nixos garbage collection breaks home-manager

[brianmay]

I had some problems with my zfs filesystem, which I think are fixed now.

However ever since, on a daily basis my home-manager config is broken (probably after automatic nixos garbage collection) and I have to run "nix run home-manager/master -- switch --flake ." to repair it.

Problem is that my /home/brian/.nix-profile/bin directory is missing. And home-manager installed binaries can't be found.

So I suspect something important isn't getting added to /nix/var/nix/gcroots/auto.

Good computer:

[brian@canidae:~]$ ls -l /nix/var/nix/gcroots/auto | grep profiles
lrwxrwxrwx 1 root root  53 Jun  2 13:43 9iqib07jhzc3ilslwgd3lsrpfwwx4hp2 -> /nix/var/nix/profiles/per-user/brian/profile-212-link
lrwxrwxrwx 1 root root  59 Jun  2 13:43 f9x1m06ain1510k1r3gcj9c9x58bxja6 -> /home/brian/.local/state/nix/profiles/home-manager-326-link
lrwxrwxrwx 1 root root  52 Mar 21  2023 fi5bwbwpzbj3zgw3758rzgp1dslz9nxf -> /nix/var/nix/profiles/per-user/brian/channels-2-link
lrwxrwxrwx 1 root root  53 Jul  7 08:18 iarzzw4dbaji73sppqb46jvjrb6c4562 -> /nix/var/nix/profiles/per-user/brian/profile-213-link
lrwxrwxrwx 1 root root  59 Jul  7 08:18 ixa1ac8lhjgsszpxama09nbss189rbkd -> /home/brian/.local/state/nix/profiles/home-manager-327-link
lrwxrwxrwx 1 root root  53 Dec 16  2023 kg5w32dg9zaw07mzpa2wlc0zigzdkw1l -> /home/brian/.local/state/nix/profiles/channels-1-link
lrwxrwxrwx 1 root root  52 Sep 25  2024 ra0kn174ha6xhypii0izc7sjqc2i3nv8 -> /nix/var/nix/profiles/per-user/root/channels-15-link
lrwxrwxrwx 1 root root  37 Jun  2 13:42 sps7fhbnys26yqraa5p7qy33dbww04r3 -> /nix/var/nix/profiles/system-202-link

Bad computer, after running home-manager switch (so it is now working until tomorrow):

[brian@miacis:~/.config/home-manager]$ ls -l /nix/var/nix/gcroots/auto | grep profiles
lrwxrwxrwx 1 root root  37 Jun 17 13:48 0gg3csxrwq7lx8ijiikvm6icx89j1x2f -> /nix/var/nix/profiles/system-147-link
lrwxrwxrwx 1 root root  37 Jul  7 08:02 952m4w437wpcfc2ll2fybpgnam1i5m8g -> /nix/var/nix/profiles/system-150-link
lrwxrwxrwx 1 root root  37 Jul  4 07:40 dgw2z782bpj65hgiziik4pf8qxfgkdw1 -> /nix/var/nix/profiles/system-148-link
lrwxrwxrwx 1 root root  37 Jul  4 07:59 mj8j9l91skl0lrpd9h72q65qvp2ksrv2 -> /nix/var/nix/profiles/system-149-link
lrwxrwxrwx 1 root root  51 Jul 29  2025 phm61mw9l2zpvj3fj6pmmyk22b1l3qg8 -> /nix/var/nix/profiles/per-user/root/channels-2-link

It is also kind of off that the .nix-profile symlink is different between identical computers:

[brian@canidae:~]$ home-manager switch
Starting Home Manager activation
Activating checkFilesChanged
Activating checkLinkTargets
Activating writeBoundary
Activating createGpgHomedir
Activating installPackages
replacing old 'home-manager-path'
installing 'home-manager-path'
Activating dconfSettings
Activating linkGeneration
Cleaning up orphan links from /home/brian
Creating home file links in /home/brian
Activating onFilesChange
Activating reloadSystemd
Activating vscodeProfiles

There are 404 unread and relevant news items.
Read them by running the command "home-manager news".


[brian@canidae:~]$ ls -l ~/.nix-profile
lrwxrwxrwx 1 brian users 44 Mar 19  2023 /home/brian/.nix-profile -> /nix/var/nix/profiles/per-user/brian/profile
[brian@canidae:~]$ ls -l  /nix/var/nix/profiles/per-user/brian/profile
lrwxrwxrwx 1 brian brian 16 Jul  7 08:52 /nix/var/nix/profiles/per-user/brian/profile -> profile-213-link

[brian@miacis:~/.config/home-manager]$ home-manager switch
Starting Home Manager activation
Activating checkFilesChanged
Activating checkLinkTargets
Activating writeBoundary
Activating createGpgHomedir
Activating installPackages
replacing old 'home-manager-path'
installing 'home-manager-path'
Activating dconfSettings
Activating linkGeneration
Cleaning up orphan links from /home/brian
Creating home file links in /home/brian
Activating onFilesChange
Activating reloadSystemd
Starting units: blueman-applet.service
Activating vscodeProfiles

There are 193 unread and relevant news items.
Read them by running the command "home-manager news".


[brian@miacis:~/.config/home-manager]$ ls -l ~/.nix-profile
lrwxrwxrwx 1 brian brian 45 Jul  7 08:27 /home/brian/.nix-profile -> /home/brian/.local/state/nix/profiles/profile
[brian@miacis:~/.config/home-manager]$ ls -l /home/brian/.local/state/nix/profiles/profile
lrwxrwxrwx 1 brian brian 16 Jul  7 08:52 /home/brian/.local/state/nix/profiles/profile -> profile-152-link

I asked LLM for help, but it got totally confused and gave up.

I would expect "home-manager switch" should populate /nix/var/nix/gcroots/auto - but that doesn't seem to be happening. Is this something I have to repair manually?

Any ideas?

[brianmay]

Possibly due to 2 bad/missing symlinks:

[brian@miacis:~/.config/home-manager]$ ls -l ~/.nix-profile
lrwxrwxrwx 1 brian brian 45 Jul  7 08:27 /home/brian/.nix-profile -> /home/brian/.local/state/nix/profiles/profile
[brian@miacis:~/.config/home-manager]$ ls -la /nix/var/nix/gcroots/profiles/per-user/
total 11
drwxr-xr-x 3 root root 3 Oct 19  2024 .
drwxr-xr-x 3 root root 9 Jul  9 06:05 ..
drwxr-xr-x 2 root root 4 Jul  9 06:05 root

Fixed with:

ln -sfn ~/.local/state/nix/profiles/home-manager ~/.nix-profile
sudo ln -s /home/brian/.local/state/nix/profiles /nix/var/nix/gcroots/per-user/brian

Not 100% convinced the .nix-profile symlink was wrong, but he other one makes sense. Garbage collection may have deleted it when my home directory was not automatically mounted at boot. Yuck. Would have hoped home-manager switch would notice the problem, I guess it does not.

Fingers crossed.

[brianmay]

Also, looks like I was comparing new/old installs, which has different symlinks. Yuck.

Old install has:

[brian@canidae:~]$ ls -ld /home/brian/.nix-profile
lrwxrwxrwx 1 brian users 44 Mar 19  2023 /home/brian/.nix-profile -> /nix/var/nix/profiles/per-user/brian/profile

Apparently this is normal for older installs.

[glmlm]

Not exactly the same, but I recently went through something similar.

This might be related: nix-community/nh#722