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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:49:42
Showing3 changed files

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@@ -9,7 +9,7 @@ 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: 1.23.0
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+Version: 1.23.1
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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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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@@ -41,8 +41,8 @@ destDir = ".", license = "Artistic-2.0", pkgName)
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 library(gmapR)
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 if (!require(BSgenome.Dmelanogaster.UCSC.dm3)) {
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-  library(BiocInstaller)
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-  biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
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+  library(BiocManager)
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+  BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
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   library(BSgenome.Dmelanogaster.UCSC.dm3)
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 }
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@@ -125,8 +125,9 @@ example demonstrates:
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 library(gmapR)
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 if (!suppressWarnings(require(BSgenome.Dmelanogaster.UCSC.dm3))) {
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-  source("http://bioconductor.org/biocLite.R")
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-  biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
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+  if (!requireNamespace("BiocManager", quietly=TRUE))
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+      install.packages("BiocManager")
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+  BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
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   library(BSgenome.Dmelanogaster.UCSC.dm3)
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 }
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@@ -348,8 +349,9 @@ object:
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 <<create_hg19_GmapGenome, eval=FALSE>>=
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 if (!suppressWarnings(require(BSgenome.Hsapiens.UCSC.hg19))) {
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-  source("http://bioconductor.org/biocLite.R")
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-  biocLite("BSgenome.Hsapiens.UCSC.hg19")
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+  if (!requireNamespace("BiocManager", quietly=TRUE))
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+      install.packages("BiocManager")
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+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
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   library(BSgenome.Hsapiens.UCSC.hg19)
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 }
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 gmapGenome <- GmapGenome(genome=Hsapiens,