Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Work-around for bug (https://github.com/hadley/testthat/issues/144)
  > Sys.setenv("R_TESTS" = "")
  > 
  > # library 
  > library(testthat)
  > library(HTSSIP)
  > 
  > # test check
  > test_check('HTSSIP')
  -- 1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordination
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: physeq_list_betaDiv(physeq_S2D2_l) at testthat/test-BD_ordinations.R:2
  2: plyr::llply(physeq_l, phyloseq::distance, method = method, weighted = weighted, fast = fast, 
         normalized = normalized, parallel = parallel)
  3: phyloseq::distance
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  -- 2. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)  -----
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: DESeq2_l2fc(physeq_S2D2_l[[1]], sparsity_threshold = 0.25, density_min = 1.71, density_max = 1.75, 
         design = ~Substrate) at testthat/test-DESeq2_l2fc.R:2
  2: phyloseq::sample_data
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 3. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: DESeq2_l2fc(physeq_S2D2_l[[1]], sparsity_threshold = 0.25, density_min = 1.71, density_max = 1.75, 
         design = ~Substrate, sparsity_apply = "heavy") at testthat/test-DESeq2_l2fc.R:15
  2: phyloseq::sample_data
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 4. Error: HRSIP runs with default (@test-HRSIP.R#3)  ------------------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: HRSIP(physeq_S2D2_l[[1]], sparsity_threshold = c(0, 0.15, 0.3), design = ~Substrate) at testthat/test-HRSIP.R:3
  2: plyr::mdply(m, DESeq2_l2fc, physeq = physeq, design = design, l2fc_threshold = l2fc_threshold, 
         sparsity_apply = sparsity_apply, .parallel = parallel)
  3: adply(.data = .data, .margins = 1, .fun = f, ..., .expand = .expand, .progress = .progress, 
         .inform = .inform, .parallel = .parallel, .paropts = .paropts)
  4: ldply(.data = pieces, .fun = .fun, ..., .progress = .progress, .inform = .inform, 
         .parallel = .parallel, .paropts = .paropts, .id = .id)
  5: llply(.data = .data, .fun = .fun, ..., .progress = .progress, .inform = .inform, 
         .parallel = .parallel, .paropts = .paropts)
  6: loop_apply(n, do.ply)
  7: (function (i) 
     {
         piece <- pieces[[i]]
         if (.inform) {
             res <- try(.fun(piece, ...))
             if (inherits(res, "try-error")) {
                 piece <- paste(utils::capture.output(print(piece)), collapse = "\n")
                 stop("with piece ", i, ": \n", piece, call. = FALSE)
             }
         }
         else {
             res <- .fun(piece, ...)
         }
         progress$step()
         res
     })(1L)
  8: .fun(piece, ...)
  9: do.call(flat, c(args, list(...)))
  10: (function (physeq, density_min, density_max, design, l2fc_threshold = 0.25, sparsity_threshold = 0.25, 
         sparsity_apply = "all", size_factors = "geoMean") 
     {
         l2fc_threshold = as.numeric(l2fc_threshold)
         stopifnot(l2fc_threshold >= 0 & l2fc_threshold <= 1)
         sparsity_apply = tolower(sparsity_apply)
         stopifnot(sparsity_apply %in% c("all", "heavy"))
         physeq.md = phyloseq::sample_data(physeq)
         stopifnot(!is.null(physeq.md$Buoyant_density))
         cat("Sparsity threshold:", sparsity_threshold, "\n")
         cat("Density window:", paste(c(density_min, density_max), collapse = "-"), "\n")
         prn = function(x) sum(x > 0) > sparsity_threshold * length(x)
         if (sparsity_apply == "all") {
             physeq = phyloseq::filter_taxa(physeq, prn, TRUE)
         }
         physeq = phyloseq::prune_samples((physeq.md$Buoyant_density >= density_min) & 
             (physeq.md$Buoyant_density <= density_max), physeq)
         physeq = phyloseq::filter_taxa(physeq, function(x) sum(x > 0) > 0 * length(x), 
             TRUE)
         if (sparsity_apply == "heavy") {
             physeq = phyloseq::filter_taxa(physeq, prn, TRUE)
         }
         dds = phyloseq::phyloseq_to_deseq2(physeq, design)
         if (tolower(size_factors) == "geomean") {
             geoMeans = apply(DESeq2::counts(dds), 1, gm_mean)
             dds = DESeq2::estimateSizeFactors(dds, geoMeans = geoMeans)
         }
         else if (tolower(size_factors) == "default") {
             dds = DESeq2::estimateSizeFactors(dds)
         }
         else if (tolower(size_factors) == "iterate") {
             dds = DESeq2::estimateSizeFactors(dds, type = "iterate")
         }
         else {
             stop("size_factors parameter not recognized")
