD] on /usr/local/llvm19/lib/clang/19/include/arm_bf16.h

I tried locking the packages, manually removing the conflicting files, and removing some of the packages (which I refused, because some of them will autoremove 3/4 of my system and I couldn't find a way of not pulling the dependencies with them).

How I solve this mess? Worse case scenario I could reinstall, as I want to upgrade to a bigger disk, but for now I am stuck on holidays far away from the new disk and I would like this system to work, plus I don't want to nuke my future install.

Any ideas? Thanks in advance!
 
Show us the complete output of pkg upgrade. The output may exceed the maximum number of characters allowed by the forum editor, if that is the case, redirect into a file, attach file to your post.


pkg upgrade -n > pkgupg.txt
 
Vladimir1922 said:
I upgraded from 14.2 to 15 a few days ago, it screwed up and managed to fix it with an pkg update -f
Click to expand...
nothing was screwed up - you are supposed to upgrade all packages after a major release upgrade.
Did you follow the upgrade instructions from the handbook and checked the release notes?

Vladimir1922 said:
stupidly followed this guide: https://www.siberoloji.com/how-to-set-up-bluetooth-support-on-freebsd-operating-system/
Click to expand...
Why follow some AI-generatet garbage if you already identified at the *second* step that it is hallucinated BS as usual?
Just follow the instructions in the handbook, this works for all supported devices as mentioned in the very first paragraph (34.7.1) in that section. If your device isn't supported (you checked the hardware notes?) no 'how to' from some random collection of AI-slop will change that...
 
Error log wasn't too big, actually, but here it is, it is good idea

About following the AI-slop... I guess impatience? Yes, I followed many official guides and the manual. Device is supported and detected, just never handshakes. It might be a hardware issue, but I know the think works on Linux (just that I decided to make my main computer FreeBSD, not having headphones is annoying, but not a deal breaker). In any case, that is an issue for another day. I never had any luck using Bluetooth on BSD, to the point that in the past I used dongles technically on the supported and working list but still, I never had any Bluetooth device working on any FreeBSD.

I did follow the instructions to upgrade, after rebooting with the new kernel is when I had the issues. I suspect that I had some port installed package which I didn't remember installing.
 

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Vladimir1922 said:
I did follow the instructions to upgrade, after rebooting with the new kernel is when I had the issues. I suspect that I had some port installed package which I didn't remember installing.
Click to expand...
How exactly did you upgrade?
This sounds as if you stopped halfway through the OS upgrade and just ran pkg upgrade
 
None of the issues you have with the packages had anything to do with the OS update (or upgrade).

I would suggest just removing one or more of the conflicting packages, and make a note if it wants to remove something you wanted to keep. Then make sure to upgrade whatever is left, remove old dependencies (pkg-autoremove(8)), then see if you can reinstall the things you still want to have that got removed with the clean up.

Or just start over; pkg delete -a and reinstall the things you need.
 
Vladimir1922 said:
in this case I did
freebsd-update fetch && freebsd-update install
pkg update
pkg upgrade
Click to expand...
If you still have issue my suggestion is.
1- Replace the old packages with new one .. --> pkg delete jpeg-turbo && pkg install mozjpeg
2- Ignore the conflicting packages?
3- Use -f flag --> pkg upgrade -f
4- Try to fix :
pkg check -Ba
pkg autoremove
pkg update -f
pkg upgrade
 
Hey, thanks for the replies!

I considered the reinstalling, I resisted because I am using at the moment WindowMaker and I was feeling lazy about hunting down and reinstalling all the small docking applets.

I solved that issue by doing creating a list of installed packages (pkg info | awk '{print $1}' > packages.txt)

then I did the pkg delete -a (thanks, SirDice, didn't knew that! ), and reinstalled with "cat packages.txt > xargs pkg install -y".

Now I got 13 conflicts instead of 11 :') . I noted there where some packages I also had to remove from the list because they are not in the repo: Something relying on timidity++, which can be found with a pkg search and something like virtual_oss, which I see has now other virtual like bluetooth, but didn't see anything updated in the docs).

About the incomplete update: I didn't see any kernel update from 15.0 to 15.0-p1, and rebooting and running freebsd-update install after reboot only prompted a "nothing to do" message, so not sure if I did something wrong as I am not that familiar with FreeBSD, or there is something off.

