Update test_updateSeqlevelsStyle.R

gagneurlab · Jan 16, 2025 · 3715c1f · 3715c1f
1 parent feff38d
commit 3715c1f
Showing 1 changed file with 21 additions and 7 deletions.
diff --git a/tests/testthat/test_updateSeqlevelsStyle.R b/tests/testthat/test_updateSeqlevelsStyle.R
@@ -1,11 +1,13 @@
 context("Test updateSeqlevelsStyle function")
 
 test_that("hg38, UCSC to NCBI", {
-  #if (!require("BiocManager", quietly = TRUE))
-  #  install.packages("BiocManager")
-
+  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")
   genome <- getBSgenome("hg38")
   bsgenome <- genome
 
@@ -17,7 +19,12 @@ test_that("hg38, UCSC to NCBI", {
 })
 
 test_that("hg38, NCBI to UCSC", {
-  #BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38")
+  if (!requireNamespace('BiocManager', quietly = TRUE)) {
+    install.packages('BiocManager')
+  }
+
+  BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38", ask=FALSE, update=FALSE)
+
   genome <- getBSgenome("GRCh38")
   bsgenome <- genome
 
@@ -29,7 +36,11 @@ test_that("hg38, NCBI to UCSC", {
 })
 
 test_that("hg19, NCBI to UCSC", {
-  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
+  if (!requireNamespace('BiocManager', quietly = TRUE)) {
+    install.packages('BiocManager')
+  }
+
+  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5", ask=FALSE, update=FALSE)
   genome <- getBSgenome("hs37d5")
   bsgenome <- genome
 
@@ -41,7 +52,10 @@ test_that("hg19, NCBI to UCSC", {
 })
 
 test_that("hg19, UCSC to NCBI", {
-  BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
+  if (!requireNamespace('BiocManager', quietly = TRUE)) {
+    install.packages('BiocManager')
+  }
+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", ask=FALSE, update=FALSE)
   genome <- getBSgenome("hg19")
   bsgenome <- genome