Installation leaves me in interactive R session

[Midnighter]

I'm on an Ubuntu derivative

No LSB modules are available.
Distributor ID:	Pop
Description:	Pop!_OS 22.04 LTS
Release:	22.04
Codename:	jammy

When I install a new R version with rig, it's stuck in an interactive R session. I then need to type "enter" to see the prompt followed by q() to quit, another "enter" to see the prompt Save workspace image? [y/n/c]:.

That doesn't seem normal. Please let me know what more information you need to debug this.

[gaborcsardi]

What version of rig did you use?

[Midnighter]

Installed today

RIG -- The R Installation Manager 0.5.2

[gaborcsardi]

Interesting. Did you see any messages from R before this happened? Can you copy the full output here? Do you have anything in your .Rprofile that could cause this?

[Midnighter]

Don't have any .Rprofile on the machine, will get you the full output tomorrow.

[Midnighter]

Sorry, I got lost in work for a while. Output of rig add 4.1.1:

[INFO] Running `sudo` for adding new R versions. This might need your password.
[INFO] r-4.1.1_1_amd64.deb is cached at /tmp/rig/r-4.1.1_1_amd64.deb
[INFO] Running apt-get update
[INFO] > Hit:7 http://apt.pop-os.org/proprietary jammy InRelease
[INFO] > Hit:8 http://apt.pop-os.org/release jammy InRelease
[INFO] > Hit:9 http://apt.pop-os.org/ubuntu jammy InRelease
[INFO] > Hit:11 http://apt.pop-os.org/ubuntu jammy-security InRelease
[INFO] > Hit:12 http://apt.pop-os.org/ubuntu jammy-updates InRelease
[INFO] > Hit:13 http://apt.pop-os.org/ubuntu jammy-backports InRelease
[INFO] > Reading package lists...
[INFO] Running apt install
[INFO] >
[INFO] > WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
[INFO] >
[INFO] > Reading package lists...
[INFO] > Building dependency tree...
[INFO] > Reading state information...
[INFO] > The following NEW packages will be installed:
[INFO] >   r-4.1.1
[INFO] > 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
[INFO] > Need to get 0 B/59.1 MB of archives.
[INFO] > After this operation, 87.8 MB of additional disk space will be used.
[INFO] > Get:1 /tmp/rig/r-4.1.1_1_amd64.deb r-4.1.1 amd64 1 [59.1 MB]
[INFO] > Selecting previously unselected package r-4.1.1.
[INFO] > (Reading database ... 283782 files and directories currently installed.)
[INFO] > Preparing to unpack /tmp/rig/r-4.1.1_1_amd64.deb ...
[INFO] > Unpacking r-4.1.1 (1) ...
[INFO] > Setting up r-4.1.1 (1) ...
[INFO] Adding /usr/local/bin/R-4.1.1 -> /opt/R/4.1.1/bin/R
[INFO] Setting default CRAN mirror
[INFO] Setting up RSPM
[INFO] Setting up automatic system requirements installation.
[INFO] Installing pak for R 4.1.1 (if not installed yet)
[INFO] > ARGUMENT ' -s --vanilla -e invisible()' __ignored__
[INFO] >
[INFO] >
[INFO] > R version 4.1.1 (2021-08-10) -- "Kick Things"
[INFO] > Copyright (C) 2021 The R Foundation for Statistical Computing
[INFO] > Platform: x86_64-pc-linux-gnu (64-bit)
[INFO] >
[INFO] > R is free software and comes with ABSOLUTELY NO WARRANTY.
[INFO] > You are welcome to redistribute it under certain conditions.
[INFO] > Type 'license()' or 'licence()' for distribution details.
[INFO] >
[INFO] >   Natural language support but running in an English locale
[INFO] >
[INFO] > R is a collaborative project with many contributors.
[INFO] > Type 'contributors()' for more information and
[INFO] > 'citation()' on how to cite R or R packages in publications.
[INFO] >
[INFO] > Type 'demo()' for some demos, 'help()' for on-line help, or
[INFO] > 'help.start()' for an HTML browser interface to help.
[INFO] > Type 'q()' to quit R.
[INFO] >

[gaborcsardi]

Hmmm, it does not happen for me, can you run these are show me the output?

dpkg -l | grep sudo
sudo --version

Thanks!

[Midnighter]

Okay, it has something to do with zsh or oh-my-zsh. When I create a bash shell and run rig add, it works as expected.

[gaborcsardi]

I can indeed reproduce it with oh-my-zsh.

root@27f1e394aaf1:~# su bashuser -- /opt/R/4.1.3/bin/R -s --vanilla -e 'getRversion()'
[1] '4.1.3'
root@27f1e394aaf1:~# su -s /bin/sh gaborcsardi -- /opt/R/4.1.3/bin/R -s --vanilla -e 'getRversion()'
[1] '4.1.3'

root@27f1e394aaf1:~# su gaborcsardi -- /opt/R/4.1.3/bin/R -s --vanilla -e 'getRversion()'
ARGUMENT ' -s --vanilla -e getRversion()' __ignored__

[gaborcsardi]

Even simpler:

root@27f1e394aaf1:~# bash /opt/R/4.1.3/bin/R -s --vanilla -e 'getRversion()'
[1] '4.1.3'
root@27f1e394aaf1:~# zsh /opt/R/4.1.3/bin/R -s --vanilla -e 'getRversion()'
ARGUMENT ' -s --vanilla -e getRversion()' __ignored__

[gaborcsardi]

We could probably pass -s /bin/sh to su, that should work as long as /bin/sh is present, and it should be present. We'll do this in the next version.

[Midnighter]

Awesome, glad you found the cause and solution.

[gaborcsardi]

Well, thanks to the oh my zsh tip, I would have never thought of that.... and it probably should not matter, meaning that it is a bug in oh my zsh?

[Midnighter]

It must be one of the plugins evaluating the command options but I wouldn't know which one. It seems like a bug to me, too.

I'm on a different system now. Have you tried the following?

zsh -c "/opt/R/4.1.3/bin/R -s --vanilla -e 'getRversion()'"

[gaborcsardi]

Yeah, -c does work, I could do su -c, but the issue with that is that I'll have to pass a full command line, escaped for the shell.

It is much easier to pass the plain unescaped arguments.