Legacy files fail to run. Permission error

[rubenelshof]

Using the latest version v3.0.0.0-1 files in legacy file locations fail to run. See the output below.
I didn't have this issue using v2.2.0.3.

Expected output

Using v2.2.0.3

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] 20-config: executing... 
[cont-init.d] 20-config: exited 0.
[cont-init.d] done.
[services.d] starting services
[24-Jan-2022 09:50:51] NOTICE: fpm is running, pid 216
[24-Jan-2022 09:50:51] NOTICE: ready to handle connections
[services.d] done.

Actual output

Using v3.0.0.0-1

s6-rc: info: service s6rc-oneshot-runner: starting
s6-rc: info: service s6rc-oneshot-runner successfully started
s6-rc: info: service fix-attrs: starting
s6-rc: info: service fix-attrs successfully started
s6-rc: info: service legacy-cont-init: starting
cont-init: info: running /etc/cont-init.d/20-config
/package/admin/s6-overlay-3.0.0.0-1/etc/s6-rc/scripts/cont-init: line 14: /etc/cont-init.d/20-config: Permission denied
cont-init: info: /etc/cont-init.d/20-config exited 126
cont-init: warning: some scripts exited nonzero
s6-rc: warning: unable to start service legacy-cont-init: command exited 1
/run/s6/basedir/scripts/rc.init: warning: s6-rc failed to properly bring all the services up! Check your logs (in /run/uncaught-logs/current if you have in-container logging) for more information.
/run/s6/basedir/scripts/rc.init: fatal: stopping the container.
s6-rc: info: service fix-attrs: stopping
s6-rc: info: service fix-attrs successfully stopped
s6-rc: info: service s6rc-oneshot-runner: stopping
s6-rc: info: service s6rc-oneshot-runner successfully stopped

After removing cont-init.d

s6-rc: info: service s6rc-oneshot-runner: starting
s6-rc: info: service s6rc-oneshot-runner successfully started
s6-rc: info: service fix-attrs: starting
s6-rc: info: service fix-attrs successfully started
s6-rc: info: service legacy-cont-init: starting
s6-rc: info: service legacy-cont-init successfully started
s6-rc: info: service legacy-services: starting
services-up: info: copying legacy longrun cron (no readiness notification)
services-up: info: copying legacy longrun nginx (no readiness notification)
services-up: info: copying legacy longrun php-fpm (no readiness notification)
s6-supervise nginx (child): fatal: unable to exec run: Permission denied
s6-supervise nginx: warning: unable to spawn ./run - waiting 10 seconds
s6-supervise cron (child): fatal: unable to exec run: Permission denied
s6-supervise php-fpm: warning: unable to spawn ./run - waiting 10 seconds
s6-supervise cron: warning: unable to spawn ./run - waiting 10 seconds
s6-supervise php-fpm (child): fatal: unable to exec run: Permission denied
s6-rc: fatal: timed out
s6-sudoc: fatal: unable to get exit status from server: Operation timed out
/run/s6/basedir/scripts/rc.init: warning: s6-rc failed to properly bring all the services up! Check your logs (in /run/uncaught-logs/current if you have in-container logging) for more information.
/run/s6/basedir/scripts/rc.init: fatal: stopping the container.
s6-rc: info: service legacy-cont-init: stopping
s6-rc: info: service legacy-cont-init successfully stopped
s6-rc: info: service fix-attrs: stopping
s6-rc: info: service fix-attrs successfully stopped
s6-rc: info: service s6rc-oneshot-runner: stopping
s6-rc: info: service s6rc-oneshot-runner successfully stopped

[skarnet]

Looks like your files aren't executable.
Please make sure that all the files in /etc/cont-init.d and all the run scripts in /etc/services.d are executable.

