test_that("rbiom_objects", { expect_silent(hmp5$id <- hmp5$id) expect_silent(hmp5$comment <- hmp5$comment) expect_silent(hmp5$sequences <- hmp5$sequences) expect_silent(hmp5$tree <- hmp5$tree) expect_silent(hmp5$taxonomy <- hmp5$taxonomy) expect_silent(hmp5$metadata <- hmp5$metadata) expect_silent(hmp5$counts <- hmp5$counts) expect_silent(hmp5$date <- hmp5$date) expect_silent(hmp5$samples <- hmp5$samples) expect_silent(hmp5$otus <- hmp5$otus) expect_silent(hmp5$fields) expect_silent(hmp5$ranks) expect_silent(hmp5$n_otus) expect_silent(hmp5$n_samples) expect_silent(hmp5$n_fields) expect_silent(hmp5$n_ranks) expect_silent(hmp5$generated_by) expect_silent(hmp5$pkg_version) expect_silent(hmp5$depth) skip_on_cran() capture.output(expect_message(print(hmp5)), type = 'message') # rb_print capture.output(expect_message(hmp5$print()), type = 'message') expect_error(hmp5$initialize()) expect_error( hmp5$id <- 1:3) expect_warning(hmp5$id <- paste0(collapse = '', rep(letters, 5))) expect_silent( hmp5$id <- NA) expect_error( hmp5$comment <- 1:3) expect_warning(hmp5$comment <- paste0(collapse = '', rep(letters, 200))) expect_silent( hmp5$comment <- NA) expect_error(hmp5$sequences <- 1:3) expect_error(hmp5$sequences <- c('a' = 'atcg')) expect_error(rare50$tree <- hmp5$tree) expect_error(min5$counts <- matrix( integer(25), nrow = 5)) expect_error(min5$counts <- matrix(!logical(25), nrow = 5)) expect_error(min5$counts <- matrix( integer(25) - 1, nrow = 5)) expect_error(min5$counts <- matrix( integer(25) + 1, nrow = 5)) expect_error(min5$counts <- matrix( integer(25) + 1, nrow = 5, dimnames = list(NULL, letters[1:5]))) m <- min5$counts; rownames(m) %<>% paste0(' ', .); expect_warning(min5$counts <- m) m <- min5$counts; colnames(m) %<>% paste0(' ', .); expect_warning(min5$counts <- m) expect_error(min5$counts <- matrix( integer(25) + 1, nrow = 5, dimnames = list(rep('a', 5), letters[1:5]))) expect_error(min5$counts <- matrix( integer(25) + 1, nrow = 5, dimnames = list(letters[1:5], rep('a', 5)))) m <- min5$counts; rownames(m) <- paste0(seq_len(nrow(m))); expect_error(min5$counts <- m) m <- min5$counts; colnames(m) <- paste0(seq_len(ncol(m))); expect_error(min5$counts <- m) expect_error(min5$date <- 1:2) expect_error(min5$date <- 'notadate') expect_error(min5$date <- FALSE) })