#79321 A pile of problems with unprivileged Guix daemon and 'guix gc'

Message #5 received at submit@debbugs.gnu.org (full text, mbox, reply):

From: "Zack Weinberg" <zack@owlfolio.org>

To: help-guix@gnu.org, bug-guix@gnu.org

Subject: A pile of problems with unprivileged Guix daemon and 'guix gc'

Date: Tue, 26 Aug 2025 17:17:22 -0400

# guix gc
finding garbage collector roots...
cannot read potential root `/var/guix/gcroots/auto/idj3k6kjlqi7y8sc4c5xschqh8zkhfvb'
cannot read potential root `/var/guix/gcroots/auto/5si4fzk79j7v27rqaic4lc2qfpk42ilb'
cannot read potential root `/var/guix/gcroots/auto/825grbfhqdfav4g6827d2d3hb8hyhhzl'
cannot read potential root `/var/guix/gcroots/auto/6l77c1c97vij2gg3p95d9zi2k7l0yx29'
cannot read potential root `/var/guix/gcroots/auto/r2x8d211bfp2y3y6wvgp8740ram26ipv'
cannot read potential root `/var/guix/gcroots/auto/jbrxxz57056g8393kh9zyyj325lwq5c5'
guix gc: error: program `/gnu/store/6px1m9n904j8s4hyrmlds707sfnq52d9-guix-1.4.0-41.826e305/bin/guix' failed with exit code 1

So first off, these error messages fail to comply with the first law of
Unix error messages; they don't print strerror(errno), and they don't
name the actual system call that failed, so they don't tell me *why* the
GC roots can't be read.  But leave that aside for now...

# guix gc 2>&1 |
  sed -ne 's:^cannot read potential root `\([a-z0-9/]*\)'\''$:\1:p' >
  /tmp/bad-roots
# ls -l $(cat /tmp/bad-roots)
lrwxrwxrwx 1 guix-daemon guix-daemon 80 Aug 10 01:41 /var/guix/gcroots/auto/5si4fzk79j7v27rqaic4lc2qfpk42ilb -> /root/.cache/guix/inferiors/bpo6zmuuzeya74vbpqn2innq7vw4xzxn7azgjarsmg756jdrsika
lrwxrwxrwx 1 guix-daemon guix-daemon 79 Mar 16 22:20 /var/guix/gcroots/auto/6l77c1c97vij2gg3p95d9zi2k7l0yx29 -> /root/.cache/guix/profiles/simr3ylizyyss24c25azsqfl4vjtw2t4ywvgpbh3iinbrsljgfea
lrwxrwxrwx 1 guix-daemon guix-daemon 80 Jul 27 02:02 /var/guix/gcroots/auto/825grbfhqdfav4g6827d2d3hb8hyhhzl -> /root/.cache/guix/inferiors/zy7a627k6aubd32iun2ibyoy4ulbj4xas55yaibwaayctx6qehta
lrwxrwxrwx 1 guix-daemon guix-daemon 80 Jul 13 01:41 /var/guix/gcroots/auto/idj3k6kjlqi7y8sc4c5xschqh8zkhfvb -> /root/.cache/guix/inferiors/72tvmmz43muzwd4lml3xsfdxw55idd742433w4kylm7yyyohed6a
lrwxrwxrwx 1 guix-daemon guix-daemon 80 Aug  3 01:39 /var/guix/gcroots/auto/jbrxxz57056g8393kh9zyyj325lwq5c5 -> /root/.cache/guix/inferiors/qgxsppsml7olednljz273sdygm5zsxjrrpey2q7ysh5on6evneza
lrwxrwxrwx 1 guix-daemon guix-daemon 80 Jul 20 01:41 /var/guix/gcroots/auto/r2x8d211bfp2y3y6wvgp8740ram26ipv -> /root/.cache/guix/inferiors/whqagcgua6af2zpw3xpaiiifny6pvevcpque3kstsu74ufx6rrda