[rubenelshof]

After making the files executable it gives me a different error.
I get the same error as before after removing cont-init.d

s6-rc: info: service s6rc-oneshot-runner: starting
s6-rc: info: service s6rc-oneshot-runner successfully started
s6-rc: info: service fix-attrs: starting
s6-rc: info: service fix-attrs successfully started
s6-rc: info: service legacy-cont-init: starting
cont-init: info: running /etc/cont-init.d/20-config
/package/admin/s6-overlay-3.0.0.0-1/etc/s6-rc/scripts/cont-init: line 14: /etc/cont-init.d/20-config: not found
cont-init: info: /etc/cont-init.d/20-config exited 127
cont-init: warning: some scripts exited nonzero
s6-rc: warning: unable to start service legacy-cont-init: command exited 1
/run/s6/basedir/scripts/rc.init: warning: s6-rc failed to properly bring all the services up! Check your logs (in /run/uncaught-logs/current if you have in-container logging) for more information.
/run/s6/basedir/scripts/rc.init: fatal: stopping the container.
s6-rc: info: service fix-attrs: stopping
s6-rc: info: service fix-attrs successfully stopped
s6-rc: info: service s6rc-oneshot-runner: stopping
s6-rc: info: service s6rc-oneshot-runner successfully stopped

Permissions

/ # ls -al /etc/cont-init.d/
total 12
drwxr-xr-x    1 root     root          4096 Jan 24 10:00 .
drwxr-xr-x    1 root     root          4096 Jan 24 10:05 ..
-rwxr-xr-x    1 root     root           445 Jan 24 10:00 20-config
/ # ls -al /etc/services.d/cron/
total 16
drwxr-xr-x    1 root     root          4096 Sep 19 04:12 .
drwxr-xr-x    1 root     root          4096 Sep 27 20:30 ..
-rwxr-xr-x    1 root     root            83 Sep 19 04:14 run
/ # ls -al /etc/services.d/nginx/
total 16
drwxr-xr-x    1 root     root          4096 Sep 19 02:53 .
drwxr-xr-x    1 root     root          4096 Sep 27 20:30 ..
-rwxr-xr-x    1 root     root            50 Sep 19 04:17 run
/ # ls -al /etc/services.d/php-fpm/
total 16
drwxr-xr-x    1 root     root          4096 Sep 19 02:53 .
drwxr-xr-x    1 root     root          4096 Sep 27 20:30 ..
-rwxr-xr-x    1 root     root            53 Dec  2 08:22 run

[mustanggb]

Think I'm seeing a similar problem.

/etc/cont-init.d/myscript

#!/command/with-contenv sh
composer --version

This gives the error /etc/cont-init.d/myscript: line 2: composer: not found

Even though:

/ # echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
/ # ls -la /usr/local/bin/
total 2320
drwxr-xr-x    2 root     root          4096 Jan 24 13:46 .
drwxr-xr-x    1 root     root          4096 Jan 24 13:46 ..
-rwxr-xr-x    1 root     root       2358836 Jan 21 16:25 composer
/ #

[skarnet]

@rubenelshof : what does your 20-config script looks like? It looks like a PATH issue.
@mustanggb : with-contenv imports the PATH from your host, that may be the problem. We probably shouldn't do that - with-contenv should probably import the host environment except for PATH.

[rubenelshof]

@skarnet

#!/usr/bin/with-contenv bash

# create folders
mkdir -p /config/{log/{cron,nginx,php},tmp/{nginx,php}}

# nginx
rm /etc/nginx/http.d/default.conf

# logrotate
sed -i "s#/var/log/messages {}.*# #g" /etc/logrotate.conf
sed -i 's#/usr/sbin/logrotate /etc/logrotate.conf#/usr/sbin/logrotate /etc/logrotate.conf -s /config/tmp/logrotate.status#g' /etc/periodic/daily/logrotate

# permissions
chown -R diony:diony /config
chmod -R 644 /etc/logrotate.d

[skarnet]

@rubenelshof Your 20-config script looks for with-contenv in /usr/bin. Either change the shebang to #!/command/with-contenv bash, or install the s6-overlay-symlinks-noarch tarball so with-contenv remains accessible from /usr/bin.

[rubenelshof]

@skarnet So that combined with setting the script as an executable fixes the errors in both cont-init.d aswell as services.d.

What I don't understand yet is why it worked without setting the file as an executable on the older version (v2.2.0.3).

Additionally maybe this example needs to be updated with the new location for with-contenv?
https://github.com/just-containers/s6-overlay#container-environment

[skarnet]

The previous versions used a specific invocation of fix-attrs to force the run scripts and the cont-init.d scripts to be executable. We're deprecating fix-attrs so we've removed this invocation; now the permissions need to be correct from the get to. Sorry for the inconvenience.

I have updated the README.md so the shebang is correct, thanks.

[rubenelshof]

No problem.

Thanks for the information & help solving the issue.