data(enterotype) data(data_fungi) test_that("write_pq function works fine with enterotype dataset", { testFolder <- tempdir() unlink(list.files(testFolder, full.names = TRUE), recursive = TRUE) expect_silent(write_pq(enterotype, path = testFolder, silent = TRUE)) skip_on_cran() expect_silent(write_pq(enterotype, path = testFolder, silent = TRUE, sam_data_first = TRUE)) expect_silent(write_pq(enterotype, path = testFolder, silent = TRUE, write_sam_data = TRUE)) expect_message(write_pq(enterotype, path = testFolder)) expect_error(write_pq(enterotype, one_file = TRUE, path = testFolder)) expect_s4_class(read_pq(testFolder, taxa_are_rows = TRUE), "phyloseq") new_data_entero <- read_pq(testFolder, taxa_are_rows = TRUE) expect_equal(ntaxa(new_data_entero) - ntaxa(enterotype), 0) expect_equal(nsamples(new_data_entero) - nsamples(enterotype), 0) }) test_that("write_pq function works fine with data_fungi dataset", { testFolder <- tempdir() unlink(list.files(testFolder, full.names = TRUE), recursive = TRUE) expect_silent(write_pq(data_fungi, path = testFolder, silent = TRUE)) skip_on_cran() expect_silent(write_pq(data_fungi, path = testFolder, silent = TRUE, sam_data_first = TRUE)) expect_silent(write_pq(data_fungi, path = testFolder, silent = TRUE, write_sam_data = FALSE)) expect_message(write_pq(data_fungi, path = testFolder, silent = TRUE, sam_data_first = TRUE, one_file = TRUE)) expect_silent(write_pq(data_fungi, path = testFolder, silent = TRUE, write_sam_data = FALSE, one_file = TRUE)) expect_message(write_pq(data_fungi, path = testFolder)) expect_message(write_pq(data_fungi, one_file = TRUE, path = testFolder)) expect_s4_class(read_pq(testFolder), "phyloseq") new_data_fungi <- read_pq(testFolder) expect_equal(ntaxa(new_data_fungi) - ntaxa(data_fungi), 0) expect_equal(nsamples(new_data_fungi) - nsamples(data_fungi), 0) }) test_that("save_pq function works fine with data_fungi dataset", { skip_on_os("windows") skip_on_cran() testFolder <- tempdir() unlink(list.files(testFolder, full.names = TRUE), recursive = TRUE) expect_message(save_pq(data_fungi, path = testFolder, silent = TRUE)) expect_message(save_pq(data_fungi, path = testFolder)) expect_equal(length(list.files(testFolder)), 6) })