Package Manager - unable to find R

[SamEdwardes]

Background

When using the Helm charts I was having trouble with Package Manager. After doing some research:

• The helm charts and docker image expect R 3.6.2
• The docker image has R 4.2.0

docker run -it --rm rstudio/rstudio-package-manager:jammy-2022.11.4 /bin/sh
ls -la /opt/R
# drwxr-xr-x 5 root root 4096 Apr  3 00:37 4.2.0

Reprex

docker run -it \
    -p 4242:4242 \
    -e RSPM_LICENSE=$RSPM_LICENSE \
    rstudio/rstudio-package-manager:jammy-2022.11.4

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
+ trap deactivate EXIT
+ RSPM_LICENSE_FILE_PATH=/etc/rstudio-pm/license.lic
+ /opt/rstudio-pm/bin/license-manager initialize --userspace
TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to ''.
Error beginning a trial: (51): The trial has expired. You must request a trial extension from RStudio customer support.
+ true
+ '[' -z ES3X-AD28-92YJ-PBKR-FCN3-G2M8-GSTA ']'
+ /opt/rstudio-pm/bin/license-manager activate ES3X-AD28-92YJ-PBKR-FCN3-G2M8-GSTA --userspace
TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to ''.

Status: Activated
Product-Key: ES3X-AD28-92YJ-PBKR-FCN3-G2M8-GSTA
Has-Key: Yes
Has-Trial: Yes
Max-Repo-Count: 0
Expiration: 2024-03-03 00:00:00
Days-Left: 321
License-Engine: 4.4.3.0
License-Scope: User

