load biocmoanager

gagneurlab · Jan 13, 2025 · b3f7762 · b3f7762
1 parent 55bb048
commit b3f7762
Showing 1 changed file with 6 additions and 5 deletions.
diff --git a/tests/testthat/test_updateSeqlevelsStyle.R b/tests/testthat/test_updateSeqlevelsStyle.R
@@ -1,7 +1,8 @@
 context("Test updateSeqlevelsStyle function")
+library(BiocManager)
 
 test_that("hg38, UCSC to NCBI", {
-  install("BSgenome.Hsapiens.UCSC.hg38")
+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
   genome <- getBSgenome("hg38")
   bsgenome <- genome
 
@@ -13,19 +14,19 @@ test_that("hg38, UCSC to NCBI", {
 })
 
 test_that("hg38, NCBI to UCSC", {
-  install("BSgenome.Hsapiens.NCBI.GRCh38")
+  BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38")
   genome <- getBSgenome("GRCh38")
   bsgenome <- genome
 
   seqlevelsStyle(bsgenome) <- "UCSC"
-  genome <- updateSeqlevelsStyle(genome, metadata(genome)$genome, "UCSC", metadata(genome)$provider, "./")
+  BiocManager::genome <- updateSeqlevelsStyle(genome, metadata(genome)$genome, "UCSC", metadata(genome)$provider, "./")
 
   expect_equal(seqnames(genome), seqnames(bsgenome))
 
 })
 
 test_that("hg19, NCBI to UCSC", {
-  install("BSgenome.Hsapiens.1000genomes.hs37d5")
+  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
   genome <- getBSgenome("hs37d5")
   bsgenome <- genome
 
@@ -37,7 +38,7 @@ test_that("hg19, NCBI to UCSC", {
 })
 
 test_that("hg19, UCSC to NCBI", {
-  install("BSgenome.Hsapiens.UCSC.hg19")
+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
   genome <- getBSgenome("hg19")
   bsgenome <- genome