@@ -1,14 +1,14 @@

 Package: GSVA

-Version: 1.39.14

+Version: 1.39.15

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),

              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),

              person("Alexey", "Sergushichev", role="ctb", email="alsergbox@gmail.com"),

              person("Pablo Sebastian", "Rodriguez", role="ctb", email="pablosebastian.rodriguez@upf.edu"))

 Depends: R (>= 3.5.0)

-Imports: methods, stats, utils, graphics, S4Vectors,

+Imports: methods, stats, utils, graphics, S4Vectors, IRanges,

          Biobase, SummarizedExperiment, GSEABase, Matrix,

-         parallel, BiocParallel, fastmatch, SingleCellExperiment, 

+         parallel, BiocParallel, SingleCellExperiment, 

          sparseMatrixStats, DelayedArray, DelayedMatrixStats,

          HDF5Array, BiocSingular

 Suggests: 

@@ -18,6 +18,7 @@ importMethodsFrom(Biobase, featureNames,

 importMethodsFrom(S4Vectors, metadata,

                              "metadata<-")

+importMethodsFrom(IRanges, match)

 importMethodsFrom(SummarizedExperiment, assays,

                                         colData)

@@ -40,6 +41,7 @@ importFrom(utils, installed.packages,

                   read.csv,

                   write.csv)

 importFrom(S4Vectors, SimpleList)

+importFrom(IRanges, CharacterList)

 importFrom(GSEABase, AnnoOrEntrezIdentifier,

                      mapIdentifiers,

                      getGmt)

@@ -825,7 +825,7 @@ ks_test_Rcode <- function(gene.density, gset_idxs, tau=1, make.plot=FALSE){

 .fastRndWalk <- function(gSetIdx, geneRanking, j, Ra) {

     n <- length(geneRanking)

     k <- length(gSetIdx)

-    idxs <- sort.int(fastmatch::fmatch(gSetIdx, geneRanking))

+    idxs <- sort.int(match(gSetIdx, geneRanking))

     stepCDFinGeneSet2 <- 

         sum(Ra[geneRanking[idxs], j] * (n - idxs + 1)) /

@@ -28,20 +28,12 @@

 ## features in both input objects follow the same nomenclature,

 .mapGeneSetsToFeatures <- function(gsets, features) {

-  ## fastmatch::fmatch() modifies the 'table' argument (i.e., the

-  ## second argument) in place by adding the attribute '.match.hash'

-  ## https://github.com/rcastelo/GSVA/issues/39

-  ## to avoid that undesired feature we duplicate 'features'

-  ## by adding an "impossible value" at the end and let

-  ## fastmatch::match() work with the duplicated object

-  features2 <- c(features, "&!%impossiblevalue%!&")

+  ## Aaron Lun's suggestion at

+  ## https://github.com/rcastelo/GSVA/issues/39#issuecomment-765549620

+  gsets2 <- CharacterList(gsets)

+  mt <- match(gsets2, features)

+  mapdgenesets <- as.list(mt[!is.na(mt)])

-  ## map to the actual features for which expression data is available

-  mapdgenesets <- lapply(gsets,

-                         function(x, y)

-                           as.vector(na.omit(fastmatch::fmatch(x, y))),

-                         features2)

-  

   if (length(unlist(mapdgenesets, use.names=FALSE)) == 0)

     stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")