diff --git a/tests/testthat/test_updateSeqlevelsStyle.R b/tests/testthat/test_updateSeqlevelsStyle.R index 1d6730a..506a874 100644 --- 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