length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`).

  `actual`: 0
`expected`: 2

res_cut <- cutadapt_remove_primers("inst/extdata", "TTC", "GAA",

"cutadapt_remove_primers()  can't be
    tested when cutadapt is not installed"

Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.4/lme4/libs/x64/lme4.dll':
  `maximal number of DLLs reached...

data_basidio <- subset_taxa(data_fungi, Phylum == "Basidiomycota")
subset_samples(data_basidio, Tree_name %in% c("A10-005", "AD30-abm-X"))
subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
expect_message(circle_pq(data_basidio_2trees, fact = "Tree_name", nproc = 1))
expect_silent(graph_test_pq(data_fungi_mini, fact = "Tree_name", na_remove = TRUE))
expect_silent(graph_test_pq(data_fungi_mini, fact = "Tree_name", return_plot = FALSE))
test_that("sankey_pq works with GlobalPatterns dataset", {
test_that("sankey_pq works with data_fungi_mini dataset", {
test_that("venn_pq works with data_fungi_mini dataset", {
expect_silent(venn_pq(data_fungi_mini, "Height", min_nb_seq = 10))
expect_silent(venn_pq(data_fungi_mini, "Height", print_values = FALSE))
expect_silent(venn_pq(data_fungi_mini, "Height", print_values = FALSE) +
expect_silent(venn_pq(data_fungi_mini, "Height", print_values = TRUE) +
venn_pq(data_fungi_mini, "Height", print_values = TRUE) + scale_fill_hue(),
venn_pq(data_fungi_mini, "Height", print_values = FALSE) + scale_fill_hue(),
test_that("ggvenn_pq works with data_fungi_mini dataset", {
expect_message(ggvenn_pq(data_fungi_mini, "Height", rarefy_before_merging = TRUE))
expect_message(suppressWarnings(ggvenn_pq(data_fungi_mini, "Height", rarefy_after_merging = TRUE)))
expect_message(ggvenn_pq(data_fungi_mini, "Height", add_nb_seq = TRUE))
expect_silent(suppressMessages(ggvenn_pq(data_fungi_mini, "Height", rarefy_nb_seqs = TRUE)))
expect_message(ggvenn_pq(data_fungi_mini, "Height", min_nb_seq = 2))
expect_message(ggvenn_pq(data_fungi_mini, "Height", taxonomic_rank = 4))
expect_silent(suppressMessages(ggvenn_pq(data_fungi_mini, "Height", split_by = "Time")))
test_that("upset_pq works with data_fungi dataset", {
expect_s3_class(upset_pq(data_fungi_mini, "Height", taxa_fill = "Class"), "ggplot")
expect_s3_class(upset_pq(data_fungi_mini, "Time", min_nb_seq = 10), "ggplot")
upset_pq(data_fungi_mini, "Time", numeric_fonction = mean),
test_that("upset_test_pq works with data_fungi_mini dataset", {
upset_test_pq(data_fungi_mini, "Time", min_nb_seq = 10),
upset_test_pq(data_fungi_mini, "Time", numeric_fonction = mean),
var_to_test = c("OTU", "Guild", "Genus")
expect_error(upset_test_pq(data_fungi_mini, "Height", var_to_test = "GUILDDDS"))
test_that("plot_LCBD_pq works with data_fungi dataset", {
test_that("LCBD_pq works with data_fungi_mini dataset", {
expect_s3_class(LCBD_pq(data_fungi_mini, nperm = 100), "beta.div")
LCBD_pq(data_fungi_mini, nperm = 100, method = "jaccard"),
test_that("plot_LCBD_pq works with data_fungi_mini dataset", {
test_that("plot_SCBD_pq works with data_fungi_mini dataset", {
test_that("multipatt_pq works with data_fungi_mini dataset", {