+ unset RSPM_LICENSE
+ unset RSPM_LICENSE_SERVER
+ /opt/rstudio-pm/bin/rstudio-pm --config /etc/rstudio-pm/rstudio-pm.gcfg
time="2023-04-17T19:30:49.032Z" level=info msg="Resource limits: {\"nofile\":{\"soft\":1048576,\"hard\":1048576}}"
2023/04/17 19:30:49 Starting Posit Package Manager v2022.11.4-20
2023/04/17 19:30:49 Using cache version 11
2023/04/17 19:30:49 Using metrics cache version 1
time="2023-04-17T19:30:49.046Z" level=info msg="Loading server configuration from /etc/rstudio-pm/rstudio-pm.gcfg"
2023/04/17 19:30:49 Using data directory: /var/lib/rstudio-pm
2023/04/17 19:30:49 Creating database directory: /var/lib/rstudio-pm/db
2023/04/17 19:30:49 Creating packages directory: /var/lib/rstudio-pm/packages
2023/04/17 19:30:49 Creating cran directory: /var/lib/rstudio-pm/cran
2023/04/17 19:30:49 Creating bioconductor directory: /var/lib/rstudio-pm/bioconductor
2023/04/17 19:30:49 Creating binaries directory: /var/lib/rstudio-pm/binaries
2023/04/17 19:30:49 Creating pypi directory: /var/lib/rstudio-pm/pypi
2023/04/17 19:30:49 Creating cache directory: /var/lib/rstudio-pm/cache
2023/04/17 19:30:49 Creating launcher directory: /var/lib/rstudio-pm/launcher
2023/04/17 19:30:49 Creating metrics directory: /var/lib/rstudio-pm/metrics
2023/04/17 19:30:49 Creating launcher directory: /var/lib/rstudio-pm/launcher_internal
2023/04/17 19:30:49 Using launcher directory: /var/lib/rstudio-pm/launcher
2023/04/17 19:30:49 Creating launcher_logs directory: /var/lib/rstudio-pm/launcher_internal/custom_logs
2023/04/17 19:30:49 Creating launcher_logs_user directory: /var/lib/rstudio-pm/launcher_internal/custom_logs/rstudio-pm
2023/04/17 19:30:50 Creating git directory: /var/lib/rstudio-pm/git
2023/04/17 19:30:50 Creating staging directory: /var/lib/rstudio-pm/packages/staging
2023/04/17 19:30:50 Warning: SSL is not configured. Using Package Manager over insecure HTTP is not recommended.
2023/04/17 19:30:50 A new PPM encryption key was created at '/var/lib/rstudio-pm/rstudio-pm.key'.
2023/04/17 19:30:50 Using HTTP access log: /var/log/rstudio/rstudio-pm/rstudio-pm.access.log
2023/04/17 19:30:50 No Server.Address configured, so we won't be able to direct your users back to this server.
2023/04/17 19:30:50 API Token authentication disabled
2023/04/17 19:30:50 Fetched package retention is on for CRAN
2023/04/17 19:30:50 Fetched package retention is on for Bioconductor
2023/04/17 19:30:50 Fetched package retention is on for PyPI
2023/04/17 19:30:50 Starting HTTP listener on :4242
2023/04/17 19:30:50 Starting admin service using sock file /var/run/rstudio-pm/rstudio-pm.sock
2023/04/17 19:30:50 Service ready to listen for requests
2023/04/17 19:30:50 Service mode file not found
2023/04/17 19:30:50 Starting Posit Package Manager Services
2023/04/17 19:30:50 Starting licensing...
2023/04/17 19:30:51 Usage data enabled
2023/04/17 19:30:51 Info: Unable to use user namespace sandboxing: "Error running the reexec.Command for [nsParent  echo]: fork/exec /proc/self/exe: invalid argument"
2023/04/17 19:30:51 Operating system:         ubuntu
2023/04/17 19:30:51 Operating system version: 22.04
2023/04/17 19:30:51 Kernel version:           5.15.49-linuxkit
2023/04/17 19:30:51 You are using a supported kernel (5.15.49-linuxkit), but user namespaces are not supported: reason unknown.
2023/04/17 19:30:51 Info: User namespaces are not supported on this system so Git builds will be run without process isolation/sandboxing.
2023/04/17 19:30:51 R version specified in Server.RVersion cannot be analyzed: /opt/R/3.6.2/: stat /opt/R/3.6.2/: no such file or directory
2023/04/17 19:30:51 Stopping: metrics janitor...
2023/04/17 19:30:51 Stopping: license manager...
2023/04/17 19:30:51 Stopping: metrics buffer...
2023/04/17 19:30:51 Done Stopping: license manager
2023/04/17 19:30:51 Done Stopping: metrics janitor
2023/04/17 19:30:51 Done Stopping: metrics buffer
2023/04/17 19:30:51 Stopped Posit Package Manager Online Services
2023/04/17 19:30:51 Error running services: Error: Unable to use R on this system: Could not locate an R installation
2023/04/17 19:30:51 Gracefully shutting down, received signal to terminate
2023/04/17 19:30:51 Stopping: signal dumper...
2023/04/17 19:30:51 Done Stopping: signal dumper
2023/04/17 19:30:51 Exited Posit Package Manager
+ deactivate
+ echo 'Deactivating license ...'
Deactivating license ...
+ is_deactivated=0
+ retries=0
+ [[ 0 -ne 1 ]]
+ [[ 0 -le 3 ]]
+ /opt/rstudio-pm/bin/license-manager deactivate --userspace
+ is_deactivated=1
+ (( retries+=1 ))
++ ls -A /home/rstudio-pm/.local
+ for file in $(ls -A /home/rstudio-pm/.local)
+ '[' -s /home/rstudio-pm/.local/.c773c155981f38032a617.51222781 ']'
+ [[ 1 -ne 1 ]]

[tnederlof]

I see this is in the config hard coded, does this need to be updated along with the actual version installed into /opt/R?

https://github.com/rstudio/rstudio-docker-products/blob/dev/package-manager/rstudio-pm.gcfg#L14

[SamEdwardes]

The actual version installed into /opt/R is 4.2.0. So I think we should:

• Update the docker image to hard code in 4.2.0
• Update the helm values.yaml to not override this value

[bdeitte]

Heads up @tylfin and @rodrigobrim if you have any thoughts on this

[rodrigobrim]

Hi, @SamEdwardes.

