Draft: New install r pkgs

scripts/install_r_packages.R

@@ -4,11 +4,11 @@
 ### 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)
+### Install pak packages first with somes dependencies and repos option
+install.packages(c("pak","pkgcache","pkgdepends","pillar"), dependencies= NA, repos = "https://cran.r-project.org")
 #### Load file with the list of packages
-packages_list <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = FALSE, sep = ";", stringsAsFactors = FALSE)
+packages_list <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = TRUE, sep = ";", stringsAsFactors = FALSE)
 ### Install packages with dependencies with pak packages
-pak::pkg_install(pkg=packages_list[,1])
+pak::pkg_install(pkg=packages_list$Package_name)
 # clean the cache of pak
 pak::cache_clean()