In jimrothstein/jimTools: Misc Tools I Find Useful

knitr::opts_chunk$set(echo = TRUE,  
                                            comment="      ##",  
                                            error=TRUE, 
                                            collapse=TRUE) 
library(data.table)
library(magrittr)

Problem

Normally, I use neovim + plugin nvim-R as my IDE. Recently I tried to install RStudio but ran into errors.

Directories

Seems each time I update R, I run into trouble with one or more directories that R uses. The reasons probably relate to the past of switching from RStudio to neovim or compiling from source one time and using binaries the next.

Over time, my R setup has collected diretories with various permuations of "lib", "library", "local." Rather than sort it all out, I decided to remove R and begin again.

I found this the Ubuntu/Debian instructions helpful: https://ftp.osuosl.org/pub/cran/bin/linux/debian, which explains some of R environmental variables.

Organization

So here I collect useful R environment variables I found to be important. To ease navigation, I also set shell environment variables (I use zsh ) to match R.

Of course, your experience will differ, but getting a good grasp on the R environment variables may avoid some future pain.

R_env  <- c("R_HOME", 
            "R_LIBS_USER", 
            "R_LIBS_SITE",
            NA,
            NA) 

paths  <- c("/usr/lib/R/",
            "/home/jim/R/x86_64-pc-linux-gnu-library/4.1/",
            "/usr/lib/R/library/",
            "/etc/R/Renviron",
            "~/.Renviron")

zsh_env  <- c("R_HOME", 
            "R_LIBS_USER", 
            "R_LIBS_SITE",
            NA,
            NA)



dt  <- data.table(R_env = R_env,
                  path = paths,
                  zsh_env = zsh_env)

dt %>% knitr::kable()

Special notes

Ending slash indicates a directory: (/usr/lib/R/library/)
No ending slash indicates a file: ( ~/.Renviron )
The file Renviron in directory /etc/R/ sets many environment variables, including $R_LIBS_SITE. $R_LIBS_SITE is important because it designates a base one more directories for R packages.
I pruned $R_LIBS_SITE to include only one directory: /usr/lib/R/library/
Because there are a couple of ways to install R packages (from Debian, from source, from inside R, ...) I may decide later to modify this.
(future) There are other environment variables that may be useful, for example R_ENVIRON, R_ENVIRON_USER but I did not use these.

Checking

Here is one way to confirm which directories R is using for packages.

.libPaths()

Another way is through Sys.getenv() to find R env variables

R_HOME
R_LIBS_SITE
R_LIBS_USER

s  <- Sys.getenv()
names  <- names(s)
head(names)
head(s[grep(pattern = "^R", x = names)])
s[grep(pattern = "^R_LIBS", x = names)]

s[grep(pattern = "^R_LIBS", x = names)]

if (F) help(.libPaths)

Troubleshooting

R --vanilla, skips profile and any user set R environment variables.

knitr::knit_exit()

(got me into trouble) Upgrade R from 4.0.3 to 4.0.4

on Rpi 400
from source, *.tar.gz
follow directions (R install & admin guide)
tar -rf | .configure etc
last step sudo make install, seemd to put it together (so running R opens 4.0.4
Directories ! Still confused. No need to sweat.
3 directories most important, ~/R/armv71.....-library/4.0/ (pkgs I add) /usr/local/lib/R/ where R prefers R_HOME be (leave it alone!)
run try_things_here/0088_base package commands. (shows which dir/which pkgs)

{
file <- "/home/jim/code/jimTools/rmd/0999_R_upgrade_notes.rmd"
file <- "rmd/0999_R_upgrade_notes.rmd"
file  <- basename(file)
file
file  <- paste0("rmd/",file)
file
}
file <- "rmd/0999_R_upgrade_notes.rmd"
rmarkdown::render(file, 
                  output_format="html_document",
                  #output_format="pdf_document",
                  output_dir="~/Downloads/print_and_delete")