resync with stuff moving from IRanges to S4Vectors

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@89154 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Apr 17, 2014 · 79ab292 · 79ab292
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commit 79ab292
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Showing 7 changed files with 20 additions and 19 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,14 +7,14 @@ Description: The ability to efficiently represent and manipulate genomic
 	intervals. Specialized containers for representing and manipulating
 	short alignments against a reference genome are defined in the
 	GenomicAlignments package.
-Version: 1.17.5
+Version: 1.17.6
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation
-Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7), IRanges (>= 1.23.5),
-	GenomeInfoDb (>= 0.99.17)
+Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7),
+	S4Vectors, IRanges (>= 1.99.0), GenomeInfoDb (>= 0.99.17)
 Imports: methods, utils, stats, BiocGenerics, IRanges, XVector
-LinkingTo: IRanges, XVector (>= 0.3.4)
+LinkingTo: S4Vectors, IRanges, XVector (>= 0.5.2)
 Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub,
 	BSgenome, BSgenome.Hsapiens.UCSC.hg19,
 	BSgenome.Scerevisiae.UCSC.sacCer2,

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,7 @@ import(methods)
 import(utils)  # for as.roman()
 importFrom(stats, setNames)
 import(BiocGenerics)
+import(S4Vectors)
 import(IRanges)
 import(XVector)  # only for the "Views" method for integer vectors, the
                  # XIntegerViews class, and the "viewMins", "viewMaxs", and

diff --git a/R/GRanges-class.R b/R/GRanges-class.R
@@ -72,7 +72,7 @@ newGRanges <- ## hidden constructor shared with other GRanges-like objects
     if (!is.factor(runValue(strand)) ||
         !identical(levels(runValue(strand)), levels(strand())))
         runValue(strand) <- strand(runValue(strand))
-    if (IRanges:::anyMissing(runValue(strand))) {
+    if (S4Vectors:::anyMissing(runValue(strand))) {
         warning("missing values in strand converted to \"*\"")
         runValue(strand)[is.na(runValue(strand))] <- "*"
     }

diff --git a/R/GenomicRanges-class.R b/R/GenomicRanges-class.R
@@ -131,7 +131,7 @@ setMethod("fixedColumnNames", "GenomicRanges", function(x) {
 {
     if (!is.factor(runValue(seqnames(x))))
         return("'seqnames' should be a 'factor' Rle")
-    if (IRanges:::anyMissing(runValue(seqnames(x))))
+    if (S4Vectors:::anyMissing(runValue(seqnames(x))))
         return("'seqnames' contains missing values")
     NULL
 }
@@ -153,7 +153,7 @@ setMethod("fixedColumnNames", "GenomicRanges", function(x) {
                  ")")
         return(paste(msg, collapse=""))
     }
-    if (IRanges:::anyMissing(runValue(strand(x))))
+    if (S4Vectors:::anyMissing(runValue(strand(x))))
         return("'strand' contains missing values")
     NULL
 }
@@ -492,7 +492,7 @@ setReplaceMethod("start", "GenomicRanges",
         starts <- start(ranges)
         starts[] <- value
         ## TODO: Revisit this to handle circularity (maybe).
-        if (!IRanges:::anyMissing(seqlengths(x))) {
+        if (!S4Vectors:::anyMissing(seqlengths(x))) {
             if (IRanges:::anyMissingOrOutside(starts, 1L)) {
                 warning("trimmed start values to be positive")
                 starts[starts < 1L] <- 1L
@@ -513,7 +513,7 @@ setReplaceMethod("end", "GenomicRanges",
         ends[] <- value
         seqlengths <- seqlengths(x)
         ## TODO: Revisit this to handle circularity.
-        if (!IRanges:::anyMissing(seqlengths)) {
+        if (!S4Vectors:::anyMissing(seqlengths)) {
             seqlengths <- seqlengths[seqlevels(x)]
             maxEnds <- seqlengths[as.integer(seqnames(x))]
             trim <- which(ends > maxEnds)
@@ -532,7 +532,7 @@ setReplaceMethod("width", "GenomicRanges",
     {
         if (!is.integer(value))
             value <- as.integer(value)
-        if (!IRanges:::anyMissing(seqlengths(x))) {
+        if (!S4Vectors:::anyMissing(seqlengths(x))) {
             end(x) <- start(x) + (value - 1L)
         } else {
             ranges <- ranges(x)

