@@ -55,11 +55,11 @@

 ## We want to deal with chromosomes in a reasonable way. This coerces likely inputs to a unified

 ## chromosome name as understood by UCSC. Accepted inputs are:

-##    - a single integer or a character coercable to one or integer-character combinations

+##    - a single integer or a character coercible to one or integer-character combinations

 ##    - a character, starting with 'chr' (case insensitive)

 ## Arguments:

 ##    o x: a character string to be converted to a valid UCSC chromosome name

-##    o force: a logical flag, force prepending of 'chr' if missing

+##    o force: a logical flag, force pre-pending of 'chr' if missing

 ## Value: the UCSC character name

 .chrName <- function(x, force = FALSE) {

     if (!getOption("ucscChromosomeNames") || length(x) == 0) {

@@ -86,10 +86,9 @@

             head <- TRUE

         }

         if (!head) {

-            stop(sprintf(paste(

-                "Invalid chromosome identifier '%s'\nPlease consider setting options(ucscChromosomeNames=FALSE)",

-                "to allow for arbitrary chromosome identifiers."

-            ), y))

+            stop(sprintf("Invalid chromosome identifier '%s'\n", y),

+                 "Please consider setting options(ucscChromosomeNames=FALSE) ",

+                 "to allow for arbitrary chromosome identifiers.")

         }

         substring(y, 1, 3) <- tolower(substring(y, 1, 3))

         y

@@ -113,7 +112,7 @@

 ## unimplemented types...

 ## Arguments:

 ##    o GdObject: an object inheriting from class GdObject

-## Value: a logical skalar indicating whether stacking is needed or not

+## Value: a logical scalar indicating whether stacking is needed or not

 .needsStacking <- function(GdObject) stacking(GdObject) %in% c("squish", "pack", "full")

@@ -1430,42 +1429,29 @@ addScheme <- function(scheme, name) {

 .getBiomart <- function(genome) {

     map <- .ucsc2Ensembl(genome)

     if (map$date == "head") {

-        bm <- useMart("ensembl", dataset = map$dataset)

+        bm <- useEnsembl(biomart="ensembl", dataset = map$dataset)

         ds <- listDatasets(bm)

         mt <- ds[match(map$dataset, ds$dataset), "version"]

         if (is.na(mt)) {

-            stop(sprintf(paste(

-                "Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

-                "\nPlease manually provide biomaRt object"

-            ), genome, map$dataset))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

+                         genome, map$dataset), "\nPlease manually provide biomaRt object")

         }

         if (mt != map$value) {

-            stop(sprintf(

-                paste(

-                    "Gviz thinks that the UCSC genome identifier '%s' should map to the current Biomart head as '%s',",

-                    "but its current version is '%s'.\nPlease manually provide biomaRt object"

-                ),

-                genome, map$value, mt

-            ))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to the current Biomart head as '%s', ",

+                         genome, map$value, mt), "but its current version is '%s'.\nPlease manually provide biomaRt object.")

         }

     } else {

-        bm <- useMart(host = sprintf("%s.archive.ensembl.org", tolower(sub(".", "", map$date, fixed = TRUE))), biomart = "ENSEMBL_MART_ENSEMBL", dataset = map$dataset)

+        bm <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", dataset = map$dataset, host = sprintf("%s.archive.ensembl.org", tolower(sub(".", "", map$date, fixed = TRUE))))

         ds <- listDatasets(bm)

         mt <- ds[match(map$dataset, ds$dataset), "version"]

         if (is.na(mt)) {

-            stop(sprintf(paste(

-                "Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

-                "\nPlease manually provide biomaRt object"

-            ), genome, map$dataset))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

+                         genome, map$dataset), "\nPlease manually provide biomaRt object")

         }

         if (mt != map$value) {

-            stop(sprintf(

-                paste(

-                    "Gviz thinks that the UCSC genome identifier '%s' should map to Biomart archive %s (version %s) as '%s',",

-                    "but its version is '%s'.\nPlease manually provide biomaRt object"

-                ),

-                genome, sub(".", " ", map$date, fixed = TRUE), map$version, map$value, mt

-            ))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to Biomart archive %s (version %s) as '%s',",

+                         genome, sub(".", " ", map$date, fixed = TRUE), map$version, map$value, mt),

+                 "but its version is '%s'.\nPlease manually provide biomaRt object")

         }

     }

     return(bm)

@@ -2216,7 +2202,7 @@ availableDisplayPars <- function(class) {

       }

     class <- match.arg(class, c(

         "GdObject", "GenomeAxisTrack", "RangeTrack", "NumericTrack", "DataTrack", "IdeogramTrack", "StackedTrack",

-        "AnnotationTrack", "DetailsAnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack", 

+        "AnnotationTrack", "DetailsAnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack",

         "AlignmentsTrack", "SequenceTrack", "SequenceBSgenomeTrack", "SequenceDNAStringSetTrack", "SequenceRNAStringSetTrack"

     ))

     parents <- names(getClassDef(class)@contains)

@@ -2372,10 +2358,8 @@ availableDisplayPars <- function(class) {

         dat

     })

     if (is(res, "try-error")) {

-        warning(sprintf(paste(

-            "File '%s' is not valid according to the GFF3 standard and can not be properly parsed.",

-            "Results may not be what you expected!"

-        ), file))

+        warning(sprintf("File '%s' is not valid according to the GFF3 standard and can not be properly parsed.",

+                        file), "\nResults may not be what you expected!")

         res <- dat

     }

     return(res)

@@ -2804,13 +2788,8 @@ availableDefaultMapping <- function(file, trackType) {

         vm[[inputType]] <- setNames(list(list(".stream" = stream)), trackType)

     } else {

         if (is.null(vm[[inputType]]) || is.null(vm[[inputType]][[trackType]])) {

-            warning(sprintf(

-                paste(

-                    "There are no default mappings from %s files to %s. Please provide a manual mapping",

-                    "in the track constructor if you haven't already done so."

-                ),

-                inputType, trackType

-            ))

+            warning(sprintf("There are no default mappings from %s files to %s. Please provide a manual mapping",

+                            inputType, trackType), " in the track constructor if you haven't already done so.")

             vm[[inputType]] <- setNames(list(list(".stream" = stream)), trackType)

         }

     }