Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bioset)
  > 
  > test_check("bioset")
  -- 1. Error: sets are read correctly (@test_set.R#5)  --------------------------
  undefined exports: add_count, add_count_, add_rownames, add_tally, add_tally_, all_equal, all_vars, anti_join, any_vars, arrange, arrange_, arrange_all, arrange_at, arrange_if, as.tbl, as.tbl_cube, auto_copy, bench_tbls, between, bind_cols, bind_rows, case_when, changes, check_dbplyr, coalesce, collect, combine, common_by, compare_tbls, compare_tbls2, compute, copy_to, count, count_, cumall, cumany, cume_dist, cummean, current_vars, db_analyze, db_begin, db_commit, db_create_index, db_create_indexes, db_create_table, db_data_type, db_desc, db_drop_table, db_explain, db_has_table, db_insert_into, db_list_tables, db_query_fields, db_query_rows, db_rollback, db_save_query, db_write_table, dense_rank, desc, dim_desc, distinct, distinct_, distinct_all, distinct_at, distinct_if, distinct_prepare, do, do_, dr_dplyr, eval_tbls, eval_tbls2, explain, failwith, filter_, filter_all, filter_at, filter_if, first, full_join, funs, funs_, group_by, group_by_, group_by_all, group_by_at, group_by_if, group_by_prepare, group_cols, group_data, group_indices, group_indices_, group_keys, group_map, group_nest, group_rows, group_size, group_split, group_trim, group_vars, group_walk, grouped_df, groups, hybrid_call, id, ident, if_else, inner_join, is.grouped_df, is.src, is.tbl, is_grouped_df, last, lead, left_join, location, make_tbl, min_rank, mutate, mutate_, mutate_all, mutate_at, mutate_each, mutate_each_, mutate_if, n, n_distinct, n_groups, na_if, near, nest_join, new_grouped_df, nth, ntile, order_by, percent_rank, progress_estimated, pull, rbind_all, rbind_list, recode, recode_factor, rename, rename_, rename_all, rename_at, rename_if, rename_vars, rename_vars_, right_join, row_number, rowwise, same_src, sample_frac, sample_n, select, select_, select_all, select_at, select_if, select_var, select_vars, select_vars_, semi_join, show_query, slice, slice_, sql, sql_escape_ident, sql_escape_string, sql_join, sql_select, sql_semi_join, sql_set_op, sql_subquery, sql_translate_env, src, src_df, src_local, src_mysql, src_postgres, src_sqlite, src_tbls, summarise, summarise_, summarise_all, summarise_at, summarise_each, summarise_each_, summarise_if, summarize, summarize_, summarize_all, summarize_at, summarize_each, summarize_each_, summarize_if, tally, tally_, tbl, tbl_cube, tbl_df, tbl_nongroup_vars, tbl_vars, top_n, transmute, transmute_, transmute_all, transmute_at, transmute_if, ungroup, union_all, validate_grouped_df, vars, with_order, wrap_dbplyr_obj
  1: set_read(num = 1, additional_vars = c("name")) at testthat/test_set.R:5
  2: data_raw %>% dplyr::slice(1:rows)
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: withVisible(function_list[[k]](value))
  9: function_list[[k]](value)
  10: dplyr::slice
  11: getExportedValue(pkg, name)
  12: asNamespace(ns)
  13: getNamespace(ns)
  14: tryCatch(loadNamespace(name), error = function(e) stop(e))
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: value[[3L]](cond)
  
  -- 2. Error: sets with additional variables are read correctly (@test_set.R#14) 
  undefined exports: add_count, add_count_, add_rownames, add_tally, add_tally_, all_equal, all_vars, anti_join, any_vars, arrange, arrange_, arrange_all, arrange_at, arrange_if, as.tbl, as.tbl_cube, auto_copy, bench_tbls, between, bind_cols, bind_rows, case_when, changes, check_dbplyr, coalesce, collect, combine, common_by, compare_tbls, compare_tbls2, compute, copy_to, count, count_, cumall, cumany, cume_dist, cummean, current_vars, db_analyze, db_begin, db_commit, db_create_index, db_create_indexes, db_create_table, db_data_type, db_desc, db_drop_table, db_explain, db_has_table, db_insert_into, db_list_tables, db_query_fields, db_query_rows, db_rollback, db_save_query, db_write_table, dense_rank, desc, dim_desc, distinct, distinct_, distinct_all, distinct_at, distinct_if, distinct_prepare, do, do_, dr_dplyr, eval_tbls, eval_tbls2, explain, failwith, filter_, filter_all, filter_at, filter_if, first, full_join, funs, funs_, group_by, group_by_, group_by_all, group_by_at, group_by_if, group_by_prepare, group_cols, group_data, group_indices, group_indices_, group_keys, group_map, group_nest, group_rows, group_size, group_split, group_trim, group_vars, group_walk, grouped_df, groups, hybrid_call, id, ident, if_else, inner_join, is.grouped_df, is.src, is.tbl, is_grouped_df, last, lead, left_join, location, make_tbl, min_rank, mutate, mutate_, mutate_all, mutate_at, mutate_each, mutate_each_, mutate_if, n, n_distinct, n_groups, na_if, near, nest_join, new_grouped_df, nth, ntile, order_by, percent_rank, progress_estimated, pull, rbind_all, rbind_list, recode, recode_factor, rename, rename_, rename_all, rename_at, rename_if, rename_vars, rename_vars_, right_join, row_number, rowwise, same_src, sample_frac, sample_n, select, select_, select_all, select_at, select_if, select_var, select_vars, select_vars_, semi_join, show_query, slice, slice_, sql, sql_escape_ident, sql_escape_string, sql_join, sql_select, sql_semi_join, sql_set_op, sql_subquery, sql_translate_env, src, src_df, src_local, src_mysql, src_postgres, src_sqlite, src_tbls, summarise, summarise_, summarise_all, summarise_at, summarise_each, summarise_each_, summarise_if, summarize, summarize_, summarize_all, summarize_at, summarize_each, summarize_each_, summarize_if, tally, tally_, tbl, tbl_cube, tbl_df, tbl_nongroup_vars, tbl_vars, top_n, transmute, transmute_, transmute_all, transmute_at, transmute_if, ungroup, union_all, validate_grouped_df, vars, with_order, wrap_dbplyr_obj
  1: set_read(num = 2, additional_vars = c("id", "prop1")) at testthat/test_set.R:14
  2: data_raw %>% dplyr::slice(1:rows)
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: withVisible(function_list[[k]](value))
  9: function_list[[k]](value)
  10: dplyr::slice
  11: getExportedValue(pkg, name)
  12: asNamespace(ns)
  13: getNamespace(ns)
  14: tryCatch(loadNamespace(name), error = function(e) stop(e))
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: value[[3L]](cond)
  
  -- 3. Error: sets without additional names are read correctly (@test_set.R#29)  
  undefined exports: add_count, add_count_, add_rownames, add_tally, add_tally_, all_equal, all_vars, anti_join, any_vars, arrange, arrange_, arrange_all, arrange_at, arrange_if, as.tbl, as.tbl_cube, auto_copy, bench_tbls, between, bind_cols, bind_rows, case_when, changes, check_dbplyr, coalesce, collect, combine, common_by, compare_tbls, compare_tbls2, compute, copy_to, count, count_, cumall, cumany, cume_dist, cummean, current_vars, db_analyze, db_begin, db_commit, db_create_index, db_create_indexes, db_create_table, db_data_type, db_desc, db_drop_table, db_explain, db_has_table, db_insert_into, db_list_tables, db_query_fields, db_query_rows, db_rollback, db_save_query, db_write_table, dense_rank, desc, dim_desc, distinct, distinct_, distinct_all, distinct_at, distinct_if, distinct_prepare, do, do_, dr_dplyr, eval_tbls, eval_tbls2, explain, failwith, filter_, filter_all, filter_at, filter_if, first, full_join, funs, funs_, group_by, group_by_, group_by_all, group_by_at, group_by_if, group_by_prepare, group_cols, group_data, group_indices, group_indices_, group_keys, group_map, group_nest, group_rows, group_size, group_split, group_trim, group_vars, group_walk, grouped_df, groups, hybrid_call, id, ident, if_else, inner_join, is.grouped_df, is.src, is.tbl, is_grouped_df, last, lead, left_join, location, make_tbl, min_rank, mutate, mutate_, mutate_all, mutate_at, mutate_each, mutate_each_, mutate_if, n, n_distinct, n_groups, na_if, near, nest_join, new_grouped_df, nth, ntile, order_by, percent_rank, progress_estimated, pull, rbind_all, rbind_list, recode, recode_factor, rename, rename_, rename_all, rename_at, rename_if, rename_vars, rename_vars_, right_join, row_number, rowwise, same_src, sample_frac, sample_n, select, select_, select_all, select_at, select_if, select_var, select_vars, select_vars_, semi_join, show_query, slice, slice_, sql, sql_escape_ident, sql_escape_string, sql_join, sql_select, sql_semi_join, sql_set_op, sql_subquery, sql_translate_env, src, src_df, src_local, src_mysql, src_postgres, src_sqlite, src_tbls, summarise, summarise_, summarise_all, summarise_at, summarise_each, summarise_each_, summarise_if, summarize, summarize_, summarize_all, summarize_at, summarize_each, summarize_each_, summarize_if, tally, tally_, tbl, tbl_cube, tbl_df, tbl_nongroup_vars, tbl_vars, top_n, transmute, transmute_, transmute_all, transmute_at, transmute_if, ungroup, union_all, validate_grouped_df, vars, with_order, wrap_dbplyr_obj
