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follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12

Hervé Pagès authored on 22/01/2018 00:24:43
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@@ -9,13 +9,13 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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         methods to work with GMAP and GSNAP from within R. In addition,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.21.2
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+Version: 1.21.3
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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-        GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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-Imports: S4Vectors (>= 0.13.13), IRanges, BiocGenerics (>= 0.25.1),
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-        rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
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-        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
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-        GenomicAlignments (>= 1.1.9), BiocParallel
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+        GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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+Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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+        rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings,
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+        VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome,
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+        GenomicAlignments (>= 1.15.6), BiocParallel
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 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
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         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
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@@ -19,15 +19,15 @@ setMethod("path", "GmapBamReader", function(object) object@path)
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 ## setReplaceMethod("bamWhich", c("GmapBamReader", "ANY"),
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 ##                  function(object, value) {
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-##                    bamWhich(object) <- as(value, "RangesList")
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+##                    bamWhich(object) <- as(value, "IntegerRangesList")
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 ##                    object
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 ##                  })
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-## setReplaceMethod("bamWhich", c("GmapBamReader", "RangesList"),
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+## setReplaceMethod("bamWhich", c("GmapBamReader", "IntegerRangesList"),
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 ##                  function(object, value) {
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 ##                    if (length(value) != 1L || length(value[[1]]) != 1L)
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-##                      stop("'value' must be a RangesList with a single, ",
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-##                           "length-one element")
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+##                      stop("'value' must be an IntegerRangesList with a ",
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+##                           "single, length-one element")
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 ##                    .Call(R_Bamread_limit_region, object, names(value),
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 ##                          start(value[[1]]), end(value[[1]]))
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 ##                  })
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@@ -28,7 +28,7 @@
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 }
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 \arguments{
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   \item{genome}{A \code{GmapGenome} object, or something coercible to one.}
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-  \item{which}{A \code{RangesList} or something coercible to
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+  \item{which}{A \code{IntegerRangesList} or something coercible to
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     one that limits the tally to that range or set of ranges. By
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     default, the entire genome is processed.
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   }