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elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@113044 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/01/2016 01:22:03
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@@ -9,12 +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: 1.13.8
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+Version: 1.13.9
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12)
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-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
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-        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
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-        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
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+Imports: S4Vectors (>= 0.9.25), IRanges, Rsamtools (>= 1.17.8),
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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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 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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@@ -31,7 +31,7 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "character", "VCF"),
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                    iitFile <- file.path(iitPath, paste(name, "iit", sep = "."))
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                    alt <- values(gr)$ALT
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                    if (is(alt, "List")) {
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-                     gr <- rep(gr, elementLengths(alt))
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+                     gr <- rep(gr, elementNROWS(alt))
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                      alt <- unlist(alt)
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                    }
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                    ref <- values(gr)$REF