Add quiet install of CRAN packages

XPRESSyourself · Apr 5, 2020 · 1a3f48f · 1a3f48f
1 parent 6c673e1
commit 1a3f48f
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Showing 5 changed files with 12 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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)