# ls -ld /root /root/.cache /root/.cache/guix /root/.cache/guix/{inferiors,profiles}
drwx------ 5 root root 4096 Aug 26 20:46 /root/
drwxr-xr-x 4 root root 4096 Jul 22  2024 /root/.cache/
drwxr-xr-x 6 root root 4096 Mar 16 22:19 /root/.cache/guix/
drwxr-xr-x 2 root root 4096 Aug 10 01:41 /root/.cache/guix/inferiors/
drwxr-xr-x 2 root root 4096 Mar 16 22:21 /root/.cache/guix/profiles/

After seeing this I suspected the problem might be that the *Guix daemon*,
which is running unprivileged, cannot access these files.  And indeed, if
I do `chmod 711 /root`, then `guix gc` stops printing the "cannot read
potential root" messages.  But it still doesn't _work_:

# guix gc
finding garbage collector roots...
guix gc: error: program `/gnu/store/6px1m9n904j8s4hyrmlds707sfnq52d9-guix-1.4.0-41.826e305/bin/guix' failed with exit code 1

So that's _really_ bad UX, but again, not the immediate problem.  Since I
do now know that it's the daemon that's having problems, I check the logs:

# tail -3 /var/log/guix-daemon.log
2025-08-26 20:56:21 accepted connection from pid 172, user root
2025-08-26 20:56:21 accepted connection from pid 176, user guix-daemon
2025-08-26 20:56:21 guix gc: error: creating directory `/var/guix/profiles/per-user/guix-daemon': Permission denied

Well, that's suggestive...

# ls -la /var/guix/profiles/per-user
total 28
drwxr-xr-x 7 root         root         4096 Apr 25 20:03 ./
drwxr-xr-x 3 root         root         4096 Aug 26 20:25 ../
drwxr-xr-x 2 root         root         4096 Aug 26 20:25 root/
drwxr-xr-x 2 user1        user1        4096 Apr 25 20:03 user1/
drwxr-xr-x 2 user2        user2        4096 Apr 25 20:03 user2/
drwxr-xr-x 2 user3        user3        4096 Apr 25 20:03 user3/

(actual user names redacted)

# mkdir /var/guix/profiles/per-user/guix-daemon
# chown guix-daemon:guix-daemon /var/guix/profiles/per-user/guix-daemon
# guix gc
finding garbage collector roots...
deleting garbage...
[7 MiB] deleting '/gnu/store/r993z4wdyqqwzxlif1hvqzp6cqhqr2bw-rustc-1.76.0-src.tar.zst.drv'
[7 MiB] deleting '/gnu/store/afnyx8a8qj4wlhywv0zsf57lmk8yskzc-rustc-1.76.0-src.tar.gz.drv'
...
[38344 MiB] deleting '/gnu/store/yd1hpyjjmzmq5qmlv6q2ycqlymsma9rh-freeglut-3.4.0-builder'
[38344 MiB] deleting '/gnu/store/3z0np2ad898193wws74k54rzppr356cv-ipxe-qemu-1.21.1-3.24db39f-builder'
deleting `/gnu/store/trash'
guix gc: error: making `var/empty' writable: Operation not permitted

Well yeah! /var/empty is supposed to be empty at all times!  Is this
not how it's supposed to be?

# ls -ld /var/empty
dr-xr-xr-x 2 root root 4096 Jul 22  2024 /var/empty/

But if I set it to be world-writable I still get the same error.  In
fact, even if I make it *owned by guix-daemon*, I still get the same
error!

