doc: guix: Troubleshooting zdiff3 issue and uninstalling.

davidgumberg commented at 9:13 pm on May 7, 2025: contributor

Add a note about guix issues with git merge.conflictstyle being set to zdiff3, and add information about how to uninstall for users of guix-install.sh

DrahtBot commented at 9:13 pm on May 7, 2025: contributor

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Possible typos and grammar issues:

purge guix->sudo apt purge guix` [closing backtick appears without an opening; the package-remove command should be enclosed in backticks for clarity]

2025-12-12

DrahtBot added the label Docs on May 7, 2025

davidgumberg force-pushed on May 7, 2025

in contrib/guix/INSTALL.md:838 in 726dd9ccc5 outdated

832@@ -784,7 +833,9 @@ an irreversible way, you may want to completely purge Guix from your system and
833 start over.
834 
835 1. Uninstall Guix itself according to the way you installed it (e.g. `sudo apt
836-   purge guix` for Ubuntu packaging, `sudo make uninstall` for a build from source).
837+   purge guix` for Ubuntu packaging, `sudo make uninstall` for a build from
838+   source), or running the GUIX [install script][install-script] with the
839+   `--unininstall` [flag](https://guix.gnu.org/manual/devel/en/guix.html#index-uninstalling-Guix).

fanquake commented at 10:12 am on May 8, 2025:

0   `--uninstall` [flag](https://guix.gnu.org/manual/devel/en/guix.html#index-uninstalling-Guix).

davidgumberg commented at 6:03 pm on May 8, 2025:

Fixed, thanks.

in contrib/guix/INSTALL.md:768 in 726dd9ccc5 outdated

795@@ -763,6 +796,22 @@ Please see the following links for more details:
796 - A commit to skip this test in Guix has been merged into the core-updates branch:
797 [savannah/guix@6ba1058](https://git.savannah.gnu.org/cgit/guix.git/commit/?id=6ba1058df0c4ce5611c2367531ae5c3cdc729ab4)
798 
799+## zdiff3
800+
801+[Currently](https://issues.guix.gnu.org/72942) `guix` builds may fail if the

fanquake commented at 10:12 am on May 8, 2025:

This is an interesting bug

laanwj commented at 1:27 pm on May 8, 2025:

Would it be possible to work around this in the build script somehow?

i guess not, i mean except by changing a global git setting there, which would be awful behavior…

maflcko commented at 9:48 am on May 14, 2025:

Are there steps to reproduce on a fresh install? I tried Ubuntu 24.04, but it seems to pass:

0    1  export DEBIAN_FRONTEND=noninteractive && apt update && apt install git vim htop guix bash curl make -y  && groupadd --system guixbuild && for i in `seq -w 1 10`; do useradd -g guixbuild -G guixbuild -d /var/empty -s `which nologin` -c "Guix build user $i" --system guixbuilder$i; done 
1    2  git config --global merge.conflictstyle zdiff3 
2    3  guix-daemon --build-users-group=guixbuild &
3    4  guix time-machine --url=https://git.savannah.gnu.org/git/guix.git --commit=53396a22afc04536ddf75d8f82ad2eafa5082725  -- install hello

davidgumberg commented at 7:09 pm on December 10, 2025:

You can reproduce this issue as follows with podman:

Ubuntu container

 0# The reason a Dockerfile is needed is to get systemd installed and running in
 1# the container.
 2mkdir -p /tmp/ubuntu-systemd-container && cd /tmp/ubuntu-systemd-container
 3cat > ./Dockerfile << 'EOF'
 4FROM ubuntu:24.04
 5ENV DEBIAN_FRONTEND=noninteractive
 6
 7RUN apt-get update
 8RUN apt-get install -y curl git gpg systemd make uidmap wget xz-utils
 9CMD ["/lib/systemd/systemd"]
10EOF
11
12# I haven't confirmed, but I don't think getting systemd running is as easy
13# with docker
14podman build -t ubuntu-systemd .
15podman run -d --replace --name ubuntu-systemd --systemd=always ubuntu-systemd
16podman exec -it ubuntu-systemd /bin/bash

