Cannot find compatible Local environment version of R when deploying to RStudio Connect

[mthomas]

Getting a seemingly obvious error (that I can't figure out how to troubleshoot) when trying to deploy any content to RStudio Connect on Apache Ubuntu 20.04 server.

"Cannot find compatible environment: no compatible Local environment with R version 4.1.2"

We specified R 4.1.2 in the manifest.json file, and R 4.1.2 is on PATH of the server. Any help would be greatly appreciated!

[rstub]

Which versions of R do you have installed on the server and where are they located? Which R versions are recognized by Connect, i.e. which are shown at the bottom of the "Documentation" tab? Do you use any RVersion* settings in /etc/rstudio-connect/rstudio-connect.gcfg?

[mthomas]

I see R installed in 2 places:

/usr/lib/R -- version 3.6.3 (this is the version of R that RStudio Connect is using)
/opt/R -- version 4.1.2 (this is the version of R that I would like RStudio Connect to use instead)

Note that the version of R on the PATH is also 4.1.2.

The "Documentation" tab shows only version 3.6.3 recognized.

Is it an acceptable solution to update the version of R at /usr/lib/R to a newer version (e.g., 4.1.2)? If so, are there any best practices for executing that update safely?

I did try adding the following line to the /etc/rstudio-connect/rstudio-connect.gcfg file:

[Server]
RVersion = /opt/R/4.1.2

And I restarted the service via sudo systemctl restart rstudio-connect, but the issue still remains (can only find 3.6.3 on deployment from RStudio IDE, and the "Documentation" tab still only shows 3.6.3)

However, when I add RVersionScanning = false to that block, it breaks RStudio Connect altogether (I receive a 503 error in the browser)

[rstub]

Interesting, do you get any errors in the log file? Maybe some of the file permissions are to tight? You can check that with namei -l $(which R).

[mthomas]

Here's what I get when I try checking the file permissions as you described:

root@inresgb-0002:/# namei -l $(which R)
f: /usr/local/bin/R
drwxr-xr-x root root /
drwxr-xr-x root root usr
drwxr-xr-x root root local
drwxr-xr-x root root bin
lrwxrwxrwx root root R -> /opt/R/4.1.2/bin/R
drwxr-xr-x root root   /
drwxr-xr-x root root   opt
drwxr-xr-x root root   R
drwxr-xr-x root root   4.1.2
drwxr-xr-x root root   bin
-rwxr-xr-x root root   R

[rstub]

Thanks, the permissions seem to be correct. Any error messages in the server log?

[mthomas]

I really appreciate the continued help, Ralf!

Here's what I see for error messages in the server log -- this might be helpful:

2022/04/06 17:15:18 Could not detect R at /opt/R/4.1.2/bin/R: Could not run R as rstudio-connect; exit status 1; received output: '/opt/R/4.1.2/bin/R: line 1                  93: /usr/bin/sed: No such file or directory
ERROR: option '-e' requires a non-empty argument'
2022/04/06 17:15:18 Could not detect R at /opt/R/4.1.2/bin/R: Could not run R as rstudio-connect; exit status 1; received output: '/opt/R/4.1.2/bin/R: line 1                  93: /usr/bin/sed: No such file or directory
ERROR: option '-e' requires a non-empty argument'
2022/04/06 17:15:18 Detected R version 3.6.3 at /usr/lib/R/bin/R
2022/04/06 17:15:18 Warning: Using system-provided R (/usr/lib/R/bin/R, discovered via Server.RVersionScanning) is not recommended. Installing the desired R                   versions from source will help avoid unexpected version changes. Use Server.RVersion to enumerate the different R installations on this server. See https://d                  ocs.rstudio.com/connect/admin/getting-started/#installation.

I assume it is trying to use the R version I specified in the rstudio-connect.gcfg file, but is expecting some directory (usr/bin/sed) that doesn't exist?

[mthomas]

I'm not sure if this helps either, but there are a lot more files in /usr/lib/R/bin (which is where RStudio Connect is getting R) than there are in /opt/R/4.1.2/bin/ (which is where I want RStudio Connect to get R from)

[rstub]

It is looking for the sed program in /usr/bin/sed. It is unusual that this file does not exist. Is sed installed? You can test that with which sed and dpkg -l sed. If it is not installed, you can use sudo apt-get install sed to install it.

[mthomas]

Here's what I get from running those two commands:

root@inresgb-0002:/# which sed
/bin/sed

and

root@inresgb-0002:/# dpkg -l sed
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name           Version      Architecture Description
+++-==============-============-============-=================================================
ii  sed            4.7-1        amd64        GNU stream editor for filtering/transforming text

It looks like sed is installed at /bin/sed (but not at /usr/bin/sed, where RStudio Connect is looking for it), but perhaps it is also corrupt based upon some of the output from the second command above?

[aron]

This is really interesting. The script that launches R expects /usr/bin/sed, which is determined when R is configured and built. How was your server provisioned? What R install are you using?

For reference, the ubuntu:20.04 Docker image has /bin as a symbolic link to /usr/bin, meaning /bin/sed and /usr/bin/sed are both valid paths, even though the sed package only installs into /bin/sed.

The symlinking of /bin and /usr/bin appears to be the case for new Ubuntu installs, but perhaps not upon upgrades. Why are /bin and /sbin now symlinks in Ubuntu 20.04? - Ask Ubuntu

For now, I would recommend creating a symlink from /usr/bin/sed to /bin/sed.

[aron]

One other breadcrumb: R determines the location of sed when it is configured and built; that system probably finds /usr/bin/sed first and uses that going forward.
https://github.com/wch/r-source/blob/7c286ab419c0be5fddfd50c71a3fd8b228751631/configure.ac#L679-L680

[mthomas]

Creating the symlink solved the issue! I can't thank you enough for the help @aron & @rstub ! This was clearly over my head and a good reminder to always check the logs first...

Thank you again so much.