And now I'm stuck.  guix gc moved all the trash to /gnu/store/trash,
but it didn't actually delete any of it.  There's 11G in there, and
I can't delete it by hand because the store is mounted read-only
and I don't know how to temporarily override that for this kind of
manual repair job.  Any advice would be most appreciated.

zw

Message #8 received at 79321@debbugs.gnu.org (full text, mbox, reply):

From: Rutherther <rutherther@ditigal.xyz>

To: help-guix@gnu.org, Zack Weinberg <zack@owlfolio.org>, 79321@debbugs.gnu.org

Subject: Re: A pile of problems with unprivileged Guix daemon and 'guix gc'

Date: Wed, 27 Aug 2025 08:23:41 +0200

Hi, 

On August 26, 2025 11:17:22 PM GMT+02:00, Zack Weinberg <zack@owlfolio.org> wrote:
># guix gc
>finding garbage collector roots...
>cannot read potential root `/var/guix/gcroots/auto/idj3k6kjlqi7y8sc4c5xschqh8zkhfvb'
>cannot read potential root `/var/guix/gcroots/auto/5si4fzk79j7v27rqaic4lc2qfpk42ilb'
>cannot read potential root `/var/guix/gcroots/auto/825grbfhqdfav4g6827d2d3hb8hyhhzl'
>cannot read potential root `/var/guix/gcroots/auto/6l77c1c97vij2gg3p95d9zi2k7l0yx29'
>cannot read potential root `/var/guix/gcroots/auto/r2x8d211bfp2y3y6wvgp8740ram26ipv'
>cannot read potential root `/var/guix/gcroots/auto/jbrxxz57056g8393kh9zyyj325lwq5c5'
>guix gc: error: program `/gnu/store/6px1m9n904j8s4hyrmlds707sfnq52d9-guix-1.4.0-41.826e305/bin/guix' failed with exit code 1
>
>So first off, these error messages fail to comply with the first law of
>Unix error messages; they don't print strerror(errno), and they don't
>name the actual system call that failed, so they don't tell me *why* the
>GC roots can't be read.  But leave that aside for now...
>
># guix gc 2>&1 |
>  sed -ne 's:^cannot read potential root `\([a-z0-9/]*\)'\''$:\1:p' >
>  /tmp/bad-roots
># ls -l $(cat /tmp/bad-roots)
>lrwxrwxrwx 1 guix-daemon guix-daemon 80 Aug 10 01:41 /var/guix/gcroots/auto/5si4fzk79j7v27rqaic4lc2qfpk42ilb -> /root/.cache/guix/inferiors/bpo6zmuuzeya74vbpqn2innq7vw4xzxn7azgjarsmg756jdrsika
>lrwxrwxrwx 1 guix-daemon guix-daemon 79 Mar 16 22:20 /var/guix/gcroots/auto/6l77c1c97vij2gg3p95d9zi2k7l0yx29 -> /root/.cache/guix/profiles/simr3ylizyyss24c25azsqfl4vjtw2t4ywvgpbh3iinbrsljgfea
>lrwxrwxrwx 1 guix-daemon guix-daemon 80 Jul 27 02:02 /var/guix/gcroots/auto/825grbfhqdfav4g6827d2d3hb8hyhhzl -> /root/.cache/guix/inferiors/zy7a627k6aubd32iun2ibyoy4ulbj4xas55yaibwaayctx6qehta
>lrwxrwxrwx 1 guix-daemon guix-daemon 80 Jul 13 01:41 /var/guix/gcroots/auto/idj3k6kjlqi7y8sc4c5xschqh8zkhfvb -> /root/.cache/guix/inferiors/72tvmmz43muzwd4lml3xsfdxw55idd742433w4kylm7yyyohed6a
>lrwxrwxrwx 1 guix-daemon guix-daemon 80 Aug  3 01:39 /var/guix/gcroots/auto/jbrxxz57056g8393kh9zyyj325lwq5c5 -> /root/.cache/guix/inferiors/qgxsppsml7olednljz273sdygm5zsxjrrpey2q7ysh5on6evneza
>lrwxrwxrwx 1 guix-daemon guix-daemon 80 Jul 20 01:41 /var/guix/gcroots/auto/r2x8d211bfp2y3y6wvgp8740ram26ipv -> /root/.cache/guix/inferiors/whqagcgua6af2zpw3xpaiiifny6pvevcpque3kstsu74ufx6rrda
>
># ls -ld /root /root/.cache /root/.cache/guix /root/.cache/guix/{inferiors,profiles}
>drwx------ 5 root root 4096 Aug 26 20:46 /root/
>drwxr-xr-x 4 root root 4096 Jul 22  2024 /root/.cache/
>drwxr-xr-x 6 root root 4096 Mar 16 22:19 /root/.cache/guix/
>drwxr-xr-x 2 root root 4096 Aug 10 01:41 /root/.cache/guix/inferiors/
>drwxr-xr-x 2 root root 4096 Mar 16 22:21 /root/.cache/guix/profiles/
>
>After seeing this I suspected the problem might be that the *Guix daemon*,
>which is running unprivileged, cannot access these files.  And indeed, if
>I do `chmod 711 /root`, then `guix gc` stops printing the "cannot read
>potential root" messages.  But it still doesn't _work_:
>
># guix gc
>finding garbage collector roots...
>guix gc: error: program `/gnu/store/6px1m9n904j8s4hyrmlds707sfnq52d9-guix-1.4.0-41.826e305/bin/guix' failed with exit code 1
>
>So that's _really_ bad UX, but again, not the immediate problem.  Since I
>do now know that it's the daemon that's having problems, I check the logs:
>
># tail -3 /var/log/guix-daemon.log
>2025-08-26 20:56:21 accepted connection from pid 172, user root
>2025-08-26 20:56:21 accepted connection from pid 176, user guix-daemon
>2025-08-26 20:56:21 guix gc: error: creating directory `/var/guix/profiles/per-user/guix-daemon': Permission denied
>
>Well, that's suggestive...
>
># ls -la /var/guix/profiles/per-user
>total 28
>drwxr-xr-x 7 root         root         4096 Apr 25 20:03 ./
>drwxr-xr-x 3 root         root         4096 Aug 26 20:25 ../
>drwxr-xr-x 2 root         root         4096 Aug 26 20:25 root/
>drwxr-xr-x 2 user1        user1        4096 Apr 25 20:03 user1/
>drwxr-xr-x 2 user2        user2        4096 Apr 25 20:03 user2/
>drwxr-xr-x 2 user3        user3        4096 Apr 25 20:03 user3/
>
>(actual user names redacted)

