rig fails to install R due to libraries referred to in .Rprofile with user library set in .profile

[MilesMcBain]

The package it's looking for is referred to in my .Rprofile and is stored in my user library. I set my user library in my ~/.profile.

So rig probably needs to run the R session for installation of {pak} as --vanilla?

Install output from server running Ubuntu 18.04:

rig add 4.2.1
[INFO] r-4.2.1_1_amd64.deb is cached at /tmp/rig/r-4.2.1_1_amd64.deb
[INFO] Running apt-get update
[INFO] > Get:1 file:/var/cuda-repo-9-0-local  InRelease
[INFO] > Ign:1 file:/var/cuda-repo-9-0-local  InRelease
[INFO] > Get:2 file:/var/cuda-repo-9-0-local  Release [574 B]
[INFO] > Get:2 file:/var/cuda-repo-9-0-local  Release [574 B]
[INFO] > Get:3 https://nvidia.github.io/libnvidia-container/ubuntu18.04/amd64  InRelease [1,484 B]
[INFO] > Get:4 https://nvidia.github.io/nvidia-container-runtime/ubuntu18.04/amd64  InRelease [1,481 B]
[INFO] > Get:5 https://nvidia.github.io/nvidia-docker/ubuntu18.04/amd64  InRelease [1,474 B]
[INFO] > Hit:7 https://download.docker.com/linux/ubuntu bionic InRelease
[INFO] > Hit:8 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ InRelease
[INFO] > Ign:9 https://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/3.4 InRelease
[INFO] > Hit:10 http://archive.ubuntu.com/ubuntu bionic InRelease
[INFO] > Hit:11 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic InRelease
[INFO] > Hit:12 https://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/3.4 Release
[INFO] > Get:13 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
[INFO] > Get:14 https://pkgs.tailscale.com/stable/ubuntu bionic InRelease
[INFO] > Get:15 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
[INFO] > Hit:16 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu bionic InRelease
[INFO] > Get:17 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
[INFO] > Hit:19 http://ppa.launchpad.net/timescale/timescaledb-ppa/ubuntu bionic InRelease
[INFO] > Hit:20 http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu bionic InRelease
[INFO] > Fetched 262 kB in 3s (83.8 kB/s)
[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] > 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 99 not upgraded.
[INFO] > After this operation, 0 B of additional disk space will be used.
[INFO] > Get:1 /tmp/rig/r-4.2.1_1_amd64.deb r-4.2.1 amd64 1 [59.6 MB]
[INFO] > (Reading database ... 299620 files and directories currently installed.)
[INFO] > Preparing to unpack /tmp/rig/r-4.2.1_1_amd64.deb ...
[INFO] > Unpacking r-4.2.1 (1) over (1) ...
[INFO] > Setting up r-4.2.1 (1) ...
[INFO] Setting default CRAN mirror
[INFO] Setting up RSPM
[INFO] Setting up automatic system requirements installation.
[INFO] Installing pak for R 4.2.1 (if not installed yet)
[INFO] > Error in loadNamespace(x) : there is no package called ‘paint’
[INFO] > Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
[INFO] > Execution halted
[ERROR] Failed to to install pak for R 4.2.1: command ["su", "mmcbain", "--", "/opt/R/4.2.1/bin/R", "-s", "-e", "invisible()"] exited with code 1

[MilesMcBain]

As a temporary work around I renamed ~/.Rprofile.

[gaborcsardi]

This is specific to Linux, when not running as root. The rest of the cases have --vanilla already.