From 3a82fa736901897fe60122df9981b7a46cc148a0 Mon Sep 17 00:00:00 2001
From: Elodie Chapeaublanc <elodie.chapeaublanc@pasteur.fr>
Date: Thu, 22 Aug 2024 14:59:10 +0200
Subject: [PATCH] =?UTF-8?q?=F0=9F=93=A6=20=F0=9F=94=A7=20Modify=20configur?=
=?UTF-8?q?ation=20file=20for=20installation=20of=20R=20packages?=
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---
scripts/install_r_packages.R | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/scripts/install_r_packages.R b/scripts/install_r_packages.R
index b7c4659..f3e42e9 100644
--- a/scripts/install_r_packages.R
+++ b/scripts/install_r_packages.R
@@ -1,10 +1,10 @@
#!/usr/bin/env Rscript
### Name : install_r_packages.R
### Folder : ~/scripts
-### Date : 17/04/2023
+### Date : 22/08/2024 from previous version 17/04/2023
### Aim : Install all packages from CRAN, BioConductor or github, requiered in the Shiny app.
-### Install pak packages first
+### Install some first pakcages included pak
# Specify your packages
my_packages <- c("pak","pkgcache","pkgdepends","pillar", "shinipsum")
# Extract not installed packages
@@ -18,16 +18,20 @@ if(length(not_installed)){
print("packages previously installed in the basic image")
}
-#### Load file with the list of packages
-packages_list <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = TRUE, sep = ";", stringsAsFactors = FALSE)
+#### Load file with the list of packages for installation of supplementary packages
+#### Part used in shiny-example docker images for install packages needed for shiny app
+additional_packages <- read.csv(file = "/opt/scripts/packages_to_install.csv", header = TRUE, sep = ";", stringsAsFactors = FALSE)
+packages_name <- additional_packages$Package_name
+#### Selection of packages not yet installed
+packages_needed <- packages_name[!(packages_name %in% installed.packages()[ , "Package"])]
print("Installation for other packages needed : ")
-print(paste(packages_list$Package_name, sep = "",collapse = ","))
+print(paste(packages_needed, sep = "",collapse = ","))
### Install packages with dependencies with pak packages
-for (i in 1:length(packages_list$Package_name)) {
+for (i in 1:length(packages_needed)) {
print("Installation of: ")
- print(packages_list$Package_name[i])
- pak::pkg_install(pkg = packages_list$Package_name[i])
+ print(packages_needed[i])
+ pak::pkg_install(pkg = packages_needed[i])
print("Installation done!!")
}
# clean the cache of pak
--
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