hanging bash scripts

[avraam-inside]

when running standard scripts (for example:) run('bash', c('-c', 'ls')) the session sometimes hangings.

I've already tried everything: cleanup_tree, and using R6 methods with rm(p) and gc() and kill() reading outputs:

stderr <-p$read_all_error_lines()
stdout <-p$read_all_output_lines()

and etc/etc

NOTHING IS WORKING.

Please tell me a sane way to clear buffers, caches, etc. before/after the script so that run does not hang. This has never happened with the system() command at all.

[gaborcsardi]

Can you try to create a reproducible example? E.g. you mention run() but p$read_all_error_lines() is about the R6 class and not run(). Hopefully a reproducible example will clarify this.

[avraam-inside]

Yes, I just tried both through run and through R6.

Crashes on any code.

It takes and hangs sometimes. It is expected to work in 4 seconds usually, sometimes it hangs after a couple of minutes.

An example of how I did:

processx::run('bash', c('-c', 'cd /home && R --no-save --no-restore-data --quiet -e "print(\'123\')"'))

and

p <- processx::process$new('bash', c('-c', 'cd /home && R --no-save --no-restore-data --quiet -e "print(\'123\')"')), stdout = "|", stderr = "|", wd = here())
    p$poll_io(50000000)

    stderr <- p$read_all_error_lines()
    stdout <- p$read_all_output_lines()

    close(p$get_output_connection())
    close(p$get_error_connection())

    p$kill_tree()

    p$kill()

[gaborcsardi]

An example of how I did:

This runs in ~ 150ms for me, so that is definitely weird, even if it runs. It also never crashes or hangs for me. What is your platform?

system.time({
  p <- processx::process$new('bash', c('-c', 'cd /home && R --no-save --no-restore-data --quiet -e "print(\'123\')")'), stdout = "|", stderr = "|", wd = here::here())
  p$wait()
})

This also does not crash, but finishes in ~5ms.

[avraam-inside]

It falls only occasionally. But even this is sometimes enough to cause problems.

Ubuntu in container

[gaborcsardi]

It falls only occasionally.

I just ran it ~8000 times...

Ubuntu in container

That's great, so then can you create a Dockerfile that reproduces this?

[avraam-inside]

It won't work, there's too much code, the service is on a shiny-proxy, with its own package and oun autotests and renv, the error repeats relatively rarely and there is no clear pattern how to cause it.

But after waiting for n time, I probably found the area with which it is connected - most likely with renv...

It's very strange why it climbs into CRAN. When restarting - everything works normally, the error is not repeated.

If you suddenly have ideas or have encountered them before, I will be glad to help. But it seems that the problem is not in the processx.