From 1a3f48ffda6208b4213efab3f3ad21b33272b3ab Mon Sep 17 00:00:00 2001
From: j-berg <j-berg@users.noreply.github.com>
Date: Sat, 4 Apr 2020 21:32:59 -0600
Subject: [PATCH] Add quiet install of CRAN packages

---
 xpresspipe/RbuildIndex.r  | 4 ++--
 xpresspipe/Rcomplexity.r  | 4 ++--
 xpresspipe/Rdiffxpress.r  | 2 +-
 xpresspipe/Rmetagene.r    | 6 +++---
 xpresspipe/Rperiodicity.r | 8 ++++----
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/xpresspipe/RbuildIndex.r b/xpresspipe/RbuildIndex.r
index b53e082..6822111 100644
--- a/xpresspipe/RbuildIndex.r
+++ b/xpresspipe/RbuildIndex.r
@@ -54,7 +54,7 @@ sub_license <- function() {
 # Install dependencies
 if (!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager", repos = "http://cran.us.r-project.org")}
 
-install.packages("stringi", repos = "http://cran.us.r-project.org")
+install.packages("stringi", repos = "http://cran.us.r-project.org", quiet = TRUE)
 library(stringi)
 
 if ("GenomicFeatures" %in% rownames(installed.packages()) == FALSE) {
@@ -68,7 +68,7 @@ library(GenomicFeatures)
 
 if ("data.table" %in% rownames(installed.packages()) == FALSE) {
   print("Installing data.table...")
-  install.packages("data.table", repos = "http://cran.us.r-project.org")
+  install.packages("data.table", repos = "http://cran.us.r-project.org", quiet = TRUE)
 } else {
   print("data.table package already installed")
 }
diff --git a/xpresspipe/Rcomplexity.r b/xpresspipe/Rcomplexity.r
index 41357ed..4f55966 100644
--- a/xpresspipe/Rcomplexity.r
+++ b/xpresspipe/Rcomplexity.r
@@ -23,12 +23,12 @@ license <- function() {
   }
 
 # Measure library complexity of RNA-seq sample
-install.packages("stringi", repos = "http://cran.us.r-project.org")
+install.packages("stringi", repos = "http://cran.us.r-project.org", quiet = TRUE)
 library(stringi)
 
 # Install dependencies
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
-  install.packages("BiocManager", repos = "http://cran.us.r-project.org")
+  install.packages("BiocManager", repos = "http://cran.us.r-project.org", quiet = TRUE)
 }
 
 if ("Rsubread" %in% rownames(installed.packages()) == FALSE) {
diff --git a/xpresspipe/Rdiffxpress.r b/xpresspipe/Rdiffxpress.r
index 721678a..d1f884b 100644
--- a/xpresspipe/Rdiffxpress.r
+++ b/xpresspipe/Rdiffxpress.r
@@ -23,7 +23,7 @@ license <- function() {
   }
 
 # Control batch effects for prep, chips, etc
-install.packages("stringi", repos = "http://cran.us.r-project.org")
+install.packages("stringi", repos = "http://cran.us.r-project.org", quiet = TRUE)
 library(stringi)
 
 if (!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager", repos = "http://cran.us.r-project.org")}
diff --git a/xpresspipe/Rmetagene.r b/xpresspipe/Rmetagene.r
index a97addf..fa0bd28 100644
--- a/xpresspipe/Rmetagene.r
+++ b/xpresspipe/Rmetagene.r
@@ -23,14 +23,14 @@ license <- function() {
   }
 
 # Import dependencies
-install.packages("stringi", repos = "http://cran.us.r-project.org")
+install.packages("stringi", repos = "http://cran.us.r-project.org", quiet = TRUE)
 library(stringi)
 
-if (!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager", repos = "http://cran.us.r-project.org")}
+if (!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager", repos = "http://cran.us.r-project.org", quiet = TRUE)}
 
 if ("data.table" %in% rownames(installed.packages()) == FALSE) {
   print("Installing data.table...")
-  install.packages("data.table", repos = "http://cran.us.r-project.org")
+  install.packages("data.table", repos = "http://cran.us.r-project.org", quiet = TRUE)
 } else {
   print("data.table package already installed")
 }
diff --git a/xpresspipe/Rperiodicity.r b/xpresspipe/Rperiodicity.r
index 410f6d5..c191882 100644
--- a/xpresspipe/Rperiodicity.r
+++ b/xpresspipe/Rperiodicity.r
@@ -23,7 +23,7 @@ license <- function() {
   }
 
 # Run install of data.table to make sure most recent version is installed
-install.packages("stringi", repos = "http://cran.us.r-project.org")
+install.packages("stringi", repos = "http://cran.us.r-project.org", quiet = TRUE)
 library(stringi)
 
 library(data.table)
@@ -42,9 +42,9 @@ OUTPUT_P_SITES <- args[3] # Path and filename with .txt extension
 PATH <- args[4] # File directory
 
 # Install riboWaltz functions
-source(paste(toString(PATH), "ribowaltz_annotation.R", sep=""))
-source(paste(toString(PATH), "ribowaltz_psites.R", sep=""))
-source(paste(toString(PATH), "ribowaltz_combine_bam.R", sep=""))
+source(paste(toString(PATH), "ribowaltz_annotation.r", sep=""))
+source(paste(toString(PATH), "ribowaltz_psites.r", sep=""))
+source(paste(toString(PATH), "ribowaltz_combine_bam.r", sep=""))
 
 # Get p-site offsets
 annotation_dt <- create_annotation(gtfpath=GTF)