From 8fe82ba64d94f57829ee71f00b006bc1cb866280 Mon Sep 17 00:00:00 2001
From: echapeau <echapeau@pasteur.fr>
Date: Wed, 26 Apr 2023 14:29:17 +0200
Subject: [PATCH] Update packages_to_install.csv and install_r_packages.R

---
 scripts/install_r_packages.R    | 6 +++---
 scripts/packages_to_install.csv | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/scripts/install_r_packages.R b/scripts/install_r_packages.R
index 32a9cc5..dfa6b5c 100644
--- a/scripts/install_r_packages.R
+++ b/scripts/install_r_packages.R
@@ -5,10 +5,10 @@
 ### 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.packages(c("pak","pkgcache","pkgdepends","pillar"), 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)
+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()
diff --git a/scripts/packages_to_install.csv b/scripts/packages_to_install.csv
index 3e78250..0f0f41f 100644
--- a/scripts/packages_to_install.csv
+++ b/scripts/packages_to_install.csv
@@ -1 +1,2 @@
-shiny
+Package_name;Comments
+shiny;cran package
\ No newline at end of file
-- 
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