fix dependency error

lpantano · Apr 30, 2024 · d568504 · d568504
1 parent 3c3b779
commit d568504
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Showing 5 changed files with 4 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: isomiRs
 Version: 1.31.2
-Date: 2024-03-13
+Date: 2024-04-30
 Type: Package
 Title: Analyze isomiRs and miRNAs from small RNA-seq
 Description: Characterization of miRNAs and isomiRs, clustering and
@@ -17,11 +17,10 @@ Suggests:
     BiocStyle,
     testthat
 Depends:
-    R (>= 4.0),
+    R (>= 4.4),
     SummarizedExperiment
 Imports:
     AnnotationDbi,
-    assertive.sets,
     BiocGenerics,
     Biobase,
     broom,

diff --git a/NAMESPACE b/NAMESPACE
@@ -29,7 +29,6 @@ import(GenomicRanges)
 import(IRanges)
 import(S4Vectors)
 import(SummarizedExperiment)
-import(assertive.sets)
 import(cluster)
 import(gtools)
 import(methods)

diff --git a/NEWS b/NEWS
@@ -1,6 +1,6 @@
-
 Changes in version  1.31.2 (Ömer An)
 
+* remove `assertive.sets`
 * Add gitactions
 * Add color to PCA plot by `isoTop` function
 * Fix depreciated dplyr code

diff --git a/R/isomiRs-package.R b/R/isomiRs-package.R
@@ -11,7 +11,6 @@
 #' @import GGally
 #' @import gtools
 #' @import Biobase
-#' @import assertive.sets
 #' @import cluster
 #' @importFrom AnnotationDbi keys mget revmap
 #' @importFrom reshape melt melt.array melt.data.frame melt.list

diff --git a/R/targets.R b/R/targets.R
@@ -275,7 +275,7 @@ isoNetwork <- function(mirna_rse, gene_rse,
     net <- res %>% separate_rows("geneID") %>% 
         .[,c("ID", "Description", "geneID")] 
     # browser()
-    if (!are_intersecting_sets(net[["geneID"]], names(gene_rse))){
+    if (length(intersect(net[["geneID"]], names(gene_rse))) == 0){
         message("No matching genes between enrich and gene_rse.")
         mapping <- .is_mapping_needed(names(gene_rse), net$geneID)
         message(" Converting from ", mapping[[1]], " to ", mapping[[2]])