  1: set_read(num = 3) at testthat/test_set.R:29
  2: data_raw %>% dplyr::slice(1:rows)
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: withVisible(function_list[[k]](value))
  9: function_list[[k]](value)
  10: dplyr::slice
  11: getExportedValue(pkg, name)
  12: asNamespace(ns)
  13: getNamespace(ns)
  14: tryCatch(loadNamespace(name), error = function(e) stop(e))
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: value[[3L]](cond)
  
  -- 4. Error: concentrations are calculated correctly using ln-ln-transform (@tes
  undefined exports: add_count, add_count_, add_rownames, add_tally, add_tally_, all_equal, all_vars, anti_join, any_vars, arrange, arrange_, arrange_all, arrange_at, arrange_if, as.tbl, as.tbl_cube, auto_copy, bench_tbls, between, bind_cols, bind_rows, case_when, changes, check_dbplyr, coalesce, collect, combine, common_by, compare_tbls, compare_tbls2, compute, copy_to, count, count_, cumall, cumany, cume_dist, cummean, current_vars, db_analyze, db_begin, db_commit, db_create_index, db_create_indexes, db_create_table, db_data_type, db_desc, db_drop_table, db_explain, db_has_table, db_insert_into, db_list_tables, db_query_fields, db_query_rows, db_rollback, db_save_query, db_write_table, dense_rank, desc, dim_desc, distinct, distinct_, distinct_all, distinct_at, distinct_if, distinct_prepare, do, do_, dr_dplyr, eval_tbls, eval_tbls2, explain, failwith, filter_, filter_all, filter_at, filter_if, first, full_join, funs, funs_, group_by, group_by_, group_by_all, group_by_at, group_by_if, group_by_prepare, group_cols, group_data, group_indices, group_indices_, group_keys, group_map, group_nest, group_rows, group_size, group_split, group_trim, group_vars, group_walk, grouped_df, groups, hybrid_call, id, ident, if_else, inner_join, is.grouped_df, is.src, is.tbl, is_grouped_df, last, lead, left_join, location, make_tbl, min_rank, mutate, mutate_, mutate_all, mutate_at, mutate_each, mutate_each_, mutate_if, n, n_distinct, n_groups, na_if, near, nest_join, new_grouped_df, nth, ntile, order_by, percent_rank, progress_estimated, pull, rbind_all, rbind_list, recode, recode_factor, rename, rename_, rename_all, rename_at, rename_if, rename_vars, rename_vars_, right_join, row_number, rowwise, same_src, sample_frac, sample_n, select, select_, select_all, select_at, select_if, select_var, select_vars, select_vars_, semi_join, show_query, slice, slice_, sql, sql_escape_ident, sql_escape_string, sql_join, sql_select, sql_semi_join, sql_set_op, sql_subquery, sql_translate_env, src, src_df, src_local, src_mysql, src_postgres, src_sqlite, src_tbls, summarise, summarise_, summarise_all, summarise_at, summarise_each, summarise_each_, summarise_if, summarize, summarize_, summarize_all, summarize_at, summarize_each, summarize_each_, summarize_if, tally, tally_, tbl, tbl_cube, tbl_df, tbl_nongroup_vars, tbl_vars, top_n, transmute, transmute_, transmute_all, transmute_at, transmute_if, ungroup, union_all, validate_grouped_df, vars, with_order, wrap_dbplyr_obj
  1: tibble::tibble(value = c(1, 2, 3, 4, 5, 6), name = c("a", "b", "c", "d", "e", "f")) %>% 
         set_calc_concentrations(cal_names = c("a", "b", "c"), cal_values = c(1, 2, 3)) at testthat/test_set.R:39
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: withVisible(function_list[[k]](value))
  8: function_list[[k]](value)
  9: set_calc_concentrations(., cal_names = c("a", "b", "c"), cal_values = c(1, 2, 3))
  10: data %>% dplyr::mutate(`:=`(!(!col_real_name), NA))
  ...
