rserver executable not found

[frederikziebell]

Container image name

rocker/rstudio:4.2.1

Container image digest

No response

What operating system are you seeing the problem on?

Linux

System information

• singularity version 3.7.0-1.el7
• linux 3.10.0-1160.11.1.el7.x86_64

Bug description

Running the rserver command inside a singulartiy container gives a FATAL: "rserver": executable file not found in $PATH error.

How to reproduce this bug?

singularity pull docker://rocker/rstudio:4.2

singularity exec rstudio_4.2.sif rserver

Note: The issue does not occurr in rocker/rstudio:4.1.

[eitsupi]

Sorry for causing this.

I think we can avoid this by specifying absolute paths as like /usr/lib/rstudio-server/bin/rserver for now.

[frederikziebell]

When connecting to the session, i.e. opening localhost:8787, the server issues an error /etc/rstudio/rsession.sh: 4: exec: rsession: not found. @eitsupi could this be related to the same issue?

[eitsupi]

@frederikziebell Yes, this is because /usr/lib/rstudio-server/bin was removed from the environment variable PATH by #535.
All paths must be absolute except for rstudio-server, where a symbolic link was created by #535.
(It makes sense to use absolute path for rstudio-server as well, to be on the safe side.)

$ find /usr/lib/rstudio-server/bin -maxdepth 1 -perm -111 -type f
/usr/lib/rstudio-server/bin/crashpad_handler
/usr/lib/rstudio-server/bin/rserver-pam
/usr/lib/rstudio-server/bin/pam-helper
/usr/lib/rstudio-server/bin/crash-handler-proxy
/usr/lib/rstudio-server/bin/rpostback
/usr/lib/rstudio-server/bin/crashpad_http_upload
/usr/lib/rstudio-server/bin/rsession
/usr/lib/rstudio-server/bin/r-ldpath
/usr/lib/rstudio-server/bin/rserver
/usr/lib/rstudio-server/bin/rstudio-server

I made the change without knowing that singularity users use these.......

[frederikziebell]

Thanks, so I guess the fix is to just update https://github.com/rocker-org/rocker-versioned2/tree/master/scripts/rsession.sh

[eitsupi]

@frederikziebell Are you using this file?
As discussed here (#470 (comment)), this file is not maintained and I was thinking we should remove it.

[frederikziebell]

I don't know. I just saw that my error was related to rsession.sh and assumed it would be copied to /etc/rstudio/ when the image is created. Do you know how the R session is initiated after logging in to localhost:8787?

[BEFH]

Is there any reason we can't just revert #535 and add /usr/lib/rstudio-server/bin/ to PATH again?

[eitsupi]

I don't know. I just saw that my error was related to rsession.sh and assumed it would be copied to /etc/rstudio/ when the image is created. Do you know how the R session is initiated after logging in to localhost:8787?

The file rsession.sh does not exist in rocker/rstudio.
If you are using singularity with the procedure described on the following page, it seems to be defined in the following line
https://github.com/rocker-org/website/blob/cddd1b2f333018739712b3143c46beb3e4f7bc9d/use/singularity.md?plain=1#L90-L95

Is there any reason we can't just revert #535 and add /usr/lib/rstudio-server/bin/ to PATH again?

I do not want to add it to the PATH again for several reasons.

1. Since this repository divides functionality on a per-script basis, it should rely as little as possible on the PATH environment variable, which is impossible to set just by executing scripts.
   

   rocker-versioned2/README.md

   Lines 100 to 106 in 37b57ec

   	For instance, if one wishes to install Shiny Server on top of a base of `rocker/rstudio:4.0.0`,
   	one could write a simple Dockerfile as follows:
   	```Dockerfile
   	FROM rocker/rstudio:4.0.0
   	RUN /rocker_scripts/install_shiny_server.sh
   	```

2. RStudio Server works fine without setting PATH.
3. To reduce the effort of definition file maintenance.

[BEFH]

That seems reasonable to me. What about symlinking rserver, and maybe 1 or 2 other relevant executables into a directory on the default search path?

…

On Tue, Sep 13, 2022, 9:41 AM eitsupi ***@***.***> wrote: I don't know. I just saw that my error was related to rsession.sh and assumed it would be copied to /etc/rstudio/ when the image is created. Do you know how the R session is initiated after logging in to localhost:8787 ? The file rsession.sh does not exist in rocker/rstudio. If you are using singularity with the procedure described on the following page, it seems to be defined in the following line https://github.com/rocker-org/website/blob/cddd1b2f333018739712b3143c46beb3e4f7bc9d/use/singularity.md?plain=1#L90-L95 Is there any reason we can't just revert #535 <#535> and add /usr/lib/rstudio-server/bin/ to PATH again? I do not want to add it to the PATH again for several reasons. 1. Since this repository divides functionality on a per-script basis, it should rely as little as possible on the PATH environment variable, which is impossible to set just by executing scripts. https://github.com/rocker-org/rocker-versioned2/blob/37b57ec4c419967ce7e78105464b1b1a054cfac1/README.md?plain=1#L100-L106 2. RStudio Server works fine without setting PATH. 3. To reduce the effort of definition file maintenance. — Reply to this email directly, view it on GitHub <#538 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZ2Z2BSMNLHITCEIVHEURDV6CAABANCNFSM6AAAAAAQKIRZGM> . You are receiving this because you commented.Message ID: ***@***.***>

[eitsupi]

What about symlinking rserver, and maybe 1 or 2 other relevant executables into a directory on the default search path?

That's definitely a good idea, but I don't know which executables would be useful to have on the PATH (I don't use any of them).

@cboettig Any thoughts?

[frederikziebell]

@eitsupi Then it seems symlinking rsession in addition to rserver would solve the singularity issue.

[eitsupi]

Then it seems symlinking rsession in addition to rserver would solve the singularity issue.

I am wondering if rsession is an executable that is intended to be run directly by the users.
If it is only used on scripts, wouldn't it just be enough to use an absolute path?

[frederikziebell]

Yes that makes sense, thanks!

[BEFH]

Personally, I would only use the rserver link, but I've migrated my recipes to use the absolute path. Maybe start with just rserver unless someone does a feature request?

[eitsupi]

Ok, I am still a bit dubious about rserver being on the PATH, but I made the change to add the sym link of rserver in the PR #541 as there seems to be a lot of demand for it.