Running ‘testthat.R’ [44s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  [ FAIL 15 | WARN 2 | SKIP 3 | PASS 490 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test--heat_tree.R:21:3'): A single taxon can be plotted ─────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_true(...) at test--heat_tree.R:21:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─metacoder::heat_tree(...)
    5. ├─metacoder::filter_taxa(my_data, 1)
    6. └─metacoder:::filter_taxa.Taxmap(my_data, 1)
    7.   └─obj$filter_taxa(...)
    8.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    9.       └─metacoder (local) FUN(X[[i]], ...)
   10.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   11.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   12.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   14.               ├─base::withCallingHandlers(...)
   15.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--parsers_and_writers.R:179:3'): Parsing/writing the greengenes database ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─metacoder::parse_greengenes(tax_file = tax_in_path, seq_file = seq_in_path) at test--parsers_and_writers.R:179:2
    2.   └─result$filter_taxa(...)
    3.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    4.       └─metacoder (local) FUN(X[[i]], ...)
    5.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    6.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.               ├─base::withCallingHandlers(...)
   10.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--parsers_and_writers.R:204:3'): Converting to phyloseq ─────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─metacoder::parse_phyloseq(enterotype) at test--parsers_and_writers.R:204:2
    2.   ├─base::withCallingHandlers(...)
    3.   └─output$filter_taxa(output$taxon_names() != "NA")
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--parsers_and_writers.R:213:3'): Parsing/writing dada2 output ───
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─metacoder::parse_dada2(seq_table = seqtab.nochim, tax_table = taxa) at test--parsers_and_writers.R:213:2
    2.   └─output$filter_taxa(!is.na(taxon_names))
    3.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    4.       └─metacoder (local) FUN(X[[i]], ...)
    5.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    6.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.               ├─base::withCallingHandlers(...)
   10.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:458:3'): Default taxon filtering works ───────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(test_obj, taxon_names == "Solanum") at test--taxmap.R:458:2
    2. └─metacoder:::filter_taxa.Taxmap(test_obj, taxon_names == "Solanum")
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:466:3'): Subtaxa can be included when filtering taxa ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(test_obj, taxon_names == "Solanum", subtaxa = TRUE) at test--taxmap.R:466:2
    2. └─metacoder:::filter_taxa.Taxmap(...)
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:476:3'): Supertaxa can be included when filtering taxa ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(test_obj, taxon_names == "Solanum", supertaxa = TRUE) at test--taxmap.R:476:2
    2. └─metacoder:::filter_taxa.Taxmap(...)
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:492:3'): Observations can be preserved when filtering taxa ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(test_obj, taxon_names == "Solanum", drop_obs = FALSE) at test--taxmap.R:492:2
    2. └─metacoder:::filter_taxa.Taxmap(...)
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:510:3'): Taxon ids can be preserved when filtering taxa ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(test_obj, taxon_names != "Solanum", reassign_taxa = FALSE) at test--taxmap.R:510:2
    2. └─metacoder:::filter_taxa.Taxmap(...)
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:515:3'): The selection of taxa to be filtered can be inverted ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(...) at test--taxmap.R:515:2
    2. └─metacoder:::filter_taxa.Taxmap(...)
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:521:3'): Edge cases return reasonable outputs ────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(filter_taxa(test_obj), test_obj) at test--taxmap.R:521:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─metacoder::filter_taxa(test_obj)
    5. └─metacoder:::filter_taxa.Taxmap(test_obj)
    6.   └─obj$filter_taxa(...)
    7.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    8.       └─metacoder (local) FUN(X[[i]], ...)
    9.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   10.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   11.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   12.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   13.               ├─base::withCallingHandlers(...)
   14.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:531:3'): Filtering taxa when there are multiple obs per taxon ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_taxa(test_obj, taxon_names == "Solanum") at test--taxmap.R:531:2
    2. └─metacoder:::filter_taxa.Taxmap(test_obj, taxon_names == "Solanum")
    3.   └─obj$filter_taxa(...)
    4.     └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    5.       └─metacoder (local) FUN(X[[i]], ...)
    6.         ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    7.         └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
    8.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.               ├─base::withCallingHandlers(...)
   11.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:584:3'): Removing taxa when filtering observations work ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::filter_obs(...) at test--taxmap.R:584:2
    2. └─metacoder:::filter_obs.Taxmap(...)
    3.   └─obj$filter_obs(...)
    4.     └─self$filter_taxa(...)
    5.       └─base::lapply(seq_along(self$data), process_one)
    6.         └─metacoder (local) FUN(X[[i]], ...)
    7.           └─private$remove_obs(data = my_index, indexes = obs_subset, unname_only = !drop_obs[my_index])
    8.             ├─base::`[<-`(`*tmp*`, !indexes, "taxon_id", value = `<chr>`)
    9.             └─tibble:::`[<-.tbl_df`(`*tmp*`, !indexes, "taxon_id", value = `<chr>`)
   10.               └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   11.                 └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   12.                   ├─base::withCallingHandlers(...)
   13.                   └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:843:3'): Sampling taxa works ─────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─metacoder::sample_n_taxa(test_obj, size = 3) at test--taxmap.R:843:2
    2. └─metacoder:::sample_n_taxa.Taxmap(test_obj, size = 3)
    3.   ├─base::eval(...)
    4.   │ └─base::eval(...)
    5.   └─`<Taxmap>`$sample_n_taxa(...)
    6.     └─self$filter_taxa(sampled_rows, ...)
    7.       └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
    8.         └─metacoder (local) FUN(X[[i]], ...)
    9.           ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   10.           └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   11.             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   12.               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   13.                 ├─base::withCallingHandlers(...)
   14.                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test--taxmap.R:862:3'): Sampling observations using data from subtaxa works ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test--taxmap.R:862:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─metacoder::sample_n_taxa(test_obj, size = 3, use_subtaxa = 0) at test--taxmap.R:864:4
    5. └─metacoder:::sample_n_taxa.Taxmap(test_obj, size = 3, use_subtaxa = 0)
    6.   ├─base::eval(...)
    7.   │ └─base::eval(...)
    8.   └─`<Taxmap>`$sample_n_taxa(...)
    9.     └─self$filter_taxa(sampled_rows, ...)
   10.       └─base::lapply(seq_along(self$data)[reassign_obs], process_one)
   11.         └─metacoder (local) FUN(X[[i]], ...)
   12.           ├─base::`[<-`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   13.           └─tibble:::`[<-.tbl_df`(`*tmp*`, to_reassign, "taxon_id", value = `<chr>`)
   14.             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   15.               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16.                 ├─base::withCallingHandlers(...)
   17.                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 15 | WARN 2 | SKIP 3 | PASS 490 ]
  Error: Test failures
  Execution halted