diff --git a/R/GRangesList-class.R b/R/GRangesList-class.R index c4de00e..b2ebbd4 100644 --- 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 index b956d98..b34b40c 100644 --- 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 index 4eedee2..2d00ad1 100644 --- 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 index 1ef26e6..d1826e2 100644 --- 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 index 94ed91e..0e051d2 100644 --- 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 index 30ac0c9..ecc34c9 100644 --- a/R/constraint.R +++ b/R/constraint.R @@ -103,7 +103,7 @@ 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", @@ -111,8 +111,8 @@ suppressWarnings( 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 index af8ce90..cc715d0 100644 --- 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)))