nh clean all using home-manager on arch removes everything

[JumpIn-Git]

When i run nh clean I get this weird error:

❯ nh clean all -k 5 -K 3d
sudo: nh: command not found

When I run any other nh command it works, I needed to run it in fakeroot, sudo wont work because it checks the root account's profile, when it does work it removes home-manager and anything installed by it

[viperML]

I'll fix it asap

[viperML]

Please run the command with --verbose and paste the output.

[imvaskel]

Not the same person but I am running the same setup:

 ❯  nh clean all --verbose
TRACE nh::logging:86: Logging OK
DEBUG nh:32: Main {
    verbose: true,
    command: Clean(
        CleanProxy {
            command: All(
                CleanArgs {
                    keep: 1,
                    keep_since: Duration(
                        0ns,
                    ),
                    dry: false,
                    ask: false,
                    nogc: false,
                    nogcroots: false,
                },
            ),
        },
    ),
}
DEBUG nh:33: NH_VERSION=4.0.0-beta.5 NH_REV=Some("6a69a14")
DEBUG nh:49: "sudo" "nh" "clean" "all" "--verbose"
[sudo] password for skylar:
sudo: nh: command not found

My guess is that this has to do with the program being installed in my user profile. Running readlink $(which nh) and running the binary directly does get past the sudo issue but instead I am met with an error:

