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[R] Fix acceptance tests memory issue (#1136)
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@ebezzi
ebezzi authored May 13, 2024
1 parent c796baf commit a0bf86c
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Showing 2 changed files with 2 additions and 40 deletions.
40 changes: 0 additions & 40 deletions api/r/cellxgene.census/tests/testthat/acceptance-tests.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
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"

Expand All @@ -17,7 +16,6 @@ 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"

Expand All @@ -29,7 +27,6 @@ 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"

Expand All @@ -42,7 +39,6 @@ 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"

Expand All @@ -54,7 +50,6 @@ 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"

Expand All @@ -66,7 +61,6 @@ 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"

Expand All @@ -77,7 +71,6 @@ 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"

Expand All @@ -89,7 +82,6 @@ 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"

Expand All @@ -100,7 +92,6 @@ 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"

Expand All @@ -113,7 +104,6 @@ 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"

Expand All @@ -126,7 +116,6 @@ 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"

Expand All @@ -139,7 +128,6 @@ 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"

Expand All @@ -152,7 +140,6 @@ 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'"
Expand All @@ -171,7 +158,6 @@ 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'"
Expand All @@ -190,7 +176,6 @@ 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'"
Expand All @@ -209,7 +194,6 @@ 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'"
Expand All @@ -228,7 +212,6 @@ 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,
Expand All @@ -243,7 +226,6 @@ 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,
Expand All @@ -258,7 +240,6 @@ 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,
Expand All @@ -273,7 +254,6 @@ 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,
Expand All @@ -288,7 +268,6 @@ 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,
Expand All @@ -303,7 +282,6 @@ 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,
Expand All @@ -318,7 +296,6 @@ 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,
Expand All @@ -333,7 +310,6 @@ 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,
Expand All @@ -348,7 +324,6 @@ 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,
Expand All @@ -363,7 +338,6 @@ 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,
Expand All @@ -379,7 +353,6 @@ 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,
Expand All @@ -397,7 +370,6 @@ 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,
Expand All @@ -414,7 +386,6 @@ 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,
Expand All @@ -429,7 +400,6 @@ 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,
Expand All @@ -444,7 +414,6 @@ 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,
Expand All @@ -459,7 +428,6 @@ 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,
Expand All @@ -474,7 +442,6 @@ 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,
Expand All @@ -489,7 +456,6 @@ 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,
Expand All @@ -504,7 +470,6 @@ 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,
Expand All @@ -519,7 +484,6 @@ 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,
Expand All @@ -534,7 +498,6 @@ 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,
Expand All @@ -549,7 +512,6 @@ 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,
Expand All @@ -565,7 +527,6 @@ 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,
Expand All @@ -583,7 +544,6 @@ 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,
Expand Down
2 changes: 2 additions & 0 deletions api/r/cellxgene.census/tests/testthat/helper-acceptance.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@ table_iter_is_ok <- function(tbl_iter, stop_after = NULL) {
}

n <- n + 1
rm(tbl)
gc()
}

return(TRUE)
Expand Down

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