paste0 for paste(sep="")

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@68364 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Aug 10, 2012 · 3c6595c · 3c6595c
1 parent 7d3cb81
commit 3c6595c
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Showing 7 changed files with 18 additions and 18 deletions.
diff --git a/R/GRangesList-class.R b/R/GRangesList-class.R
@@ -568,13 +568,13 @@ setMethod("show", "GRangesList",
             cat("<0 elements>\n\n")
         } else if ((k == 1L) || ((k <= 3L) && (N <= 20L))) {
             nms <- names(object)
-            defnms <- paste("[[", seq_len(k), "]]", sep="")
+            defnms <- paste0("[[", seq_len(k), "]]")
             if (is.null(nms)) {
                 nms <- defnms
             } else {
                 empty <- nchar(nms) == 0L
                 nms[empty] <- defnms[empty]
-                nms[!empty] <- paste("$", nms[!empty], sep="")
+                nms[!empty] <- paste0("$", nms[!empty])
             }
             for (i in seq_len(k)) {
                 cat(nms[i], "\n")
@@ -594,13 +594,13 @@ setMethod("show", "GRangesList",
                 showK <- 1
             diffK <- k - showK
             nms <- names(object)[seq_len(showK)]
-            defnms <- paste("[[", seq_len(showK), "]]", sep="")
+            defnms <- paste0("[[", seq_len(showK), "]]")
             if (is.null(nms)) {
                 nms <- defnms
             } else {
                 empty <- nchar(nms) == 0L
                 nms[empty] <- defnms[empty]
-                nms[!empty] <- paste("$", nms[!empty], sep="")
+                nms[!empty] <- paste0("$", nms[!empty])
             }
             for (i in seq_len(showK)) {
                 cat(nms[i], "\n")

diff --git a/R/GappedAlignmentPairs-class.R b/R/GappedAlignmentPairs-class.R
@@ -507,7 +507,7 @@ showGappedAlignmentPairs <- function(x, margin="",
         out <- rbind(classinfo, out)
     }
     if (nrow(out) != 0L)
-        rownames(out) <- paste(margin, rownames(out), sep="")
+        rownames(out) <- paste0(margin, rownames(out))
     print(out, quote=FALSE, right=TRUE)
     if (print.seqlengths) {
         cat(margin, "---\n", sep="")

diff --git a/R/GappedAlignments-class.R b/R/GappedAlignments-class.R
@@ -648,7 +648,7 @@ showGappedAlignments <- function(x, margin="",
         out <- rbind(classinfo, out)
     }
     if (nrow(out) != 0L)
-        rownames(out) <- paste(margin, rownames(out), sep="")
+        rownames(out) <- paste0(margin, rownames(out))
     print(out, quote=FALSE, right=TRUE)
     if (print.seqlengths) {
         cat(margin, "---\n", sep="")

diff --git a/R/GenomicRanges-class.R b/R/GenomicRanges-class.R
@@ -115,7 +115,7 @@ setMethod("elementMetadata", "GenomicRanges",
         !identical(levels(runValue(strand(x))), levels(strand())))
     {
         msg <- c("'strand' should be a 'factor' Rle with levels c(",
-                 paste('"', levels(strand()), '"', sep="", collapse=", "),
+                 paste0('"', levels(strand()), '"', collapse=", "),
                  ")")
         return(paste(msg, collapse=""))
     }
@@ -134,7 +134,7 @@ INVALID.GR.COLNAMES <- c("seqnames", "ranges", "strand",
 {    
     if (any(INVALID.GR.COLNAMES %in% colnames(elementMetadata(x)))) {
         msg <- c("slot 'elementMetadata' cannot use",
-                 paste("\"", INVALID.GR.COLNAMES, "\"", sep="", collapse=", "),
+                 paste0("\"", INVALID.GR.COLNAMES, "\"", collapse=", "),
                  "as column names")
         return(paste(msg, collapse=" "))
     }
@@ -710,7 +710,7 @@ showGenomicRanges <- function(x, margin="",
         out <- rbind(classinfo, out)
     }
     if (nrow(out) != 0L)
-        rownames(out) <- paste(margin, rownames(out), sep="")
+        rownames(out) <- paste0(margin, rownames(out))
     print(out, quote=FALSE, right=TRUE)
     if (print.seqlengths) {
         cat(margin, "---\n", sep="")

