Import new txdbmaker package

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: tximeta
-Version: 1.21.4
+Version: 1.21.5
 Title: Transcript Quantification Import with Automatic Metadata
 Description: Transcript quantification import from Salmon and
     other quantifiers with automatic attachment of transcript ranges
@@ -20,7 +20,7 @@ VignetteBuilder: knitr
 Imports:
     SummarizedExperiment, tximport, jsonlite, S4Vectors,
     IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures,
-    ensembldb, BiocFileCache, AnnotationHub, Biostrings,
+    txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings,
     tibble, GenomeInfoDb, tools, utils, methods, Matrix
 Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db,
     DESeq2, fishpond, edgeR, limma, devtools
@@ -29,5 +29,5 @@ biocViews: Annotation, GenomeAnnotation, DataImport, Preprocessing,
     RNASeq, SingleCell, Transcriptomics, Transcription, GeneExpression,
     FunctionalGenomics, ReproducibleResearch, ReportWriting,
     ImmunoOncology
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8

NAMESPACE

@@ -39,8 +39,6 @@ importFrom(GenomeInfoDb,seqlevels)
 importFrom(GenomicFeatures,cdsBy)
 importFrom(GenomicFeatures,exonsBy)
 importFrom(GenomicFeatures,genes)
-importFrom(GenomicFeatures,makeTxDbFromGFF)
-importFrom(GenomicFeatures,makeTxDbFromGRanges)
 importFrom(GenomicFeatures,transcripts)
 importFrom(GenomicRanges,"end<-")
 importFrom(GenomicRanges,"start<-")
@@ -73,6 +71,8 @@ importFrom(methods,is)
 importFrom(tibble,tibble)
 importFrom(tools,R_user_dir)
 importFrom(tools,file_ext)
+importFrom(txdbmaker,makeTxDbFromGFF)
+importFrom(txdbmaker,makeTxDbFromGRanges)
 importFrom(tximport,summarizeToGene)
 importFrom(tximport,tximport)
 importFrom(utils,head)

R/tximeta.R

@@ -179,7 +179,8 @@ NULL
 #' @importFrom tximport tximport summarizeToGene
 #' @importFrom jsonlite fromJSON toJSON
 #' @importFrom AnnotationDbi loadDb saveDb select keys mapIds
-#' @importFrom GenomicFeatures makeTxDbFromGFF makeTxDbFromGRanges transcripts genes exonsBy cdsBy
+#' @importFrom GenomicFeatures transcripts genes exonsBy cdsBy
+#' @importFrom txdbmaker makeTxDbFromGFF makeTxDbFromGRanges
 #' @importFrom ensembldb ensDbFromGtf EnsDb
 #' @importFrom BiocFileCache BiocFileCache bfcquery bfcnew bfcadd bfccount bfcrpath
 #' @importFrom AnnotationHub AnnotationHub query dbconn dbfile
@@ -739,7 +740,7 @@ this may produce errors if the GTF is not from Ensembl, or has been modified")
     # 1) Neither Ensembl or GENCODE source
     # 2) GENCODE source but AHub didn't work
     if ((!srcName %in% hubSources) | (srcName == "GENCODE" & !hubWorked)) {
-      message("building TxDb with 'GenomicFeatures' package")
+      message("building TxDb with 'txdbmaker' package")
       # allow .rds instead of GTF
       if (tools::file_ext(txomeInfo$gtf) == "rds") {
         gtf2gr <- readRDS(txomeInfo$gtf)

vignettes/tximeta.Rmd

@@ -150,7 +150,7 @@ coming from the annotation source, and not easily avoided by
 `tximeta` makes use of Bioconductor packages for storing
 transcript databases as *TxDb* or *EnsDb* objects, which both are 
 connected by default to `sqlite` backends.
-For GENCODE and RefSeq GTF files, `tximeta` uses the *GenomicFeatures*
+For GENCODE and RefSeq GTF files, `tximeta` uses the *txdbmaker*
 package [@granges] to parse the GTF and build a *TxDb*. For Ensembl
 GTF files, `tximeta` will first attempt to obtain the correct *EnsDb*
 object using *AnnotationHub*. The *ensembldb* package [@ensembldb]