Merge branch 'install_r_packages' into 'main'

Install r packages

See merge request hub/rshiny-k8s!10

example_proj/my_packages_to_install.csv

-Package_name;Deposit_name
-shiny;cran
-shinythemes;cran
+shiny
+shinythemes

scripts/install_r_packages.R

-### Name : script_install_r_packages.R
-### Folder : /home/echapeau/Languages/rshiny/in_docker_image/first_app/scripts_R
-### Date : 20/03/2023
-### Aim : Install all packages from CRAN and BioConductor, requiered in the Shiny app.
-
-
-#### Load file with the list of packages and the name of the deposit
-packages_list <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = TRUE, sep = ";", stringsAsFactors = FALSE )
-
-### CRAN Packages
-cran_pkgs <- packages_list[which(packages_list$Deposit_name == "cran"),"Package_name"]
-### Bioconductor Packages
-bioconductor_pkgs <- packages_list[which(packages_list$Deposit_name == "bioconductor"),"Package_name"]
-
-
-### Install Packages
-if (length(cran_pkgs) >= 1) {
-  install.packages(cran_pkgs, dependencies = NA)
-}
-if (length(bioconductor_pkgs) >= 1) {
-  requireNamespace("BiocManager")
-  BiocManager::install(bioconductor_pkgs, ask = FALSE)
-}
+#!/usr/bin/env Rscript
+### Name : install_r_packages.R
+### Folder : ~/scripts
+### Date : 17/04/2023
+### Aim : Install all packages from CRAN, BioConductor or github, requiered in the Shiny app.
+
+### Install pak packages first
+install.packages(c("pak","pkgcache","pkgdepends"), dependencies= NA)
+#### Load file with the list of packages
+packages_list <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = FALSE, sep = ";", stringsAsFactors = FALSE)
+### Install packages with dependencies with pak packages
+pak::pkg_install(pkg=packages_list[,1])
+# clean the cache of pak
+pak::cache_clean()

scripts/packages_to_install.csv

-Package_name;Deposit_name
-shiny;cran
-shinythemes;cran
+shiny
+ggplot2
+limma
+tidyverse/tibble