Furthermore, everytime I say yes to the update, it reinstalls gettext-runtime

root@Think420:/home/alvarez # pkg upgrade
Updating FreeBSD-ports repository catalogue...
FreeBSD-ports repository is up to date.
Updating FreeBSD-ports-kmods repository catalogue...
FreeBSD-ports-kmods repository is up to date.
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
Updating FreeBSD-kmods repository catalogue...
FreeBSD-kmods repository is up to date.
All repositories are up to date.
Checking for upgrades (343 candidates): 100%
Processing candidates (343 candidates): 100%
Checking integrity... done (13 conflicting)
- luajit-openresty-2.1.20250826 [FreeBSD-ports] conflicts with luajit-2.1.0.20251208 [installed] on /usr/local/bin/luajit
- luajit-openresty-2.1.20250826 [FreeBSD-ports] conflicts with luajit-2.1.0.20251208 [FreeBSD] on /usr/local/bin/luajit
- mozjpeg-4.1.5 [FreeBSD-ports] conflicts with jpeg-turbo-3.1.2 [installed] on /usr/local/bin/cjpeg
- mozjpeg-4.1.5 [FreeBSD-ports] conflicts with jpeg-turbo-3.1.2 [FreeBSD] on /usr/local/bin/cjpeg
- mozjpeg-4.1.5 [FreeBSD-ports] conflicts with jpeg-turbo-3.1.2 [FreeBSD-ports] on /usr/local/bin/cjpeg
- svt-av1-hdr-3.1.3 [FreeBSD-ports] conflicts with svt-av1-3.1.2 [installed] on /usr/local/bin/SvtAv1EncApp
- svt-av1-hdr-3.1.3 [FreeBSD-ports] conflicts with svt-av1-3.1.2 [FreeBSD] on /usr/local/bin/SvtAv1EncApp
- libebur128-1.2.6 [FreeBSD-ports] conflicts with ebur128-0.1.10_9 [installed] on /usr/local/include/ebur128.h
- libebur128-1.2.6 [FreeBSD-ports] conflicts with ebur128-0.1.10_9 [FreeBSD] on /usr/local/include/ebur128.h
- ja-libslang-1.4.5.j2_1 [FreeBSD-ports] conflicts with libslang2-2.3.3_2 [installed] on /usr/local/lib/libslang.a
- ja-libslang-1.4.5.j2_1 [FreeBSD-ports] conflicts with libslang2-2.3.3_2 [FreeBSD] on /usr/local/lib/libslang.a
- llvm19-lite-19.1.7_1 [FreeBSD-ports] conflicts with llvm19-19.1.7_1 [installed] on /usr/local/llvm19/lib/clang/19/include/arm_bf16.h
- llvm19-lite-19.1.7_1 [FreeBSD-ports] conflicts with llvm19-19.1.7_1 [FreeBSD] on /usr/local/llvm19/lib/clang/19/include/arm_bf16.h
Checking integrity... done (0 conflicting)
The following 1 package(s) will be affected (of 0 checked):

Installed packages to be REINSTALLED:
gettext-runtime-0.26 [FreeBSD]

Number of packages to be reinstalled: 1

Proceed with this action? [y/N]: y
 
Vladimir1922 said:
I solved that issue by doing creating a list of installed packages (pkg info | awk '{print $1}' > packages.txt)
Click to expand...
Use the list from pkg prime-list. The command you used is a full list of everything you have installed, including all the conflicting packages. So reinstalling this list will simply result in the same conflicts. The "prime-list" only contains a list of packages you 'manually' installed, everything else is a dependency (or a dependency of a dependency of a ... etc) of those "prime" packages. Dependency chains can be quite long, complex and intertwined. Those dependencies will get automatically pulled in anyway, so there's no need for you to keep track of them.

Vladimir1922 said:
About the incomplete update: I didn't see any kernel update from 15.0 to 15.0-p1, and rebooting and running freebsd-update install after reboot only prompted a "nothing to do" message, so not sure if I did something wrong as I am not that familiar with FreeBSD, or there is something off.
Click to expand...
P1 fixed a couple of kernel modules (not included in the GENERIC kernel) and a few userspace tools. So the GENERIC kernel wasn't updated, hence it still shows the original 'version'. The kernel won't be recompiled for something that's purely cosmetic (a changed version string).
So that's fine. You did nothing wrong.

To fix the current situation, because you already did a pkg delete -a and started installing from that packages.txt file, can you post that file here? Might be too big to post though, so cat packages.txt | nc termbin.com 9999 would be useful too. I'll have a look through it, see what can be removed and clean it up a bit.
 
SirDice said:
Use the list from pkg prime-list. The command you used is a full list of everything you have installed, including all the conflicting packages. So reinstalling this list will simply result in the same conflicts. The "prime-list" only contains a list of packages you 'manually' installed, everything else is a dependency (or a dependency of a dependency of a ... etc) of those "prime" packages. Dependency chains can be quite long, complex and intertwined. Those dependencies will get automatically pulled in anyway, so there's no need for you to keep track of them.


P1 fixed a couple of kernel modules (not included in the GENERIC kernel) and a few userspace tools. So the GENERIC kernel wasn't updated, hence it still shows the original 'version'. The kernel won't be recompiled for something that's purely cosmetic (a changed version string).
So that's fine. You did nothing wrong.

To fix the current situation, because you already did a pkg delete -a and started installing from that packages.txt file, can you post that file here? Might be too big to post though, so cat packages.txt | nc termbin.com 9999 would be useful too. I'll have a look through it, see what can be removed and clean it up a bit.
Click to expand...
Wow, that is very generous, thank you!
I realized that when you do a version upgrade you had to count the ports. At the time of doing it, I ignored that steps, because I thought I installed everything from packages... I was wrong. At least Timidity++ is not installable from packages and only works from ports, so that is something I should had taken care off. I had to remove it from the list too, as it will make it fail.

The packages.txt file in question: and thanks again for the nc trick

https://termbin.com/g0s0
 
Pfew. That's quite the list you have. Hang on, that's going to take me a bit of time to sort through it all. A lot I can do from memory and experience, but you have some things installed I'm not familiar with.
 
Don't worry, and I hope I don't inconvenience anyone. I know I have a lot installed, and all on a 150GB SSD! 😅 .

Btw, I just finished with the pkg prime-list, and I found myself with a weird issue:
df reports I have -4.4G free.
WTF?
I can try to clear what any package does if that helps
screenshot_2025-12-19_at_16:50:17.png
 
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