Update test_updateSeqlevelsStyle.R

gagneurlab · Jan 16, 2025 · d1b023b · d1b023b
1 parent 5ed90d3
commit d1b023b
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Showing 2 changed files with 3 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -81,10 +81,6 @@ Imports:
     VGAM
 Suggests:
     magick,
-    BSgenome.Hsapiens.UCSC.hg38,
-    BSgenome.Hsapiens.NCBI.GRCh38,
-    BSgenome.Hsapiens.1000genomes.hs37d5,
-    BSgenome.Hsapiens.UCSC.hg19,
     BiocStyle,
     knitr,
     rmarkdown,

diff --git a/tests/testthat/test_updateSeqlevelsStyle.R b/tests/testthat/test_updateSeqlevelsStyle.R
@@ -4,10 +4,6 @@ if (!requireNamespace('BiocManager', quietly = TRUE)) {
    }
 
 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)
 
@@ -26,7 +22,7 @@ test_that("hg38, NCBI to UCSC", {
   #  install.packages('BiocManager')
   #}
 
-  #BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38", ask=FALSE, update=FALSE)
+  BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38", ask=FALSE, update=FALSE)
 
   genome <- getBSgenome("GRCh38")
   bsgenome <- genome
@@ -43,7 +39,7 @@ test_that("hg19, NCBI to UCSC", {
   #  install.packages('BiocManager')
   #}
 
-  #BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5", ask=FALSE, update=FALSE)
+  BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5", ask=FALSE, update=FALSE)
   genome <- getBSgenome("hs37d5")
   bsgenome <- genome
 
@@ -58,7 +54,7 @@ test_that("hg19, UCSC to NCBI", {
   #if (!requireNamespace('BiocManager', quietly = TRUE)) {
   #  install.packages('BiocManager')
   #}
-  #BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", ask=FALSE, update=FALSE)
+  BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", ask=FALSE, update=FALSE)
   genome <- getBSgenome("hg19")
   bsgenome <- genome