This doesn't look okay, I think both /var/guix/profiles and /var/guix/profiles/per-user should be owned by guix-daemon. This goes basically for everything under /var/guix, except for profiles/per-user/X, where the owner should be X. Though now looking into guix-ownership service it seems it doesn't try to change this ownership, only of /var/guix. While on the other hand the guix-install.sh script does - it chowns everything and then reverts root's profile to root. An oversight? 

>
># mkdir /var/guix/profiles/per-user/guix-daemon
># chown guix-daemon:guix-daemon /var/guix/profiles/per-user/guix-daemon
># guix gc
>finding garbage collector roots...
>deleting garbage...
>[7 MiB] deleting '/gnu/store/r993z4wdyqqwzxlif1hvqzp6cqhqr2bw-rustc-1.76.0-src.tar.zst.drv'
>[7 MiB] deleting '/gnu/store/afnyx8a8qj4wlhywv0zsf57lmk8yskzc-rustc-1.76.0-src.tar.gz.drv'
>...
>[38344 MiB] deleting '/gnu/store/yd1hpyjjmzmq5qmlv6q2ycqlymsma9rh-freeglut-3.4.0-builder'
>[38344 MiB] deleting '/gnu/store/3z0np2ad898193wws74k54rzppr356cv-ipxe-qemu-1.21.1-3.24db39f-builder'
>deleting `/gnu/store/trash'
>guix gc: error: making `var/empty' writable: Operation not permitted
>
>Well yeah! /var/empty is supposed to be empty at all times!  Is this
>not how it's supposed to be?
>
># ls -ld /var/empty
>dr-xr-xr-x 2 root root 4096 Jul 22  2024 /var/empty/
>
>But if I set it to be world-writable I still get the same error.  In
>fact, even if I make it *owned by guix-daemon*, I still get the same
>error!

