[rsession-rstudio] Verify-installation, Error 4 & Endless PATH inserts on restart

[azaryc2m]

Hi!
I'm having some issues after updating to rocker/rstudio:latest recently. In order to pin the error down i was checking configs etc. in a new container. I think there might be something wrong with the configurations or the code itself. When i run a fresh container using:

docker run -e PASSWORD=somePassword -p 8787:8787 -P rocker/rstudio:latest

then "go inside" using

docker exec -it container_name bash

and run

rstudio-server verify-installation

i only get "Terminated" as an output. I thought this was a good thing (no error shown = no error) but this also could mean it terminated while trying to check - > so i looked up the system output of the container, and every time i run the verification it says:

rsession: no process found

and sometimes additionally:

s6-supervise rstudio: warning: finish script lifetime reached maximum value - sending it a SIGKILL

If this was not enough, when i log in as "rstudio" to the rstudio it works, but i get this error inside the editor:

25 Feb 2019 08:50:56 [rsession-rstudio] ERROR r error 4 (R code execution error) [errormsg=]; OCCURRED AT: rstudio::core::Error rstudio::r::exec::executeSafely(rstudio_boost::function<void()>) /home/ubuntu/rstudio/src/cpp/r/RExec.cpp:212; LOGGED FROM: void rstudio::session::{anonymous}::processEvents() /home/ubuntu/rstudio/src/cpp/session/SessionHttpMethods.cpp:91

I would provide more logs, but i cannot find those...all the information regarding the location of the log files seem to be invalid for running rstudio inside docker.

Also: I don't know if this is somehow related (i supposed it might be), but every time i restart the container, the same PATH variable gets inserted into the /usr/local/lib/R/etc/Renviron file:

PATH=/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

and this over and over again. After 4 restarts i got

PATH=/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PATH=/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PATH=/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PATH=/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

sitting there.

[cboettig]

@azaryc2s Thanks for the reports. Sounds like you have a few separate and unrelated issues here.

Regarding the repeated PATH, can you open an issue in https://github.com/rocker-org/rocker-versioned instead? That's caused by the append behavior of the userconf script, https://github.com/rocker-org/rocker-versioned/blob/master/rstudio/3.5.2/userconf.sh#L12, and while it's not hurting anything (unless you do a million restarts), it is ugly and unnecessary, so we should fix that.

Regarding the error message you see when you log in, /home/ubuntu/rstudio/src/cpp/r/RExec.cpp: etc, are you linking volumes to the local host? Are you seeing that with a fresh pull, or only when restoring / restarting the container? I ask because as you'll note, that path is not related to the Rocker image directly (there is no /home/ubuntu) but I suspect you're seeing this error due to RStudio's file-locking protocol instead. Like the above behavior, this message is completely harmless but also annoying. We switched the default locking behavior so you should see this less in recent images. I also don't think you should see this if you aren't linking to the host or another container where RStudio cannot manage the file permission locks?

It sounds like you have correctly entered the container and run rstudio-server verify-installation, and verified that you see no error messages. I agree the message Terminated is a little opaque way to say RStudio has installed correctly with no errors, but as you already gathered, that is exactly the expected behavior and no cause for concern. I couldn't quite follow what you did after that, I haven't come across s6-supervise rstudio: warning: finish script lifetime reached maximum value before, but it sounds like your RStudio instance is working just fine other than the annoying-but-harmless error message regarding the permission locks.

Hope this helps, sorry some of these things are more confusing than they need to be.