Inside the container:

0git config --global merge.conflictstyle zdiff3
1
2# https://guix.gnu.org/manual/en/html_node/Binary-Installation.html#Binary-Installation-1
3cd /tmp
4wget -O guix-install.sh https://guix.gnu.org/install.sh
5chmod +x guix-install.sh
6yes '' | ./guix-install.sh
7
8git clone https://github.com/bitcoin/bitcoin.git --depth 1 && cd bitcoin
9HOSTS=x86_64-linux-gnu ./contrib/guix/guix-build

Fedora Container

Running the same commands as above once inside the container:

 0mkdir -p /tmp/fedora-systemd-container && cd /tmp/fedora-systemd-container
 1cat > ./Dockerfile << 'EOF'
 2FROM registry.fedoraproject.org/fedora:43
 3RUN dnf update -y
 4RUN dnf -y install git make systemd wget
 5CMD ["/lib/systemd/systemd"]
 6EOF
 7
 8# I haven't confirmed, but I don't think getting systemd running is as easy
 9# with docker
10podman build -t fedora-systemd .
11podman run -d --replace --name fedora-systemd --systemd=always fedora-systemd
12podman exec -it fedora-systemd /bin/bash

davidgumberg force-pushed on May 8, 2025

fanquake commented at 3:14 pm on October 17, 2025: member

Related upstream issue: https://codeberg.org/guix/guix/issues/3576

fanquake commented at 1:59 pm on December 5, 2025: member

A commit has landed upstream: https://codeberg.org/guix/guix/commit/bd2edc9e435402b48fd201b56ab486151512717a.

fanquake commented at 10:16 am on December 8, 2025: member

Probably also related: https://codeberg.org/guix/guix/pulls/4737

in contrib/guix/INSTALL.md:635 in 2de60ed140

630+easiest solution is to set `SELinux` to permissive for guix-daemon:
631+
632+```bash
633+# as root
634+semanage permissive -a guix_daemon.guix_daemon_t
635+```

hebasto commented at 1:56 pm on December 8, 2025:

I believe this is no longer necessary.

On my Fedora 43 installation with the working Guix:

 0$ sestatus
 1SELinux status:                 enabled
 2SELinuxfs mount:                /sys/fs/selinux
 3SELinux root directory:         /etc/selinux
 4Loaded policy name:             targeted
 5Current mode:                   enforcing
 6Mode from config file:          enforcing
 7Policy MLS status:              enabled
 8Policy deny_unknown status:     allowed
 9Memory protection checking:     actual (secure)
10Max kernel policy version:      35
11$ guix describe
12Generation 27	Dec 05 2025 14:13:44	(current)
13  guix bd2edc9
14    repository URL: https://git.guix.gnu.org/guix.git
15    branch: master
16    commit: bd2edc9e435402b48fd201b56ab486151512717a

davidgumberg commented at 7:12 pm on December 10, 2025:

Thanks for testing this, I’ve dropped this commit.

davidgumberg force-pushed on Dec 10, 2025

davidgumberg commented at 7:14 pm on December 10, 2025: contributor

Pushed to drop the SELinux note since the issue seems to have been resolved upstream.

davidgumberg renamed this:
~~doc: Add troubleshooting note about Guix on SELinux systems~~
doc: guix: Troubleshooting zdiff3 issue and uninstalling.
on Dec 10, 2025

in contrib/guix/INSTALL.md:772 in cb4c677ef5

769+
770+[Currently](https://issues.guix.gnu.org/72942) `guix` builds may fail if the
771+global git config has `merge.conflictstyle` set to `zdiff3` as follows:
772+
773+```
774+Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'...

hebasto commented at 7:35 pm on December 10, 2025:

The default URL of the repository has been updated recently:

