@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.23.0

+Version: 1.23.1

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)

 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),

@@ -41,8 +41,8 @@ destDir = ".", license = "Artistic-2.0", pkgName)

 library(gmapR)

 if (!require(BSgenome.Dmelanogaster.UCSC.dm3)) {

-  library(BiocInstaller)

-  biocLite("BSgenome.Dmelanogaster.UCSC.dm3")

+  library(BiocManager)

+  BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")

   library(BSgenome.Dmelanogaster.UCSC.dm3)

 }

@@ -125,8 +125,9 @@ example demonstrates:

 library(gmapR)

 if (!suppressWarnings(require(BSgenome.Dmelanogaster.UCSC.dm3))) {

-  source("http://bioconductor.org/biocLite.R")

-  biocLite("BSgenome.Dmelanogaster.UCSC.dm3")

+  if (!requireNamespace("BiocManager", quietly=TRUE))

+      install.packages("BiocManager")

+  BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")

   library(BSgenome.Dmelanogaster.UCSC.dm3)

 }

@@ -348,8 +349,9 @@ object:

 <<create_hg19_GmapGenome, eval=FALSE>>=

 if (!suppressWarnings(require(BSgenome.Hsapiens.UCSC.hg19))) {

-  source("http://bioconductor.org/biocLite.R")

-  biocLite("BSgenome.Hsapiens.UCSC.hg19")

+  if (!requireNamespace("BiocManager", quietly=TRUE))

+      install.packages("BiocManager")

+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")

   library(BSgenome.Hsapiens.UCSC.hg19)

 }

 gmapGenome <- GmapGenome(genome=Hsapiens,