I can't attach any R session to VS Code when using a remote server via SSH and it can't find the binary either.

I am using a conda virtual environment for a research project conducted at a remote server which I access via SSH.

I use the [Remote SSH] (https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh) extension to connect to the host and then I need to edit R files there. The code below shows that both R and radian are correctly set, I believe:

(r_conda) [rgr6291@klc0201 bin]$ conda env list
# conda environments:
#
fomc                     /home/rgr6291/.conda/envs/fomc
r_conda               *  /home/rgr6291/.conda/envs/r_conda
rfe_paper                /home/rgr6291/.conda/envs/rfe_paper
base                     /software/python-anaconda3/2019.10

(r_conda) [rgr6291@klc0201 bin]$ which R
~/.conda/envs/r_conda/bin/R
(r_conda) [rgr6291@klc0201 bin]$ which radian
~/.conda/envs/r_conda/bin/radian

In the settings for the R extension, I have set these binaries as the RPath and the Rterm:

{
    "r.rpath.linux": "~/.conda/envs/r_conda/bin/R",
    "r.rterm.linux": "~/.conda/envs/r_conda/bin/radian"
}

However, I get errors like this one when I try to attach an R session:

Cannot find R client at ~/.conda/envs/r_conda/bin/radian. Please check r.rterm setting.

And also it complains that it can’t find the jsonlite package although it has been installed:

Failed to get list of R functions. Make sure that jsonlite is installed and r.rpath.linux points to a valid R executable.

What am I missing here?

[pgramme]

Hi !

My environment is the same as raulguarini (OP): VsCode + R extension + SSH remote shell (Linux) + R only available through a Conda environment on the remote. I haven’t tried to use radiant. After struggling a bit I just found how to use the Conda env properly, so I’m sharing it here.

In my case, the Conda environment also contains R packages (tidyverse etc) and an ODBC driver that I need to use from R. In order to use syntax highlighting from VsCode, I installed r-languageserver and r-jsonlite in my Conda environment.

Three options: the first one is a bit easier but not complete enough for me. I went for Option 3.

I hope this can help someone else! If so, maybe document it somewhere? Pierre

Option 1

In the settings for the R extension, set RPath and the Rterm: (NB: I avoided “~” in the paths, not sure if expansion would work or not)

{
    "r.rpath.linux": "/home/myself/conda/envs/my_conda_env/bin/R",
    "r.rterm.linux": "/home/myself/conda/envs/my_conda_env/bin/R"
}

Result: R is available, tidyverse also OK but not the ODBC driver is not accessible from R.

Option 2

As suggested in #623, you can try to set "r.alwaysUseActiveTerminal": true in the VsCode settings. Then manually start a terminal, Conda-activate and start R. After that you should be able to submit R commands (e.g. with Ctrl+Enter). I find it less comfortable and didn’t try it.

Option 3

Write a little shell script which first activates Conda and then starts R. I wrote it in /path/to/myproject/R-conda.sh and made it executable (chmod +x R-conda.sh)

#!/bin/bash
MY_CONDA_ENV=my_conda_env

# Optional and not related to Conda: cd to the script's dir
cd $(dirname $0)

# First we need to init conda bc ~/.bashrc is not executed when starting non-interactive shells. 
# Assuming PATH was already set by parent shell, and reusing script in profile.d/ if possible...
__conda_init_file=$(dirname $(which conda))/../etc/profile.d/conda.sh
if [ -f "$__conda_init_file" ]; then
    source "$__conda_init_file"
else
    eval "$(conda shell.bash hook 2> /dev/null)"
fi    

# Now we can activate
conda deactivate && conda activate $MY_CONDA_ENV

# And start R, passing through all command-line arguments
R "$@"

Then I pointed VsCode-R to this script in the settings:

{
    "r.rpath.linux": "/path/to/myproject/R-conda.sh",
    "r.rterm.linux": "/path/to/myproject/R-conda.sh"
}

Result: R is available, tidyverse and the ODBC driver are accessible from R.