0Updating channel 'guix' from Git repository at 'https://git.guix.gnu.org/guix.git'...

davidgumberg commented at 7:56 pm on December 10, 2025:

I’m not sure which is the “canonical” one, but git.guix.gnu.org redirects to codeberg and that is what I actually see in the error message:

0Updating channel 'guix' from Git repository at 'https://codeberg.org/guix/guix.git'...
1guix time-machine: error: Git error: unknown style 'zdiff3' given for 'merge.conflictstyle'

davidgumberg commented at 8:04 pm on December 10, 2025:

Thanks for catching this, I’ve updated the error message to what is actually printed. I think fixing the rest of the savannah->codeberg links could be done in a follow-up that also changes the guix time-machine --url in /contrib/guix/libexec/prelude.bash

davidgumberg force-pushed on Dec 10, 2025

DrahtBot added the label CI failed on Dec 10, 2025

DrahtBot removed the label CI failed on Dec 10, 2025

guix: doc: Suggest guix-install.sh --uninstall ea1be38677

guix: doc: zdiff3 doesn't work e76e886581

in contrib/guix/INSTALL.md:803 in 15ebdb4044

798@@ -782,7 +799,9 @@ an irreversible way, you may want to completely purge Guix from your system and
799 start over.
800 
801 1. Uninstall Guix itself according to the way you installed it (e.g. `sudo apt
802-   purge guix` for Ubuntu packaging, `sudo make uninstall` for a build from source).
803+   purge guix` for Ubuntu packaging, `sudo make uninstall` for a build from
804+   source), or running the GUIX [install script][install-script] with the

maflcko commented at 8:25 am on December 11, 2025:

running -> run [The sentence starts with an imperative ("Uninstall Guix itself...") and needs a parallel imperative verb; "or running" is a fragment — "or run" makes the coordination grammatical.]

davidgumberg commented at 4:53 pm on December 12, 2025:

The mistake I made was that or running... should be inside of the parentheses. The items in the parentheses don’t “need” to be parallel with “Uninstall” even if you respect the parallel structure device as a rule (which it isn’t.)

I moved the guix install script instructions inside the parentheses.

davidgumberg force-pushed on Dec 12, 2025

in contrib/guix/INSTALL.md:766 in e76e886581

759@@ -758,13 +760,28 @@ Please see the following links for more details:
760 
761 - An upstream coreutils bug has been filed: [debbugs#47940](https://debbugs.gnu.org/cgi/bugreport.cgi?bug=47940)
762 - A Guix bug detailing the underlying problem has been filed: [guix-issues#47935](https://issues.guix.gnu.org/47935), [guix-issues#49985](https://issues.guix.gnu.org/49985#5)
763-- A commit to skip this test is included since Guix 1.4.0:
764-[codeberg/guix@6ba1058](https://codeberg.org/guix/guix/commit/6ba1058df0c4ce5611c2367531ae5c3cdc729ab4)
765+- A commit to skip this test in Guix has been merged into the core-updates branch:
766+[savannah/guix@6ba1058](https://git.savannah.gnu.org/cgit/guix.git/commit/?id=6ba1058df0c4ce5611c2367531ae5c3cdc729ab4)
767 
768+## zdiff3

hebasto commented at 2:04 pm on January 8, 2026:

0### zdiff3

in contrib/guix/INSTALL.md:803 in e76e886581

798@@ -782,7 +799,9 @@ an irreversible way, you may want to completely purge Guix from your system and
799 start over.
800 
801 1. Uninstall Guix itself according to the way you installed it (e.g. `sudo apt
802-   purge guix` for Ubuntu packaging, `sudo make uninstall` for a build from source).
803+   purge guix` for Ubuntu packaging, `sudo make uninstall` for a build from
804+   source, or running the GUIX [install script][install-script] with the

hebasto commented at 2:04 pm on January 8, 2026:

0   source, or running the Guix [install script][install-script] with the

hebasto approved

hebasto commented at 2:04 pm on January 8, 2026: member