diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 88d5598..d78ee95 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -22,7 +22,6 @@ jobs: - {os: windows-latest, r: 'release'} - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R new file mode 100644 index 0000000..d36b3bc --- /dev/null +++ b/tests/testthat/setup.R @@ -0,0 +1,4 @@ +# Creating temporary directory +tmpdir <- testthat::test_path("_TEMP") +if (!dir.exists(tmpdir)) dir.create(tmpdir) +tmpdir <- normalizePath(tmpdir, mustWork = TRUE) diff --git a/tests/testthat/teardown.R b/tests/testthat/teardown.R new file mode 100644 index 0000000..55c2bac --- /dev/null +++ b/tests/testthat/teardown.R @@ -0,0 +1,2 @@ +# Removing temporary directory +if (dir.exists(tmpdir)) unlink(tmpdir, recursive = TRUE) diff --git a/tests/testthat/test_Convert.R b/tests/testthat/test_Convert.R index be2564b..4d60799 100644 --- a/tests/testthat/test_Convert.R +++ b/tests/testthat/test_Convert.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path) obj <- BPCells::convert_matrix_type(obj, "uint32_t") diff --git a/tests/testthat/test_Dir.R b/tests/testthat/test_Dir.R index 237922a..4d43010 100644 --- a/tests/testthat/test_Dir.R +++ b/tests/testthat/test_Dir.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path) testthat::test_that("`BPCellsDirSeed()` works as expected", { diff --git a/tests/testthat/test_HDF5.R b/tests/testthat/test_HDF5.R index ebea65b..ae498bf 100644 --- a/tests/testthat/test_HDF5.R +++ b/tests/testthat/test_HDF5.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_hdf5( mat = as(mat, "dgCMatrix"), path = path, group = "BPCells" diff --git a/tests/testthat/test_Mask.R b/tests/testthat/test_Mask.R index e4d1ed7..482e2f2 100644 --- a/tests/testthat/test_Mask.R +++ b/tests/testthat/test_Mask.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path) mask <- matrix( sample(c(0, 1), diff --git a/tests/testthat/test_Multiply.R b/tests/testthat/test_Multiply.R index f72dd08..1f50251 100644 --- a/tests/testthat/test_Multiply.R +++ b/tests/testthat/test_Multiply.R @@ -1,6 +1,6 @@ mat <- mock_matrix(2000, 200) mat2 <- mock_matrix(ncol(mat), 5000) -path <- normalizePath(c(tempfile(), tempfile()), mustWork = FALSE) +path <- normalizePath(c(tempfile(tmpdir = tmpdir), tempfile(tmpdir = tmpdir)), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path[1L]) obj2 <- BPCells::write_matrix_dir(mat = as(mat2, "dgCMatrix"), dir = path[2L]) obj <- obj %*% obj2 diff --git a/tests/testthat/test_RankTransform.R b/tests/testthat/test_RankTransform.R index 85e1466..7b4f349 100644 --- a/tests/testthat/test_RankTransform.R +++ b/tests/testthat/test_RankTransform.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path) obj <- BPCells:::rank_transform(obj, "col") diff --git a/tests/testthat/test_RenameDims.R b/tests/testthat/test_RenameDims.R index d552293..cb440fe 100644 --- a/tests/testthat/test_RenameDims.R +++ b/tests/testthat/test_RenameDims.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path) dimnames(obj) <- list( paste0("G", seq_len(2000L)), diff --git a/tests/testthat/test_Subset.R b/tests/testthat/test_Subset.R index ee1a4b6..c6381e6 100644 --- a/tests/testthat/test_Subset.R +++ b/tests/testthat/test_Subset.R @@ -1,5 +1,5 @@ mat <- mock_matrix(2000, 200) -path <- normalizePath(tempfile(), mustWork = FALSE) +path <- normalizePath(tempfile(tmpdir = tmpdir), mustWork = FALSE) obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path) obj <- obj[1:1000L, 1:100] diff --git a/tests/testthat/test_cBindMatrix.R b/tests/testthat/test_cBindMatrix.R index 8414863..b5dab3e 100644 --- a/tests/testthat/test_cBindMatrix.R +++ b/tests/testthat/test_cBindMatrix.R @@ -1,6 +1,6 @@ mat1 <- mock_matrix(2000, 200) mat2 <- mock_matrix(2000, 200) -path <- normalizePath(c(tempfile(), tempfile()), mustWork = FALSE) +path <- normalizePath(c(tempfile(tmpdir = tmpdir), tempfile(tmpdir = tmpdir)), mustWork = FALSE) obj1 <- BPCells::write_matrix_dir(mat = as(mat1, "dgCMatrix"), dir = path[1L]) obj2 <- BPCells::write_matrix_dir(mat = as(mat2, "dgCMatrix"), dir = path[2L]) obj <- cbind(obj1, obj2) diff --git a/tests/testthat/test_rBindMatrix.R b/tests/testthat/test_rBindMatrix.R index 9199033..d2a6818 100644 --- a/tests/testthat/test_rBindMatrix.R +++ b/tests/testthat/test_rBindMatrix.R @@ -1,6 +1,6 @@ mat <- mock_matrix(2000, 200) mat2 <- mock_matrix(2000, 200) -path <- normalizePath(c(tempfile(), tempfile()), mustWork = FALSE) +path <- normalizePath(c(tempfile(tmpdir = tmpdir), tempfile(tmpdir = tmpdir)), mustWork = FALSE) mat <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path[1L]) mat2 <- BPCells::write_matrix_dir(mat = as(mat2, "dgCMatrix"), dir = path[2L]) obj <- rbind(mat, mat2)