diff --git a/R/intra-range-methods.R b/R/intra-range-methods.R
@@ -68,7 +68,7 @@ setMethod("flank", "GenomicRanges",
         ranges <-
             flank(ranges(x), width=width, start=start, both=both,
                   use.names=use.names)
-        if (!IRanges:::anyMissing(seqlengths(x))) {
+        if (!S4Vectors:::anyMissing(seqlengths(x))) {
             start(x) <- start(ranges)
             end(x) <- end(ranges)
         } else {
@@ -159,7 +159,7 @@ setMethod("resize", "GenomicRanges",
         }
         ranges <-
             resize(ranges(x), width=width, fix=fix, use.names=use.names)
-        if (!IRanges:::anyMissing(seqlengths(x))) {
+        if (!S4Vectors:::anyMissing(seqlengths(x))) {
             start(x) <- start(ranges)
             end(x) <- end(ranges)
         } else {
@@ -265,7 +265,7 @@ setMethod("trim", "GenomicRanges",
 setMethod("Ops", c("GenomicRanges", "numeric"),
     function(e1, e2)
     {
-        if (IRanges:::anyMissing(e2))
+        if (S4Vectors:::anyMissing(e2))
             stop("NA not allowed as zoom factor")
         e2 <- recycleNumericArg(e2, "e2", length(e1))
         if (.Generic == "*") {

diff --git a/R/strand-utils.R b/R/strand-utils.R
@@ -118,10 +118,10 @@ setMethod("compatibleStrand", c("factor", "factor"),  # not exported
         y <- as.integer(as.character(y))
 
         ans <- x * y != -1L
-        if (IRanges:::anyMissing(ans)) {
+        if (S4Vectors:::anyMissing(ans)) {
             fix <- which(is.na(ans))
             ans[fix] <- (x[fix] == 0L) | (y[fix] == 0L)
-            if (IRanges:::anyMissing(ans))
+            if (S4Vectors:::anyMissing(ans))
                 ans[is.na(ans)] <- FALSE
         }
         ans
@@ -145,11 +145,11 @@ setMethod("compatibleStrand", c("Rle", "Rle"),  # not exported
         runValue(y) <- as.integer(as.character(runValue(y)))
 
         ans <- x * y != -1L
-        if (IRanges:::anyMissing(runValue(ans))) {
+        if (S4Vectors:::anyMissing(runValue(ans))) {
             fix <- which(is.na(runValue(ans)))
             runValue(ans)[fix] <-
               (runValue(x) == 0L)[fix] | (runValue(y)[fix] == 0L)
-            if (IRanges:::anyMissing(runValue(ans)))
+            if (S4Vectors:::anyMissing(runValue(ans)))
                 runValue(ans)[is.na(runValue(ans))] <- FALSE
         }
         ans

diff --git a/man/constraint.Rd b/man/constraint.Rd
@@ -172,7 +172,7 @@ setMethod("checkConstraint", c("GenomicRanges", "HasRangeTypeCol"),
         rangeType <- x_mcols[[idx]]
         .LEVELS <- c("gene", "transcript", "exon", "cds", "5utr", "3utr")
         if (!is(rangeType, "Rle") ||
-            IRanges:::anyMissing(runValue(rangeType)) ||
+            S4Vectors:::anyMissing(runValue(rangeType)) ||
             !identical(levels(rangeType), .LEVELS))
         {
             msg <- c("'mcols(x)$rangeType' must be a ",
@@ -270,7 +270,7 @@ setMethod("checkConstraint", c("GenomicRanges", "HasGCCol"),
         }
         GC <- x_mcols[[idx]]
         if (!is.numeric(GC) ||
-            IRanges:::anyMissing(GC) ||
+            S4Vectors:::anyMissing(GC) ||
             any(GC < 0) || any(GC > 1))
         {
             msg <- c("'mcols(x)$GC' must be a numeric vector ",