 ❯  /nix/store/wfg7csq178khs2p640vpycgl7qrdc861-nh-4.0.0-beta.5-6a69a14/bin/nh clean all --verbose
TRACE nh::logging:86: Logging OK
DEBUG nh:32: Main {
    verbose: true,
    command: Clean(
        CleanProxy {
            command: All(
                CleanArgs {
                    keep: 1,
                    keep_since: Duration(
                        0ns,
                    ),
                    dry: false,
                    ask: false,
                    nogc: false,
                    nogcroots: false,
                },
            ),
        },
    ),
}
DEBUG nh:33: NH_VERSION=4.0.0-beta.5 NH_REV=Some("6a69a14")
! nh 4.0.0-beta.5 now uses NH_FLAKE instead of FLAKE, please modify your configuration (nh/src/main.rs:36)
DEBUG nh:49: "sudo" "/nix/store/wfg7csq178khs2p640vpycgl7qrdc861-nh-4.0.0-beta.5-6a69a14/bin/nh" "clean" "all" "--verbose"
TRACE nh::logging:86: Logging OK
DEBUG nh:32: Main {
    verbose: true,
    command: Clean(
        CleanProxy {
            command: All(
                CleanArgs {
                    keep: 1,
                    keep_since: Duration(
                        0ns,
                    ),
                    dry: false,
                    ask: false,
                    nogc: false,
                    nogcroots: false,
                },
            ),
        },
    ),
}
DEBUG nh:33: NH_VERSION=4.0.0-beta.5 NH_REV=Some("6a69a14")
DEBUG profiles_in_dir: nh::clean:240: return=[] dir="/nix/var/nix/profiles"
DEBUG profiles_in_dir: nh::clean:240: return=["/nix/var/nix/profiles/per-user/root/profile"] dir="/nix/var/nix/profiles/per-user/root"
DEBUG nh::clean:64: Scanning XDG profiles for users 0, $1000-$1100
DEBUG nh::clean:67: Adding XDG profiles for user user=User(0, root)
! Failed to read profiles directory dir="/root/.local/state/nix/profiles" error=Os { code: 2, kind: NotFound, message: "No such file or directory" } (nh/src/clean.rs:272)
DEBUG profiles_in_dir: nh::clean:240: return=[] dir="/root/.local/state/nix/profiles"
DEBUG nh::clean:67: Adding XDG profiles for user user=User(1000, skylar)
DEBUG profiles_in_dir: nh::clean:240: return=["/home/skylar/.local/state/nix/profiles/home-manager", "/home/skylar/.local/state/nix/profiles/profile"] dir="/home/skylar/.local/state/nix/profiles"
DEBUG cleanable_generations: nh::clean:341: {
    Generation {
        number: 2,
        last_modified: SystemTime {
            tv_sec: 1734814738,
            tv_nsec: 501387808,
        },
        path: "/nix/var/nix/profiles/per-user/root/profile-2-link",
    }: false,
} profile="/nix/var/nix/profiles/per-user/root/profile" keep=1 keep_since=Duration(0ns)
DEBUG cleanable_generations: nh::clean:341: {
    Generation {
        number: 45,
        last_modified: SystemTime {
            tv_sec: 1735588276,
            tv_nsec: 255411177,
        },
        path: "/home/skylar/.local/state/nix/profiles/home-manager-45-link",
    }: false,
} profile="/home/skylar/.local/state/nix/profiles/home-manager" keep=1 keep_since=Duration(0ns)
DEBUG cleanable_generations: nh::clean:341: {
    Generation {
        number: 31,
        last_modified: SystemTime {
            tv_sec: 1735588277,
            tv_nsec: 392070676,
        },
        path: "/home/skylar/.local/state/nix/profiles/profile-31-link",
    }: false,
} profile="/home/skylar/.local/state/nix/profiles/profile" keep=1 keep_since=Duration(0ns)
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/v73nmmh5d8van4ja5c8jn0gjlwhxbz3a" dst="/nix/var/nix/profiles/per-user/root/profile-2-link"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/nix/var/nix/profiles/per-user/root/profile-2-link"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/za3i593wy63jx69igv2kd596mzaj7n96" dst="/home/skylar/nixfiles/.devenv/gc/shell-30-link"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/nixfiles/.devenv/gc/shell-30-link"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/gkd5mn5f9x4rga3s81gd84v72wgrkcp4" dst="/home/skylar/.local/state/home-manager/gcroots/current-home"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/.local/state/home-manager/gcroots/current-home"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/10f9vwvjjybiwaymbryc251mns6zzg5j" dst="/home/skylar/.cache/nix/flake-registry.json"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/.cache/nix/flake-registry.json"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/g15qw8gvikc1qsz6hdq0lmi2cqvxpsfb" dst="/home/skylar/.local/state/nix/profiles/home-manager-45-link"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/.local/state/nix/profiles/home-manager-45-link"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/169phrhd10k7bz8sjnlzdr1qhdvadk8w" dst="/home/skylar/.local/state/nix/profiles/profile-30-link"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/.local/state/nix/profiles/profile-30-link"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/srpyams1lbyyrg4f1lxbbi3rxrjgq9qi" dst="/tmp/nh-os16Ds66/result"
DEBUG gcroot detection: nh::clean:159: dst doesn't exist or is not writable, skipping dst="/tmp/nh-os16Ds66/result"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/pf9wwmskhs5j5xafncd8vqnjjsaldzi4" dst="/home/skylar/.local/state/nix/profiles/home-manager-44-link"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/.local/state/nix/profiles/home-manager-44-link"
DEBUG gcroot detection: nh::clean:115: src="/nix/var/nix/gcroots/auto/szg4qhas6niv59c6rkh0bsywigllbnm9" dst="/home/skylar/.local/state/nix/profiles/profile-31-link"
DEBUG gcroot detection: nh::clean:121: dst doesn't match any gcroot regex, skipping dst="/home/skylar/.local/state/nix/profiles/profile-31-link"

Welcome to nh clean
Keeping 1 generation(s)
Keeping paths newer than 0s

legend:
OK: path to be kept
DEL: path to be removed

/nix/var/nix/profiles/per-user/root/profile
- OK  /nix/var/nix/profiles/per-user/root/profile-2-link

/home/skylar/.local/state/nix/profiles/home-manager
- OK  /home/skylar/.local/state/nix/profiles/home-manager-45-link

/home/skylar/.local/state/nix/profiles/profile
- OK  /home/skylar/.local/state/nix/profiles/profile-31-link

> Performing garbage collection on the nix store
DEBUG nh::commands:97: cmd=Exec { nix store gc }
Error:
   0: Performing garbage collection on the nix store
   1: No such file or directory (os error 2)
   2: No such file or directory (os error 2)

Location:
   src/commands.rs:101

However my guess is that this second problem is related to how I've installed nix and the default root environment not having nix on PATH.