diff --git a/R/Seqinfo-class.R b/R/Seqinfo-class.R
@@ -417,7 +417,7 @@ showCompactDataFrame <- function(x, rownames.label="", left.margin="")
     showme <- .showOutputAsCharacter(compactdf)
     if (label_nchar != 0L)
         substr(showme[1L], 1L, label_nchar) <- rownames.label
-    cat(paste(left.margin, showme, sep=""), sep="\n")
+    cat(paste0(left.margin, showme), sep="\n")
 }
 
 setMethod("show", "Seqinfo",

diff --git a/R/constraint.R b/R/constraint.R
@@ -103,16 +103,16 @@ suppressWarnings(
         for (i in seq_len(nrow(signatures))) {
             sig <- signatures[i, ]
             sigString <- paste(names(sig),
-                               paste("\"", sig, "\"", sep=""),
+                               paste0('"', sig, '"'),
                                sep="=", collapse=", ")
             if (verbose)
                 message("Calling \"checkConstraint\" method for\n",
                         "    ", sigString)
             method <- getMethod("checkConstraint", sig)
             errors <- method(x, constraint)
             if (length(errors) != 0L) {
-                errors <- paste("from \"checkConstraint\" method for c(",
-                                sigString, "): ", errors, sep="")
+                errors <- paste0("from \"checkConstraint\" method for c(",
+                                 sigString, "): ", errors)
                 ## If a constraint is not satisfied, we don't check the
                 ## remaining constraints (so when implementing a constraint
                 ## a developper can assume that the less specific constraints

diff --git a/R/utils.R b/R/utils.R
@@ -19,7 +19,7 @@ makePrettyMatrixForCompactPrinting <- function(x, makeNakedMat.FUN)
         } else if (lx == 0L) {
             ans_rownames <- character(0)
         } else {
-            ans_rownames <- paste("[", seq_len(lx), "]", sep="")
+            ans_rownames <- paste0("[", seq_len(lx), "]")
         }
     } else {
         top_idx <- 1:9
@@ -34,9 +34,9 @@ makePrettyMatrixForCompactPrinting <- function(x, makeNakedMat.FUN)
         if (!is.null(nms)) {
             ans_rownames <- c(nms[top_idx], "...", nms[bottom_idx])
         } else {
-            ans_rownames <- c(paste("[", top_idx, "]", sep=""),
+            ans_rownames <- c(paste0("[", top_idx, "]"),
                               "...",
-                              paste("[", bottom_idx, "]", sep=""))
+                              paste0("[", bottom_idx, "]"))
         }
     }
     rownames(ans) <- format(ans_rownames, justify="right")
@@ -51,11 +51,11 @@ makeClassinfoRowForCompactPrinting <- function(x, col2class)
     left_brackets <- right_brackets <- character(length(col2class))
     left_brackets[!no_bracket] <- "<"
     right_brackets[!no_bracket] <- ">"
-    ans <- paste(left_brackets, col2class, right_brackets, sep="")
+    ans <- paste0(left_brackets, col2class, right_brackets)
     names(ans) <- ans_names
     if (ncol(elementMetadata(x)) > 0L) {
         tmp <- sapply(elementMetadata(x),
-                      function(xx) paste("<", class(xx), ">", sep=""))
+                      function(xx) paste0("<", class(xx), ">"))
         ans <- c(ans, `|`="|", tmp)
     }
     matrix(ans, nrow=1L, dimnames=list("", names(ans)))