I think that resolving the /var/guix permissions might solve this issue as well. The error says var/empty, not /var/empty, implying it is under whatever the guix daemon's pwd is. Well, I unfortunately am just on phone and since recently I decided to try update emacs on it and ended up with emacs without git or anything, I cannot check now what file it is actually trying to create from source like I usually would (with search feature). So best I can tell you, if solving permissions in /var/guix doesnt work, to start guix-daemon with strace and see what file it is actually talking about, not just the relative path. 

>
>And now I'm stuck.  guix gc moved all the trash to /gnu/store/trash,
>but it didn't actually delete any of it.  There's 11G in there, and
>I can't delete it by hand because the store is mounted read-only
>and I don't know how to temporarily override that for this kind of
>manual repair job.  Any advice would be most appreciated.

It is bind mounted, that means you can just umount it. But I would strongly advise against it if it is possible to  let guix solve it on its own. Not sure if stuff in the trash is somehow tracked, if not, it would be safe to do that, yeah. 

Rutherther

PS: please dont send same emails both to guix help and bug guix. This means anyone who replies all will make a new bug report! Omitting the fact that this bug tracker is deprecated in favor of codeberg issues, you should rather use X-Debbugs-Cc to let debbugs send the email with proper email address to reply to - id of the bug. 

>
>zw

Message #11 received at 79321@debbugs.gnu.org (full text, mbox, reply):

From: "Zack Weinberg" <zack@owlfolio.org>

To: Rutherther <rutherther@ditigal.xyz>, help-guix@gnu.org, 79321@debbugs.gnu.org

Subject: Re: A pile of problems with unprivileged Guix daemon and 'guix gc'

Date: Wed, 27 Aug 2025 11:24:32 -0400

On Wed, Aug 27, 2025, at 2:23 AM, Rutherther wrote:
> On August 26, 2025 11:17:22 PM GMT+02:00, Zack Weinberg wrote:
>># guix gc
>>guix gc: error: making `var/empty' writable: Operation not permitted
>>
>>Well yeah! /var/empty is supposed to be empty at all times!  Is this
>>not how it's supposed to be?
>>
>># ls -ld /var/empty
>>dr-xr-xr-x 2 root root 4096 Jul 22  2024 /var/empty/
>>
>>But if I set it to be world-writable I still get the same error.  In
>>fact, even if I make it *owned by guix-daemon*, I still get the same
>>error!
>
> I think that resolving the /var/guix permissions might solve this issue 
> as well. The error says var/empty, not /var/empty, implying it is under 
> whatever the guix daemon's pwd is. 

The guix daemon's pwd is '/'.

> Well, I unfortunately am just on 
> phone and since recently I decided to try update emacs on it and ended 
> up with emacs without git or anything, I cannot check now what file it 
> is actually trying to create from source like I usually would (with 
> search feature).

I happen to have a full checkout of Guix on my workstation.   The computer
with all the problems was stuck on an old Guix (because unattended-upgrade
failed because the store had consumed all available disk space); if I'm
interpreting the contents of the old system profile correctly,
it was stuck on commit b7ac124f3cfadca9a6fc9829628f84c9d9d1b27b.

The string "var/empty" does not appear anywhere in the Guix source tree,
except as part of "/var/empty", either on that commit or the tip of
master (currently commit aad612c143e19c1a4b64ae066a1fdfbe16c71226).

I'm reluctant to screw with permissions without understanding what
actually went wrong here.

> PS: please dont send same emails both to guix help and bug guix. This 
> means anyone who replies all will make a new bug report! Omitting the 
> fact that this bug tracker is deprecated in favor of codeberg issues, 
> you should rather use X-Debbugs-Cc to let debbugs send the email with 
> proper email address to reply to - id of the bug. 

So noted.

zw

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