[ToyVo]

Yeah I'd agree you have a path issue to sort out.

I'd like to point out the failure to read /root/.local/state/nix/profiles similar to #202 helping to show that isn't a Darwin specific issue

[JumpIn-Git]

Please run the command with --verbose and paste the output.

sorry for the late response, (this was run in fakeroot btw)

~
# ❯ nh clean all --verbose 
TRACE nh::logging:86: Logging OK
DEBUG nh:23: args=NHParser { verbose: true, command: Clean(CleanProxy { command: All(CleanArgs { keep: 1, keep_since: Duration(0ns), dry: false, ask: false, nogc: false, nogcroots: false }) }) }
DEBUG nh:24: NH_VERSION=3.6.0
DEBUG profiles_in_dir: nh::clean:235: return=[] dir="/nix/var/nix/profiles"
DEBUG profiles_in_dir: nh::clean:235: return=["/nix/var/nix/profiles/per-user/root/profile"] dir="/nix/var/nix/profiles/per-user/root"
DEBUG nh::clean:58: Scanning XDG profiles for users 0, 1000-1100
DEBUG nh::clean:61: Adding XDG profiles for user user=User(0, root)
! Failed to read profiles directory dir="/root/.local/state/nix/profiles" error=Os { code: 13, kind: PermissionDenied, message: "Permission denied" } @ src/clean.rs:267
DEBUG profiles_in_dir: nh::clean:235: return=[] dir="/root/.local/state/nix/profiles"
DEBUG nh::clean:61: Adding XDG profiles for user user=User(1000, cinnamon)
DEBUG profiles_in_dir: nh::clean:235: return=["/home/cinnamon/.local/state/nix/profiles/profile", "/home/cinnamon/.local/state/nix/profiles/channels", "/home/cinnamon/.local/state/nix/profiles/home-manager"] dir="/home/cinnamon/.local/state/nix/profiles"
DEBUG cleanable_generations: nh::clean:336: {
    Generation {
        number: 1,
        last_modified: SystemTime {
            tv_sec: 1735403653,
            tv_nsec: 996627176,
        },
        path: "/nix/var/nix/profiles/per-user/root/profile-1-link",
    }: true,
    Generation {
        number: 2,
        last_modified: SystemTime {
            tv_sec: 1735403654,
            tv_nsec: 86627172,
        },
        path: "/nix/var/nix/profiles/per-user/root/profile-2-link",
    }: false,
} profile="/nix/var/nix/profiles/per-user/root/profile" keep=1 keep_since=Duration(0ns)
DEBUG cleanable_generations: nh::clean:336: {
    Generation {
        number: 28,
        last_modified: SystemTime {
            tv_sec: 1735935658,
            tv_nsec: 929910519,
        },
        path: "/home/cinnamon/.local/state/nix/profiles/profile-28-link",
    }: true,
    Generation {
        number: 29,
        last_modified: SystemTime {
            tv_sec: 1736001751,
            tv_nsec: 111085530,
        },
        path: "/home/cinnamon/.local/state/nix/profiles/profile-29-link",
    }: true,
    Generation {
        number: 30,
        last_modified: SystemTime {
            tv_sec: 1736001751,
            tv_nsec: 147752197,
        },
        path: "/home/cinnamon/.local/state/nix/profiles/profile-30-link",
    }: false,
} profile="/home/cinnamon/.local/state/nix/profiles/profile" keep=1 keep_since=Duration(0ns)
DEBUG cleanable_generations: nh::clean:336: {
    Generation {
        number: 1,
        last_modified: SystemTime {
            tv_sec: 1735470556,
            tv_nsec: 799886128,
        },
        path: "/home/cinnamon/.local/state/nix/profiles/channels-1-link",
    }: false,
} profile="/home/cinnamon/.local/state/nix/profiles/channels" keep=1 keep_since=Duration(0ns)
DEBUG cleanable_generations: nh::clean:336: {
    Generation {
        number: 13,
        last_modified: SystemTime {
            tv_sec: 1735935659,
            tv_nsec: 26577188,
        },
        path: "/home/cinnamon/.local/state/nix/profiles/home-manager-13-link",
    }: false,
} profile="/home/cinnamon/.local/state/nix/profiles/home-manager" keep=1 keep_since=Duration(0ns)
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/ak9698wzcgmg7jidjax3isb6r423p81z" dst="/home/cinnamon/.local/state/nix/profiles/profile-28-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.local/state/nix/profiles/profile-28-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/d41417n6i4nbci08n7xxa1kmkadr8has" dst="/home/cinnamon/.local/state/nix/profiles/channels-1-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.local/state/nix/profiles/channels-1-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/xzsaf5bcijc8kr84srapk1j7cil6v9rv" dst="/home/cinnamon/.local/state/home-manager/gcroots/current-home"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.local/state/home-manager/gcroots/current-home"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/ajbv2slxp8lsnm0bdni7h64gzxkfxc4z" dst="/home/cinnamon/.local/state/nix/profiles/home-manager-13-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.local/state/nix/profiles/home-manager-13-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/k9d5vvcmfkfsnxwv7ac4frrd9y07lh4r" dst="/home/cinnamon/.cache/nix/flake-registry.json"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.cache/nix/flake-registry.json"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/d9lddacv5m59m7azjl8nq31wms23rvaq" dst="/home/cinnamon/.local/state/nix/profiles/profile-29-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.local/state/nix/profiles/profile-29-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/lzjbmb2ry0z7lma2fvpqprb12921pnb5" dst="/nix/var/nix/profiles/per-user/root/profile-1-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/nix/var/nix/profiles/per-user/root/profile-1-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/0hdpv1mlaymcmjrir5s8m79vl8mzf9wy" dst="/home/cinnamon/.local/state/nix/profiles/profile-30-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/home/cinnamon/.local/state/nix/profiles/profile-30-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/x25ab52fcq5q68wlfk8185nl7w7jbc9h" dst="/tmp/home-manager-build.noYfNSJuxw/news.json"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/tmp/home-manager-build.noYfNSJuxw/news.json"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/v73nmmh5d8van4ja5c8jn0gjlwhxbz3a" dst="/nix/var/nix/profiles/per-user/root/profile-2-link"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/nix/var/nix/profiles/per-user/root/profile-2-link"
DEBUG gcroot detection: nh::clean:109: src="/nix/var/nix/gcroots/auto/knrjv6hmwf7lbrdrg5a71wqh5mbwr5vd" dst="/tmp/home-manager-build.noYfNSJuxw/generation"
DEBUG gcroot detection: nh::clean:115: dst doesn't match any gcroot regex, skipping dst="/tmp/home-manager-build.noYfNSJuxw/generation"

