Version bump, swap GenomicFeatures for txdbmaker

csoneson · csoneson · commit 6b6c25c2fd7f · 2024-03-13T22:13:42.000+01:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Rhisat2
 Type: Package
 Title: R Wrapper for HISAT2 Aligner
-Version: 1.19.1
+Version: 1.19.2
 Authors@R: c(person("Charlotte", "Soneson", role = c("aut", "cre"), 
     email = "charlottesoneson@gmail.com", comment = c(ORCID = "0000-0003-3833-2169")))
 SystemRequirements: GNU make
@@ -10,15 +10,15 @@ Description: An R interface to the HISAT2 spliced short-read aligner by
     genome index and to perform the read alignment to the generated index.
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.2.3
-Depends: R (>= 4.2)
+RoxygenNote: 7.3.1
+Depends: R (>= 4.4.0)
 Suggests: testthat,
     knitr,
     rmarkdown,
     BiocStyle
 VignetteBuilder: knitr
 biocViews: Alignment, Sequencing, SplicedAlignment
-Imports: GenomicFeatures,
+Imports: txdbmaker,
     SGSeq,
     GenomicRanges,
     methods,
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,7 +6,6 @@ export(hisat2_build)
 export(hisat2_build_usage)
 export(hisat2_usage)
 export(hisat2_version)
-importFrom(GenomicFeatures,makeTxDbFromGFF)
 importFrom(GenomicRanges,end)
 importFrom(GenomicRanges,seqnames)
 importFrom(GenomicRanges,start)
@@ -15,4 +14,5 @@ importFrom(GenomicRanges,width)
 importFrom(SGSeq,convertToTxFeatures)
 importFrom(SGSeq,type)
 importFrom(methods,is)
+importFrom(txdbmaker,makeTxDbFromGFF)
 importFrom(utils,write.table)
diff --git a/R/Rhisat2-package.R b/R/Rhisat2-package.R
@@ -7,13 +7,10 @@
 #'
 #' @author Charlotte Soneson, based partly on code from Florian Hahne
 #'
-#' @name Rhisat2-package
-#'
 #' @seealso hisat2, hisat2_build, hisat2_build_usage, hisat2_usage
-#'
+#' @keywords internal
 #' @references
 #' Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low
 #' memory requirements. Nature Methods 12:357-360 (2015).
 #'
-#' @docType package
-NULL
+"_PACKAGE"
diff --git a/R/extract_splice_sites.R b/R/extract_splice_sites.R
@@ -29,7 +29,7 @@
 #'                                           package="Rhisat2"),
 #'                      outfile=tmp, min_length=5)
 #'
-#' @importFrom GenomicFeatures makeTxDbFromGFF
+#' @importFrom txdbmaker makeTxDbFromGFF
 #' @importFrom SGSeq convertToTxFeatures type
 #' @importFrom GenomicRanges start end width seqnames strand
 #' @importFrom methods is
@@ -43,7 +43,7 @@ extract_splice_sites <- function(features, outfile, min_length=5) {
                  "file does not exist.")
         }
         tryCatch({
-            txdb <- GenomicFeatures::makeTxDbFromGFF(features, format = "auto")
+            txdb <- txdbmaker::makeTxDbFromGFF(features, format = "auto")
         }, error = function(e) {
             stop("'features' is a character string corresponding to an ",
                  "existing file, but the file is not compatible with ",
diff --git a/man/Rhisat2-package.Rd b/man/Rhisat2-package.Rd
diff --git a/tests/testthat/test-splice-site-extraction.R b/tests/testthat/test-splice-site-extraction.R
@@ -26,7 +26,7 @@ test_that("splice site extraction works and is consistent with HISAT2 output", {
 
   ## input in TxDb format
   tmp <- tempfile()
-  txdb <- GenomicFeatures::makeTxDbFromGFF(
+  txdb <- txdbmaker::makeTxDbFromGFF(
       system.file("extdata/refs/genes.gtf",
                   package="Rhisat2"))
   extract_splice_sites(features=txdb,
