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The path() generic has moved from Rsamtools to BiocGenerics

LiNk-NY authored on 20/12/2017 20:04:28
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@@ -9,10 +9,10 @@ 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: 1.21.1
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+Version: 1.21.2
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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, 
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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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@@ -1,6 +1,7 @@
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 useDynLib(gmapR, .registration = TRUE)
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-importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
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+importFrom(BiocGenerics, path)
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+importFrom(Rsamtools, bamPaths, "bamWhich<-", BamFile, BamFileList,
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            BamSampler)
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 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
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            list_files_with_exts)
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@@ -12,7 +13,8 @@ import(GenomicRanges)
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 import(GenomeInfoDb)
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 import(BiocParallel)
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 importMethodsFrom(GenomeInfoDb, genome)
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-importFrom(utils, packageVersion)
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+importFrom(stats, setNames)
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+importFrom(utils, packageVersion, read.table, str)
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 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
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 importMethodsFrom(GenomicRanges, seqnames, strand)
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 importMethodsFrom(Rsamtools, asBam)