[Yunuuuu]

Just came across this problem, I also used conda to manage R in a remote server. Since the server has network limitations and I have no root permission, I can only work R with a conda, and set some local CRAN or Bioconductor mirror to install packages. here is the detail usage list:

• use vscode to connect the server
• install R with conda in the user path
• install package use R function install.package (since I don’t want to use conda to manage R packages)
• use conda to manage the R package compiling dependencies
• use radian to provide Rterm

here is my sessionInfo() output:

R version 4.2.1 (2022-06-23)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/user/anaconda3/envs/R-release/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8
[12] LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils    
[5] datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.2.1   cli_3.4.1       
[3] tools_4.2.1      progressr_0.11.0
[5] jsonlite_1.8.3   digest_0.6.30   
[7] rlang_1.0.6     

I install R by command conda create --name R-release -c conda-forge r-base git radian here is my setting:

• vscode setting (don’t use “~”, it seems vscode won’t expand it, just use a absolute path)

    "r.alwaysUseActiveTerminal": true,
    "r.bracketedPaste": true,
    "r.lsp.debug": false,
    "r.rpath.linux": "/home/user/anaconda3/envs/R-release/bin/R",
    "r.rterm.linux": "/home/user/anaconda3/envs/R-release/bin/radian",
    "r.rterm.option": [
        "--r-binary=/home/user/anaconda3/envs/R-release/bin/R",
        "--local-history",
        "--no-save",
        "--no-restore"
    ]

• .Rprofile setting

# local CRAN and Bioconductor mirror
local({
    # set a CRAN mirror
    r <- getOption("repos")
    r["CRAN"] <- "https://mirrors.tuna.tsinghua.edu.cn/CRAN/"
    options(repos = r)
    options(BioC_mirror = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
    # since the network limitation of my remote server, I used a local `bioconductor_config.yaml`
    # downloaded from https://bioconductor.org/config.yaml
    options(BIOCONDUCTOR_CONFIG_FILE = "~/.bioconductor_config.yaml")
})
# this is important for the installation of package from R command
local({
    home_dir <- path.expand("~")
    conda_env_dir <- file.path(home_dir, "anaconda3/envs")
    set_envpath <- function(env_var, ...) {
        if (any(lengths(list(...)) > 1L)) {
            stop("Element of length one is expected", call. = FALSE)
        }
        add_path <- file.path(...)
        add_path <- path.expand(add_path)
        env_var_value <- Sys.getenv(env_var, unset = "")
        if (identical(env_var_value, "")) {
            path <- add_path
        } else {
            path <- paste0(add_path, switch(.Platform$OS.type,
                windows = ";",
                unix = ":"
            ), env_var_value)
        }
        expr <- quote(Sys.setenv())
        expr[[env_var]] <- path
        eval(expr)
    }

    # R-release environment path -----------------------------
    # conda create --name R-release -c conda-forge r-base git radian
    conda_renv <- file.path(conda_env_dir, "R-release")
    set_envpath("PKG_CONFIG_PATH", conda_renv, "lib", "pkgconfig")

    # pkg-specific PKG_CONFIG_PATH ---------------------------
    # these packages are not compitable with current conda R environment, install
    # this package in another conda environment and add the corresponding
    # PKG_CONFIG_PATH
    # gert environment variable
    # conda create -n libgit2 -c conda-forge libgit2
    libgit2 <- file.path(conda_env_dir, "libgit2")
    set_envpath("PKG_CONFIG_PATH", libgit2, "lib", "pkgconfig")
    set_envpath("LD_LIBRARY_PATH", libgit2, "lib")

    # textshaping environment variable
    # harfbuzz
    # conda create -n harfbuzz -c conda-forge harfbuzz
    harfbuzz <- file.path(conda_env_dir, "harfbuzz")
    set_envpath("PKG_CONFIG_PATH", harfbuzz, "lib", "pkgconfig")
    # fribidi
    # conda create -n fribidi -c conda-forge fribidi
    fribidi <- file.path(conda_env_dir, "fribidi")
    set_envpath("PKG_CONFIG_PATH", fribidi, "lib", "pkgconfig")
})

• .Renviron setting

LANGUAGE=en
R_HISTSIZE=500
# for I have no root permission, I use a user R library path
R_LIBS_USER=~/Rlibrary/%v
# add your conda R environment path to the `PATH` variable
PATH=/home/user/anaconda3/envs/R-release/bin:${PATH}

• last setting (optional), just for convenience of the usage of R in bash. .bashrc setting:

alias r="~/anaconda3/envs/R-release/bin/radian --r-binary ~/anaconda3/envs/R-release/bin/R"
alias R=~/anaconda3/envs/R-release/bin/R
alias Rscript=~/anaconda3/envs/R-release/bin/Rscript