Remove use of paste() or paste0() inside message() to resolve another…

… BiocCheck NOTE

R/corner.R

@@ -18,13 +18,25 @@
 #' lis <- list(iris, mtcars, matrix(rnorm(1000), ncol = 10))
 #' corner(lis)
 corner <- function(mat, n = 6) {
-    types <- c("list", "DataFrame", "data.frame", "GRanges", "matrix", "tbl_df")
+    types <-
+        c("list",
+            "DataFrame",
+            "data.frame",
+            "GRanges",
+            "matrix",
+            "tbl_df")
     if (!(class(mat)[1] %in% types)) {
-        stop(paste0("The class of your object (", class(mat), ") is not handled by this function."))
+        stop(
+            "The class of your object (",
+            class(mat),
+            ") is not handled by this function.",
+            call. = FALSE
+        )
     }
     if (class(mat)[1] == "list") {
         # return corners of first n items of list
-        return(lapply(mat[seq_len(min(length(mat), n))], function(x) x[seq_len(min(nrow(x), n)), seq_len(min(ncol(x), n))]))
+        return(lapply(mat[seq_len(min(length(mat), n))], function(x)
+            x[seq_len(min(nrow(x), n)), seq_len(min(ncol(x), n))]))
     } else {
         return(mat[seq_len(min(nrow(mat), n)), seq_len(min(ncol(mat), n))])
     }

R/expression_cutoff.R

@@ -166,9 +166,9 @@ expression_cutoff <- function(expr, max_cut = 1, seed = NULL, n.boot = 2000,
         "samples_nonzero_cut" = cuts[round(seg2$psi[, 2])][2]
     )
 
-    message(paste(
-        Sys.time(), "the suggested expression cutoff is",
+    message(
+        Sys.time(), " the suggested expression cutoff is ",
         round(mean(suggested), 2)
-    ))
+    )
     return(suggested)
 }

R/junctionCount.R

@@ -44,7 +44,7 @@ junctionCount <- function(junctionFiles, sampleNames = names(junctionFiles),
     stopifnot(output %in% c("Count", "Rail"))
 
     names(junctionFiles) <- sampleNames
-    message(paste(Sys.time(), "reading in data"))
+    message(Sys.time(), " reading in data")
 
     if (all(is.character(junctionFiles))) {
         theData <- mclapply(junctionFiles, function(x) {
@@ -86,7 +86,7 @@ junctionCount <- function(junctionFiles, sampleNames = names(junctionFiles),
         theData <- junctionFiles
         stopifnot(all(sapply(theData, class) == "GRanges"))
     }
-    message(paste(Sys.time(), "creating master table of junctions"))
+    message(Sys.time(), " creating master table of junctions")
 
     ## turn into GRangesList
     ### THIS STEP IS SLOW...
@@ -108,8 +108,8 @@ junctionCount <- function(junctionFiles, sampleNames = names(junctionFiles),
     fullGR <- sort(fullGR)
     fullGR$count <- NULL
 
-    message(paste(Sys.time(), "there are", length(fullGR), "total junctions"))
-    message(paste(Sys.time(), "populating count matrix"))
+    message(Sys.time(), " there are ", length(fullGR), " total junctions")
+    message(Sys.time(), " populating count matrix")
 
     jNames <- paste0(
         as.character(seqnames(fullGR)), ":", start(fullGR), "-",
@@ -127,7 +127,7 @@ junctionCount <- function(junctionFiles, sampleNames = names(junctionFiles),
     M <- length(jNames)
 
     ## fill in matrix
-    message(paste(Sys.time(), "filling in the count matrix"))
+    message(Sys.time(), " filling in the count matrix")
     for (i in seq(along = grList)) {
         if (i %% 25 == 0) message(".")
         cc <- rep(0, M)