Can you try setting the R version on your Helm values.yaml?

  config:
    Server:
      RVersion: /opt/R/4.2.0

[SamEdwardes]

Yes, I can confirm it works if you override the default with:

config:
    Server:
      RVersion: /opt/R/4.2.0

But the default config in the Dockerfile points to an old version of R:

$ docker run -it --rm rstudio/rstudio-package-manager:jammy-2022.11.4 /bin/sh

$ cat /etc/rstudio-pm/rstudio-pm.gcfg
; RStudio Package Manager configuration file

[Server]
; Address is a public URL for this RStudio Package Manager server. Must be configured
; to enable features like including links to your content in emails. If
; Package Manager is deployed behind an HTTP proxy, this should be the URL for Package Manager
; in terms of that proxy.
;
; Address = https://rstudio-pm.company.com
Address =
;
; Git sources require a configured R installation. R is often installed at `/usr/lib/R`
; or `/usr/lib64/R`.
RVersion = /opt/R/3.6.2/
;
; Customize the data directory if necessary. This is where all packages and metadata are
; stored by default. Refer to Admin Guide for details.
;DataDir = /mnt/rspm/data
;
; Use a consistent location for the Launcher directory. The default location
; is based on the hostname, and the hostname may be different in each container.
; When customizing the data directory, this should be set to {DataDir}/launcher_internal
LauncherDir = /var/lib/rstudio-pm/launcher_internal

[HTTP]
; RStudio Package Manager will listen on this network address for HTTP connections.
Listen = :4242

[HTTPS]
; Path to a TLS certificate file. If the certificate is signed by a certificate authority, the
; certificate file should be the concatenation of the server's certificate followed by the CA's
; certificate. Must be paired with `HTTPS.Key`.
;Certificate = ""
;
; Path to a private key file corresponding to the certificate specified with `HTTPS.Certificate`.
; Required when `HTTPS.Certificate` is specified.
;Key = ""

[CRAN]
; Customize the default schedule for CRAN sync.
;SyncSchedule = "0 0 * * *"

[Bioconductor]
; Customize the default schedule for Bioconductor syncs.
;SyncSchedule = "0 2 * * *"

[PyPI]
; Customize the default schedule for PyPI syncs.
;SyncSchedule = "0 1 * * *"

; Configure Git if you are intending to build and share packages stored in Git repositories.
[Git]
; The amount of time to wait between polling git repos to look for package changes.
;PollInterval = 5m
;
; The maximum number of times to attempt building a git package when the build fails.
;BuildRetries = 3
AllowUnsandboxedGitBuilds = true

[bschwedler]

Docker image fixes have been implemented. Just need helm chart released in rstudio/helm#402

[fh-mthomson]

Any updates on including this in the Helm chart? thank you!

[jvroberts]

@tylfin @shepherdjerred
Now that PPM has autodetection of R/Python, should our Helm charts default to relying on that, rather than hard-coding paths as the default, to make them more reliable/future-proof?

[shepherdjerred]

That would make sense, Joe. We can remove the Server.RVersion in our values.yaml file. This will cause the property to be unset, which will default to auto-detection.

The Docker image has R installed, so it would be successfully detected. We already take the auto-detection approach for the vanilla Docker image.

[SamEdwardes]

I made a PR to the helm chart that will by default, have PPM use the R and Python auto-detection (rstudio/helm#474).

However, we should also make changes to this repo. The two PPM config files:

• https://github.com/rstudio/rstudio-docker-products/blob/dev/package-manager/rstudio-pm.gcfg
• https://github.com/rstudio/rstudio-docker-products/blob/dev/package-manager/rstudio-pm-float.gcfg

Should be updated to use these settings:

[Server]
# An empty string will configure Package Manager to autodetect Python
PythonVersion = 
# An empty string will configure Package Manager to autodetect R
RVersion =