Install all R packages loaded in any files within a folder

Rpkginstall

#!/bin/bash

# This concatenates array values using a multi-character separater. 
# https://dev.to/meleu/how-to-join-array-elements-in-a-bash-script-303a
joinByString() {
  local separator="$1"
  shift
  local first="$1"
  shift
  printf "%s" "$first" "${@/#/$separator}"
}

# Get all packages loaded in qmd files in any subdirectory of the current directory
grep -r --include=*.qmd --include=*.R --include=*.Rmd "library(" | \
# Split filename from line of the file, keep matching line
awk -F: '{print $2}' | \
# Remove leading spaces and tabs
awk '{gsub(/^[ \t]+/,"", $0); print}' | \
# Remove comments after the library() statement
awk -F# '{print $1}' | \
# Remove any suppressXXX() commands, e.g. suppressPackageStartupMessages
sed 's/suppress.*\((.*)\)/\1/' | \
# Remove library() from around package name
sed 's/library(\(.*\)).*/\1/' | \
# Remove any quotes from around package name
sed -e 's/["()]//g' | \
sed -e "s/'//g" | \
# Remove any lines that have characters other than A-z,0-9,and .
grep -v -P '[^A-z0-9\.]' | \
# Remove any lines that have \n in the middle of the package name
grep -v -P '\n' | \
# Remove any lines that have brackets/_
grep -v -P '[\[\]_]' | \
# Remove any lines with non-ASCII characters
grep -v -P "[\x80-\xFF]" | \
# Remove any lines starting with a number -- not valid R packages
grep -v "^[0-9]" | \
# Sort packages and keep unique packages only
sort --uniq | \
# Load into a BASH Array
readarray -t pkgs

# Create an install script and make it executable as R code
echo "install.packages(c('"$(joinByString "', '" ${pkgs[@]})"'), deps=T)" > pkg_install.R
sed -i '1 i #!/usr/bin/Rscript' pkg_install.R
chmod +x pkg_install.R

# Run install script and save output/errors to separate files
./pkg_install.R > pkg_install_output.text 2> pkg_install_errors.txt