diff --git a/api/r/cellxgene.census/tests/testthat/acceptance-tests.R b/api/r/cellxgene.census/tests/testthat/acceptance-tests.R index f91a66b65..9215e4665 100644 --- a/api/r/cellxgene.census/tests/testthat/acceptance-tests.R +++ b/api/r/cellxgene.census/tests/testthat/acceptance-tests.R @@ -4,6 +4,7 @@ test_that("test_load_obs_human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" @@ -16,6 +17,7 @@ test_that("test_load_obs_human", { test_that("test_load_var_human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" @@ -27,6 +29,7 @@ test_that("test_load_var_human", { test_that("test_load_obs_mouse", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" @@ -39,6 +42,7 @@ test_that("test_load_obs_mouse", { test_that("test_load_var_mouse", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" @@ -50,6 +54,7 @@ test_that("test_load_var_mouse", { test_that("test_incremental_read_obs_human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" @@ -61,6 +66,7 @@ test_that("test_incremental_read_obs_human", { test_that("test_incremental_read_var_human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" @@ -71,6 +77,7 @@ test_that("test_incremental_read_var_human", { test_that("test_incremental_read_obs_mouse", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" @@ -82,6 +89,7 @@ test_that("test_incremental_read_obs_mouse", { test_that("test_incremental_read_var_mouse", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" @@ -92,6 +100,7 @@ test_that("test_incremental_read_var_mouse", { test_that("test_incremental_read_X_human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" @@ -104,6 +113,7 @@ test_that("test_incremental_read_X_human", { test_that("test_incremental_read_X_human-large-buffer-size", { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" @@ -116,6 +126,7 @@ test_that("test_incremental_read_X_human-large-buffer-size", { test_that("test_incremental_read_X_mouse", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" @@ -128,6 +139,7 @@ test_that("test_incremental_read_X_mouse", { test_that("test_incremental_read_X_mouse-large-buffer-size", { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" @@ -140,6 +152,7 @@ test_that("test_incremental_read_X_mouse-large-buffer-size", { test_that("test_incremental_query_human_brain", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" obs_value_filter <- "tissue == 'brain'" @@ -158,6 +171,7 @@ test_that("test_incremental_query_human_brain", { test_that("test_incremental_query_human_aorta", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "homo_sapiens" obs_value_filter <- "tissue == 'aorta'" @@ -176,6 +190,7 @@ test_that("test_incremental_query_human_aorta", { test_that("test_incremental_query_mouse_brain", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" obs_value_filter <- "tissue == 'brain'" @@ -194,6 +209,7 @@ test_that("test_incremental_query_mouse_brain", { test_that("test_incremental_query_mouse_aorta", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) organism <- "mus_musculus" obs_value_filter <- "tissue == 'aorta'" @@ -212,6 +228,7 @@ test_that("test_incremental_query_mouse_aorta", { test_that("test_seurat_small-query", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -226,6 +243,7 @@ test_that("test_seurat_small-query", { test_that("test_seurat_10K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -240,6 +258,7 @@ test_that("test_seurat_10K-cells-human", { test_that("test_seurat_100K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -254,6 +273,7 @@ test_that("test_seurat_100K-cells-human", { test_that("test_seurat_250K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -268,6 +288,7 @@ test_that("test_seurat_250K-cells-human", { test_that("test_seurat_500K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -282,6 +303,7 @@ test_that("test_seurat_500K-cells-human", { test_that("test_seurat_750K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -296,6 +318,7 @@ test_that("test_seurat_750K-cells-human", { test_that("test_seurat_1M-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -310,6 +333,7 @@ test_that("test_seurat_1M-cells-human", { test_that("test_seurat_common-tissue", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -324,6 +348,7 @@ test_that("test_seurat_common-tissue", { test_that("test_seurat_common-tissue-large-buffer-size", { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -338,6 +363,7 @@ test_that("test_seurat_common-tissue-large-buffer-size", { test_that("test_seurat_common-cell-type", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -353,6 +379,7 @@ test_that("test_seurat_common-cell-type", { test_that("test_seurat_common-cell-type-large-buffer-size", { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -370,6 +397,7 @@ test_that("test_seurat_whole-enchilada-large-buffer-size", { if (FALSE) { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -386,6 +414,7 @@ test_that("test_seurat_whole-enchilada-large-buffer-size", { test_that("test_sce_small-query", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -400,6 +429,7 @@ test_that("test_sce_small-query", { test_that("test_sce_10K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -414,6 +444,7 @@ test_that("test_sce_10K-cells-human", { test_that("test_sce_100K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -428,6 +459,7 @@ test_that("test_sce_100K-cells-human", { test_that("test_sce_250K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -442,6 +474,7 @@ test_that("test_sce_250K-cells-human", { test_that("test_sce_500K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -456,6 +489,7 @@ test_that("test_sce_500K-cells-human", { test_that("test_sce_750K-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -470,6 +504,7 @@ test_that("test_sce_750K-cells-human", { test_that("test_sce_1M-cells-human", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -484,6 +519,7 @@ test_that("test_sce_1M-cells-human", { test_that("test_sce_common-tissue", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -498,6 +534,7 @@ test_that("test_sce_common-tissue", { test_that("test_sce_common-tissue-large-buffer-size", { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -512,6 +549,7 @@ test_that("test_sce_common-tissue-large-buffer-size", { test_that("test_sce_common-cell-type", { census <- open_soma_latest_for_test() on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -527,6 +565,7 @@ test_that("test_sce_common-cell-type", { test_that("test_sce_common-cell-type-large-buffer-size", { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census, @@ -544,6 +583,7 @@ test_that("test_sce_whole-enchilada-large-buffer-size", { if (FALSE) { census <- open_soma_latest_for_test(soma.init_buffer_bytes = paste(1 * 1024**3)) on.exit(census$close(), add = TRUE) + on.exit(gc(verbose = TRUE, reset = FALSE, full = TRUE), add = TRUE) test_args <- list( census = census,