         }
         dds = DESeq2::DESeq(dds, quiet = TRUE, fitType = "local")
         theta = l2fc_threshold
         res = DESeq2::results(dds, independentFiltering = FALSE)
         res$OTU = rownames(res)
         beta = res$log2FoldChange
         betaSE = res$lfcSE
         p = stats::pnorm(beta, theta, betaSE, lower.tail = FALSE)
         res$p = p
         d = data.frame(res[, c("OTU", "log2FoldChange", "p")])
         d$padj = stats::p.adjust(p, method = "BH")
         TT = phyloseq::tax_table(physeq, errorIfNULL = FALSE)
         if (!is.null(TT)) {
             TT = as.data.frame(as.matrix(TT))
             TT$OTU = rownames(TT)
             d = dplyr::left_join(d, TT, c("OTU"))
         }
         d$density_min = density_min
         d$density_max = density_max
         d$sparsity_threshold = sparsity_threshold
         d$sparsity_apply = sparsity_apply
         d$l2fc_threshold = l2fc_threshold
         return(d)
     })(density_min = 1.7, density_max = 1.75, sparsity_threshold = 0, physeq = <S4 object of class structure("phyloseq", package = "phyloseq")>, 
         design = ~Substrate, l2fc_threshold = 0.25, sparsity_apply = "all")
  11: phyloseq::sample_data
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: tryCatch(loadNamespace(name), error = function(e) stop(e))
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: value[[3L]](cond)
  
  -- 5. Error: phyloseq sim (@test-HTSSIP_sim.R#57)  -----------------------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: HTSSIP_sim(L$locs, L$params) at testthat/test-HTSSIP_sim.R:57
  2: phyloseq::phyloseq
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 6. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#73)  -----------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: HTSSIP_sim(L$locs, L$params, meta = meta) at testthat/test-HTSSIP_sim.R:73
  2: phyloseq::phyloseq
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 7. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#9)
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: phyloseq2df(physeq_S2D2, phyloseq::sample_data) at testthat/test-Util.R:9
  2: phyloseq::sample_data
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 8. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#17) 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: phyloseq2df(physeq_S2D2, phyloseq::tax_table) at testthat/test-Util.R:17
  2: phyloseq::tax_table
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#24) 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: phyloseq2df(physeq_S2D2, phyloseq::otu_table) at testthat/test-Util.R:24
  2: phyloseq::otu_table
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 10. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: phyloseq2df(physeq_rep3, phyloseq::sample_data) at testthat/test-Util.R:34
  2: phyloseq::sample_data
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 11. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#47)
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: phyloseq2df(physeq_rep3, phyloseq::otu_table) at testthat/test-Util.R:47
  2: phyloseq::otu_table
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 12. Error: physeq_format runs (@test-chk.R#3)  ------------------------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: physeq_format(physeq_S2D2) at testthat/test-chk.R:3
  2: phyloseq::sample_data
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 13. Error: delta BD on rep3 dataset (@test-delta_BD.R#29)  ------------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: delta_BD(physeq_rep3, control_expr = "Treatment==\"12C-Con\"") at testthat/test-delta_BD.R:29
  2: qSIP_atom_excess_format(physeq, control_expr, treatment_rep = NULL)
  3: phyloseq2table(physeq, include_sample_data = TRUE, sample_col_keep = cols, control_expr = control_expr)
  4: phyloseq::otu_table
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  -- 14. Error: heavy-SIP runs on replicated dataset with default settings (@test-
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: heavy_SIP(physeq_rep3, ex = "Treatment=='12C-Con'") at testthat/test-heavy_SIP.R:7
  2: phyloseq::filter_taxa
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 15. Error: heavy-SIP runs on non-rep dataset with default settings (@test-hea
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: heavy_SIP(physeq_S2D2_l[[1]], ex = "Substrate=='12C-Con'") at testthat/test-heavy_SIP.R:31
  2: phyloseq::filter_taxa
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 16. Error: heavy-SIP runs on replicated dataset with t-test (@test-heavy_SIP.