Welcome to nh clean
Keeping 1 generation(s)
Keeping paths newer than 0s

legend:
OK: path to be kept
DEL: path to be removed

/nix/var/nix/profiles/per-user/root/profile
- OK  /nix/var/nix/profiles/per-user/root/profile-2-link
- DEL /nix/var/nix/profiles/per-user/root/profile-1-link

/home/cinnamon/.local/state/nix/profiles/channels
- OK  /home/cinnamon/.local/state/nix/profiles/channels-1-link

/home/cinnamon/.local/state/nix/profiles/home-manager
- OK  /home/cinnamon/.local/state/nix/profiles/home-manager-13-link

/home/cinnamon/.local/state/nix/profiles/profile
- OK  /home/cinnamon/.local/state/nix/profiles/profile-30-link
- DEL /home/cinnamon/.local/state/nix/profiles/profile-29-link
- DEL /home/cinnamon/.local/state/nix/profiles/profile-28-link

> Removing /nix/var/nix/profiles/per-user/root/profile-1-link
! Failed to remove path path="/nix/var/nix/profiles/per-user/root/profile-1-link" err=Os { code: 13, kind: PermissionDenied, message: "Permission denied" } @ src/clean.rs:343
> Removing /home/cinnamon/.local/state/nix/profiles/profile-29-link
> Removing /home/cinnamon/.local/state/nix/profiles/profile-28-link
> Performing garbage collection on the nix store
DEBUG nh::commands:53: cmd=Exec { nix store gc }
7727 store paths deleted, 8655.86 MiB freed

Wierd, it know doesnt remove home-manager