  16: withVisible(function_list[[k]](value))
  17: function_list[[k]](value)
  18: dplyr::mutate
  19: getExportedValue(pkg, name)
  20: asNamespace(ns)
  21: getNamespace(ns)
  22: tryCatch(loadNamespace(name), error = function(e) stop(e))
  23: tryCatchList(expr, classes, parentenv, handlers)
  24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  25: value[[3L]](cond)
  
  -- 5. Error: variability is calculated correctly (@test_set.R#56)  -------------
  undefined exports: add_count, add_count_, add_rownames, add_tally, add_tally_, all_equal, all_vars, anti_join, any_vars, arrange, arrange_, arrange_all, arrange_at, arrange_if, as.tbl, as.tbl_cube, auto_copy, bench_tbls, between, bind_cols, bind_rows, case_when, changes, check_dbplyr, coalesce, collect, combine, common_by, compare_tbls, compare_tbls2, compute, copy_to, count, count_, cumall, cumany, cume_dist, cummean, current_vars, db_analyze, db_begin, db_commit, db_create_index, db_create_indexes, db_create_table, db_data_type, db_desc, db_drop_table, db_explain, db_has_table, db_insert_into, db_list_tables, db_query_fields, db_query_rows, db_rollback, db_save_query, db_write_table, dense_rank, desc, dim_desc, distinct, distinct_, distinct_all, distinct_at, distinct_if, distinct_prepare, do, do_, dr_dplyr, eval_tbls, eval_tbls2, explain, failwith, filter_, filter_all, filter_at, filter_if, first, full_join, funs, funs_, group_by, group_by_, group_by_all, group_by_at, group_by_if, group_by_prepare, group_cols, group_data, group_indices, group_indices_, group_keys, group_map, group_nest, group_rows, group_size, group_split, group_trim, group_vars, group_walk, grouped_df, groups, hybrid_call, id, ident, if_else, inner_join, is.grouped_df, is.src, is.tbl, is_grouped_df, last, lead, left_join, location, make_tbl, min_rank, mutate, mutate_, mutate_all, mutate_at, mutate_each, mutate_each_, mutate_if, n, n_distinct, n_groups, na_if, near, nest_join, new_grouped_df, nth, ntile, order_by, percent_rank, progress_estimated, pull, rbind_all, rbind_list, recode, recode_factor, rename, rename_, rename_all, rename_at, rename_if, rename_vars, rename_vars_, right_join, row_number, rowwise, same_src, sample_frac, sample_n, select, select_, select_all, select_at, select_if, select_var, select_vars, select_vars_, semi_join, show_query, slice, slice_, sql, sql_escape_ident, sql_escape_string, sql_join, sql_select, sql_semi_join, sql_set_op, sql_subquery, sql_translate_env, src, src_df, src_local, src_mysql, src_postgres, src_sqlite, src_tbls, summarise, summarise_, summarise_all, summarise_at, summarise_each, summarise_each_, summarise_if, summarize, summarize_, summarize_all, summarize_at, summarize_each, summarize_each_, summarize_if, tally, tally_, tbl, tbl_cube, tbl_df, tbl_nongroup_vars, tbl_vars, top_n, transmute, transmute_, transmute_all, transmute_at, transmute_if, ungroup, union_all, validate_grouped_df, vars, with_order, wrap_dbplyr_obj
  1: tibble::tibble(name = c("a", "b", "c", "d", "e", "f", "a", "b", "c", "d", "e", "f", 
         "a"), raw = c(100, 200, 300, 400, 500, 600, 120, 205, 294, 426, 489, 560, 89), 
         conc = c(2, 4, 6, 8, 10, 12, 1.9, 3.7, 6.3, 7.45, 10.4, 12.1, 2.1)) %>% set_calc_variability(name, 
         conc, raw) at testthat/test_set.R:56
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: withVisible(function_list[[k]](value))
  8: function_list[[k]](value)
  9: set_calc_variability(., name, conc, raw)
  10: dplyr::n
  11: getExportedValue(pkg, name)
  12: asNamespace(ns)
  13: getNamespace(ns)
  14: tryCatch(loadNamespace(name), error = function(e) stop(e))
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: value[[3L]](cond)
  
  == testthat results  ===========================================================
  OK: 67 SKIPPED: 0 FAILED: 5
  1. Error: sets are read correctly (@test_set.R#5) 
  2. Error: sets with additional variables are read correctly (@test_set.R#14) 
  3. Error: sets without additional names are read correctly (@test_set.R#29) 
  4. Error: concentrations are calculated correctly using ln-ln-transform (@test_set.R#39) 
  5. Error: variability is calculated correctly (@test_set.R#56) 
  
  Error: testthat unit tests failed
  Execution halted