Update test_updateSeqlevelsStyle.R

gagneurlab · Jan 16, 2025 · 5ed90d3 · 5ed90d3
1 parent 87727af
commit 5ed90d3
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/tests/testthat/test_updateSeqlevelsStyle.R b/tests/testthat/test_updateSeqlevelsStyle.R
@@ -1,12 +1,15 @@
 context("Test updateSeqlevelsStyle function")
+if (!requireNamespace('BiocManager', quietly = TRUE)) {
+    install.packages('BiocManager')
+   }
 
 test_that("hg38, UCSC to NCBI", {
   #if (!requireNamespace('BiocManager', quietly = TRUE)) {
   #  install.packages('BiocManager')
   #  BiocManager::install("remotes")
   #}
 
-  #BiocManager::install("BSgenome.Hsapiens.UCSC.hg38", ask=FALSE, update=FALSE)
+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg38", ask=FALSE, update=FALSE)
 
   genome <- getBSgenome("hg38")
   bsgenome <- genome
@@ -29,7 +32,7 @@ test_that("hg38, NCBI to UCSC", {
   bsgenome <- genome
 
   seqlevelsStyle(bsgenome) <- "UCSC"
-  BiocManager::genome <- updateSeqlevelsStyle(genome, metadata(genome)$genome, "UCSC", metadata(genome)$provider, "./")
+  genome <- updateSeqlevelsStyle(genome, metadata(genome)$genome, "UCSC", metadata(genome)$provider, "./")
 
   expect_equal(seqnames(genome), seqnames(bsgenome))