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: heavy_SIP(physeq_rep3, ex = "Treatment=='12C-Con'", comparison = "H-v-L", hypo_test = "t-test") at testthat/test-heavy_SIP.R:56
  2: phyloseq::filter_taxa
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 17. Error: heavy-SIP runs on replicated dataset with wilcox (@test-heavy_SIP.
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: heavy_SIP(physeq_rep3, ex = "Treatment=='12C-Con'", comparison = "H-v-L", hypo_test = "wilcox") at testthat/test-heavy_SIP.R:80
  2: phyloseq::filter_taxa
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 18. Error: Getting params for subsetting (@test-phyloseq_subset.R#3)  -------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: get_treatment_params(physeq_S2D2, X) at testthat/test-phyloseq_subset.R:3
  2: phyloseq2df(physeq, phyloseq::sample_data)
  3: phyloseq::sample_data
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  -- 19. Error: Expression parameter extraction regardless of quotes (@test-phylos
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: expr_param_extract(x) at testthat/test-phyloseq_subset.R:20
  2: stringr::str_extract_all
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  -- 20. Error: Expression parameter extraction regardless of expr vector length (
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: expr_param_extract(x) at testthat/test-phyloseq_subset.R:30
  2: sapply(ex, expr_param_extract, collapse = collapse)
  3: lapply(X = X, FUN = FUN, ...)
  4: FUN(X[[i]], ...)
  5: stringr::str_extract_all
  6: getExportedValue(pkg, name)
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  -- 21. Error: Subsetting phyloseq object (@test-phyloseq_subset.R#43)  ---------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: get_treatment_params(physeq_S2D2, c("Substrate", "Day")) at testthat/test-phyloseq_subset.R:43
  2: phyloseq2df(physeq, phyloseq::sample_data)
  3: phyloseq::sample_data
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  -- 22. Error: Subsetting phyloseq object (@test-phyloseq_subset.R#60)  ---------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: get_treatment_params(physeq_rep3, c("Treatment", "Replicate")) at testthat/test-phyloseq_subset.R:60
  2: phyloseq2df(physeq, phyloseq::sample_data)
  3: phyloseq::sample_data
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  -- 23. Error: Naming phyloseq object (@test-phyloseq_subset.R#77)  -------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: get_treatment_params(physeq_S2D2, c("Substrate", "Day")) at testthat/test-phyloseq_subset.R:77
  2: phyloseq2df(physeq, phyloseq::sample_data)
  3: phyloseq::sample_data
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  -- 24. Error: qPCR simulation warnings (@test-qPCR.R#101)  ---------------------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: expect_warning(qPCR_sim(physeq_S2D2, control_expr = "Substrate==\"XXX\"", control_mean_fun = L$control_mean_fun, 
         control_sd_fun = L$control_sd_fun, treat_mean_fun = L$treat_mean_fun, treat_sd_fun = L$treat_sd_fun)) at testthat/test-qPCR.R:101
  2: quasi_capture(enquo(object), capture_warnings, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: qPCR_sim(physeq_S2D2, control_expr = "Substrate==\"XXX\"", control_mean_fun = L$control_mean_fun, 
         control_sd_fun = L$control_sd_fun, treat_mean_fun = L$treat_mean_fun, treat_sd_fun = L$treat_sd_fun)
  7: phyloseq2df(physeq, phyloseq::sample_data)
  8: phyloseq::sample_data
  9: getExportedValue(pkg, name)
  10: asNamespace(ns)
  11: getNamespace(ns)
  12: tryCatch(loadNamespace(name), error = function(e) stop(e))
  13: tryCatchList(expr, classes, parentenv, handlers)
  14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  15: value[[3L]](cond)
  
  -- 25. Error: bootstrap iteration is working (@test-qSIP_atom_excess.R#33)  ----
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR) at testthat/test-qSIP_atom_excess.R:33
  2: colnames(phyloseq::otu_table(physeq))
  3: is.data.frame(x)
  4: phyloseq::otu_table
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  -- 26. Error: qPCR OTU table transformation (@test-qSIP_trans.R#38)  -----------
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  1: OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR) at testthat/test-qSIP_trans.R:38
  2: colnames(phyloseq::otu_table(physeq))
  3: is.data.frame(x)
  4: phyloseq::otu_table
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  == testthat results  ===========================================================
  OK: 24 SKIPPED: 17 FAILED: 26
  1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 
  2. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  3. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  4. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  5. Error: phyloseq sim (@test-HTSSIP_sim.R#57) 
  6. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#73) 
  7. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#9) 
  8. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#17) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#24) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted