Last updated on 2024-10-06 01:49:36 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.3 | 54.09 | 642.75 | 696.84 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.9.3 | 36.18 | 454.43 | 490.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.9.3 | 1250.68 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.3 | 1090.88 | ERROR | |||
| r-devel-windows-x86_64 | 0.9.3 | 56.00 | 615.00 | 671.00 | ERROR | |
| r-patched-linux-x86_64 | 0.9.3 | 48.29 | 597.26 | 645.55 | ERROR | |
| r-release-linux-x86_64 | 0.9.3 | 47.79 | 596.81 | 644.60 | ERROR | |
| r-release-macos-arm64 | 0.9.3 | 286.00 | OK | |||
| r-release-macos-x86_64 | 0.9.3 | 539.00 | NOTE | |||
| r-release-windows-x86_64 | 0.9.3 | 58.00 | 637.00 | 695.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.3 | 9.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.9.3 | 12.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.9.3 | 74.00 | 807.00 | 881.00 | ERROR |
Version: 0.9.3
Check: examples
Result: ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tbl_sum_samdata
> ### Title: Summarize information from sample data in a table
> ### Aliases: tbl_sum_samdata
>
> ### ** Examples
>
> if (requireNamespace("gtsummary")) {
+ tbl_sum_samdata(data_fungi) %>%
+ gtsummary::as_kable()
+
+ summary_samdata <- tbl_sum_samdata(data_fungi,
+ include = c("Time", "Height"),
+ type = list(Time ~ "continuous2", Height ~ "categorical"),
+ statistic = list(Time ~ c("{median} ({p25}, {p75})", "{min}, {max}"))
+ )
+ }
Loading required namespace: gtsummary
Error in `dplyr::mutate()`:
ℹ In argument: `df_stats = list(...)`.
Caused by error in `dplyr::mutate()`:
ℹ In argument: `stat = map(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─tbl_sum_samdata(data_fungi) %>% gtsummary::as_kable()
2. ├─gtsummary::as_kable(.)
3. │ └─gtsummary:::check_class(x, "gtsummary")
4. ├─MiscMetabar::tbl_sum_samdata(data_fungi)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_categorical(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─dplyr::bind_rows(...)
41. │ └─rlang::list2(...)
42. ├─dplyr::group_map(...)
43. ├─dplyr:::group_map.data.frame(...)
44. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
45. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
46. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
47. │ ├─dplyr::mutate(...)
48. │ └─dplyr:::mutate.data.frame(...)
49. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
50. │ ├─base::withCallingHandlers(...)
51. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
52. │ └─mask$eval_all_mutate(quo)
53. │ └─dplyr (local) eval()
54. ├─gtsummary:::map(...)
55. │ └─base::lapply(.x, .f, ...)
56. │ └─gtsummary (local) FUN(X[[i]], ...)
57. │ └─glue::glue(...)
58. │ └─glue::glue_data(...)
59. │ └─base::stopifnot(is.environment(.envir))
60. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
61. └─dplyr (local) `<fn>`(`<smplErrr>`)
62. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SRS_curve_pq 8.876 0.312 10.959
LCBD_pq 5.439 0.372 6.642
ggscatt_pq 5.558 0.040 6.757
filter_trim 5.086 0.216 6.948
subset_taxa_tax_control 5.147 0.154 6.199
sankey_pq 4.290 0.042 5.660
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.9.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [113s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
══ Skipped tests (76) ══════════════════════════════════════════════════════════
• On CRAN (76): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
'test_deseq2_edgeR.R:76:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',
'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
'test_figures_beta_div.R:209:3', 'test_figures_beta_div.R:241:5',
'test_figures_beta_div.R:259:5', 'test_figures_beta_div.R:289:5',
'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',
'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',
'test_figures_beta_div.R:402:3', 'test_figures_beta_div.R:414:3',
'test_figures_taxo.R:15:3', 'test_figures_taxo.R:30:3',
'test_figures_taxo.R:45:3', 'test_figures_taxo.R:64:3',
'test_figures_taxo.R:165:3', 'test_figures_taxo.R:209:5',
'test_figures_taxo.R:252:5', 'test_figures_taxo.R:319:5',
'test_figures_taxo.R:354:3', 'test_figures_taxo.R:379:3',
'test_figures_taxo.R:414:3', 'test_figures_summary_plot.R:10:3',
'test_figures_summary_plot.R:20:3', 'test_figures_summary_plot.R:30:3',
'test_krona.R:7:3', 'test_phyloseq_class.R:10:3',
'test_phyloseq_class.R:51:3', 'test_phyloseq_class.R:94:3', 'test_rw.R:8:3',
'test_rw.R:24:3', 'test_rw.R:39:3', 'test_subset.R:7:3',
'test_subset.R:18:3', 'test_table_functions.R:6:3',
'test_table_functions.R:19:3', 'test_table_functions.R:34:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]],
.envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_continuous(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─glue::glue(...)
41. │ └─glue::glue_data(...)
42. │ └─base::stopifnot(is.environment(.envir))
43. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
44. └─dplyr (local) `<fn>`(`<smplErrr>`)
45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.9.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘metacoder’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.9.3
Check: examples
Result: ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:
> ### Name: tbl_sum_samdata
> ### Title: Summarize information from sample data in a table
> ### Aliases: tbl_sum_samdata
>
> ### ** Examples
>
> if (requireNamespace("gtsummary")) {
+ tbl_sum_samdata(data_fungi) %>%
+ gtsummary::as_kable()
+
+ summary_samdata <- tbl_sum_samdata(data_fungi,
+ include = c("Time", "Height"),
+ type = list(Time ~ "continuous2", Height ~ "categorical"),
+ statistic = list(Time ~ c("{median} ({p25}, {p75})", "{min}, {max}"))
+ )
+ }
Loading required namespace: gtsummary
Error in `dplyr::mutate()`:
ℹ In argument: `df_stats = list(...)`.
Caused by error in `dplyr::mutate()`:
ℹ In argument: `stat = map(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─tbl_sum_samdata(data_fungi) %>% gtsummary::as_kable()
2. ├─gtsummary::as_kable(.)
3. │ └─gtsummary:::check_class(x, "gtsummary")
4. ├─MiscMetabar::tbl_sum_samdata(data_fungi)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_categorical(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─dplyr::bind_rows(...)
41. │ └─rlang::list2(...)
42. ├─dplyr::group_map(...)
43. ├─dplyr:::group_map.data.frame(...)
44. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
45. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
46. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
47. │ ├─dplyr::mutate(...)
48. │ └─dplyr:::mutate.data.frame(...)
49. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
50. │ ├─base::withCallingHandlers(...)
51. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
52. │ └─mask$eval_all_mutate(quo)
53. │ └─dplyr (local) eval()
54. ├─gtsummary:::map(...)
55. │ └─base::lapply(.x, .f, ...)
56. │ └─gtsummary (local) FUN(X[[i]], ...)
57. │ └─glue::glue(...)
58. │ └─glue::glue_data(...)
59. │ └─base::stopifnot(is.environment(.envir))
60. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
61. └─dplyr (local) `<fn>`(`<smplErrr>`)
62. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.9.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [184s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
══ Skipped tests (76) ══════════════════════════════════════════════════════════
• On CRAN (76): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
'test_deseq2_edgeR.R:76:3', 'test_figures_beta_div.R:22:3',
'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
'test_figures_beta_div.R:209:3', 'test_figures_beta_div.R:241:5',
'test_figures_beta_div.R:259:5', 'test_figures_beta_div.R:289:5',
'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',
'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',
'test_figures_beta_div.R:402:3', 'test_figures_beta_div.R:414:3',
'test_figures_biplot.R:14:3', 'test_figures_biplot.R:52:3',
'test_figures_misc.R:11:3', 'test_figures_misc.R:19:3',
'test_figures_misc.R:26:3', 'test_figures_misc.R:35:3',
'test_figures_summary_plot.R:10:3', 'test_figures_summary_plot.R:20:3',
'test_figures_summary_plot.R:30:3', 'test_figures_taxo.R:15:3',
'test_figures_taxo.R:30:3', 'test_figures_taxo.R:45:3',
'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
'test_figures_taxo.R:379:3', 'test_figures_taxo.R:414:3', 'test_krona.R:7:3',
'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
'test_phyloseq_class.R:94:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',
'test_table_functions.R:6:3', 'test_table_functions.R:19:3',
'test_table_functions.R:34:5', 'test_targets.R:5:3', 'test_targets.R:56:3',
'test_targets.R:84:3', 'test_targets.R:101:3', 'test_targets.R:111:3',
'test_tuckey.R:5:3', 'test_tuckey.R:17:3', 'test_tuckey.R:26:3',
'test_misc.R:11:3', 'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]],
.envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_continuous(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─glue::glue(...)
41. │ └─glue::glue_data(...)
42. │ └─base::stopifnot(is.environment(.envir))
43. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
44. └─dplyr (local) `<fn>`(`<smplErrr>`)
45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.9.3
Check: tests
Result: ERROR
Running 'testthat.R' [56s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 77 | PASS 82 ]
══ Skipped tests (77) ══════════════════════════════════════════════════════════
• On CRAN (64): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
'test_deseq2_edgeR.R:76:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_beta_div.R:22:3',
'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
'test_figures_beta_div.R:387:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:10:3',
'test_figures_summary_plot.R:20:3', 'test_figures_summary_plot.R:30:3',
'test_krona.R:7:3', 'test_figures_taxo.R:30:3', 'test_figures_taxo.R:45:3',
'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
'test_figures_taxo.R:379:3', 'test_phyloseq_class.R:10:3',
'test_phyloseq_class.R:51:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:34:5',
'test_misc.R:11:3', 'test_misc.R:30:3', 'test_misc.R:97:3',
'test_tuckey.R:5:3', 'test_tuckey.R:17:3', 'test_tuckey.R:26:3',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:101:3',
'test_targets.R:111:3'
• On Windows (13): 'test_figures_beta_div.R:208:3',
'test_figures_beta_div.R:401:3', 'test_figures_beta_div.R:413:3',
'test_figures_misc.R:10:3', 'test_figures_misc.R:18:3',
'test_figures_taxo.R:14:3', 'test_figures_taxo.R:413:3',
'test_phyloseq_class.R:92:3', 'test_rw.R:38:3', 'test_table_functions.R:5:3',
'test_table_functions.R:18:3', 'test_targets.R:83:3', 'test_targets.R:128:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]],
.envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_continuous(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─glue::glue(...)
41. │ └─glue::glue_data(...)
42. │ └─base::stopifnot(is.environment(.envir))
43. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
44. └─dplyr (local) `<fn>`(`<smplErrr>`)
45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 1 | WARN 0 | SKIP 77 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.9.3
Check: Rd cross-references
Result: NOTE
Unknown package ‘metacoder’ in Rd xrefs
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.9.3
Check: examples
Result: ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tbl_sum_samdata
> ### Title: Summarize information from sample data in a table
> ### Aliases: tbl_sum_samdata
>
> ### ** Examples
>
> if (requireNamespace("gtsummary")) {
+ tbl_sum_samdata(data_fungi) %>%
+ gtsummary::as_kable()
+
+ summary_samdata <- tbl_sum_samdata(data_fungi,
+ include = c("Time", "Height"),
+ type = list(Time ~ "continuous2", Height ~ "categorical"),
+ statistic = list(Time ~ c("{median} ({p25}, {p75})", "{min}, {max}"))
+ )
+ }
Loading required namespace: gtsummary
Error in `dplyr::mutate()`:
ℹ In argument: `df_stats = list(...)`.
Caused by error in `dplyr::mutate()`:
ℹ In argument: `stat = map(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─tbl_sum_samdata(data_fungi) %>% gtsummary::as_kable()
2. ├─gtsummary::as_kable(.)
3. │ └─gtsummary:::check_class(x, "gtsummary")
4. ├─MiscMetabar::tbl_sum_samdata(data_fungi)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_categorical(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─dplyr::bind_rows(...)
41. │ └─rlang::list2(...)
42. ├─dplyr::group_map(...)
43. ├─dplyr:::group_map.data.frame(...)
44. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
45. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
46. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
47. │ ├─dplyr::mutate(...)
48. │ └─dplyr:::mutate.data.frame(...)
49. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
50. │ ├─base::withCallingHandlers(...)
51. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
52. │ └─mask$eval_all_mutate(quo)
53. │ └─dplyr (local) eval()
54. ├─gtsummary:::map(...)
55. │ └─base::lapply(.x, .f, ...)
56. │ └─gtsummary (local) FUN(X[[i]], ...)
57. │ └─glue::glue(...)
58. │ └─glue::glue_data(...)
59. │ └─base::stopifnot(is.environment(.envir))
60. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
61. └─dplyr (local) `<fn>`(`<smplErrr>`)
62. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.9.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [105s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
══ Skipped tests (76) ══════════════════════════════════════════════════════════
• On CRAN (76): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
'test_deseq2_edgeR.R:76:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',
'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
'test_figures_beta_div.R:209:3', 'test_figures_beta_div.R:241:5',
'test_figures_beta_div.R:259:5', 'test_figures_beta_div.R:289:5',
'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',
'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',
'test_figures_beta_div.R:402:3', 'test_figures_beta_div.R:414:3',
'test_figures_summary_plot.R:10:3', 'test_figures_summary_plot.R:20:3',
'test_figures_summary_plot.R:30:3', 'test_krona.R:7:3',
'test_figures_taxo.R:15:3', 'test_figures_taxo.R:30:3',
'test_figures_taxo.R:45:3', 'test_figures_taxo.R:64:3',
'test_figures_taxo.R:165:3', 'test_figures_taxo.R:209:5',
'test_figures_taxo.R:252:5', 'test_figures_taxo.R:319:5',
'test_figures_taxo.R:354:3', 'test_figures_taxo.R:379:3',
'test_figures_taxo.R:414:3', 'test_phyloseq_class.R:10:3',
'test_phyloseq_class.R:51:3', 'test_phyloseq_class.R:94:3', 'test_rw.R:8:3',
'test_rw.R:24:3', 'test_rw.R:39:3', 'test_subset.R:7:3',
'test_subset.R:18:3', 'test_table_functions.R:6:3',
'test_table_functions.R:19:3', 'test_table_functions.R:34:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]],
.envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_continuous(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─glue::glue(...)
41. │ └─glue::glue_data(...)
42. │ └─base::stopifnot(is.environment(.envir))
43. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
44. └─dplyr (local) `<fn>`(`<smplErrr>`)
45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.9.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [105s/65s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
══ Skipped tests (76) ══════════════════════════════════════════════════════════
• On CRAN (76): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
'test_deseq2_edgeR.R:76:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',
'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
'test_figures_beta_div.R:209:3', 'test_figures_beta_div.R:241:5',
'test_figures_beta_div.R:259:5', 'test_figures_beta_div.R:289:5',
'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',
'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',
'test_figures_beta_div.R:402:3', 'test_figures_beta_div.R:414:3',
'test_figures_summary_plot.R:10:3', 'test_figures_summary_plot.R:20:3',
'test_figures_summary_plot.R:30:3', 'test_krona.R:7:3',
'test_figures_taxo.R:15:3', 'test_figures_taxo.R:30:3',
'test_figures_taxo.R:45:3', 'test_figures_taxo.R:64:3',
'test_figures_taxo.R:165:3', 'test_figures_taxo.R:209:5',
'test_figures_taxo.R:252:5', 'test_figures_taxo.R:319:5',
'test_figures_taxo.R:354:3', 'test_figures_taxo.R:379:3',
'test_figures_taxo.R:414:3', 'test_phyloseq_class.R:10:3',
'test_phyloseq_class.R:51:3', 'test_phyloseq_class.R:94:3', 'test_rw.R:8:3',
'test_rw.R:24:3', 'test_rw.R:39:3', 'test_subset.R:7:3',
'test_subset.R:18:3', 'test_table_functions.R:6:3',
'test_table_functions.R:19:3', 'test_table_functions.R:34:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]],
.envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_continuous(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─glue::glue(...)
41. │ └─glue::glue_data(...)
42. │ └─base::stopifnot(is.environment(.envir))
43. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
44. └─dplyr (local) `<fn>`(`<smplErrr>`)
45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 83 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.9.3
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'ANCOMBC', 'mia'
Flavor: r-release-macos-x86_64
Version: 0.9.3
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘ANCOMBC’
Flavor: r-release-macos-x86_64
Version: 0.9.3
Check: package dependencies
Result: ERROR
Package required but not available: ‘dada2’
Packages suggested but not available for checking: 'ANCOMBC', 'mia'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.9.3
Check: tests
Result: ERROR
Running 'testthat.R' [82s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 77 | PASS 82 ]
══ Skipped tests (77) ══════════════════════════════════════════════════════════
• On CRAN (64): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
'test_deseq2_edgeR.R:76:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',
'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
'test_figures_beta_div.R:387:3', 'test_figures_summary_plot.R:10:3',
'test_figures_summary_plot.R:20:3', 'test_figures_summary_plot.R:30:3',
'test_krona.R:7:3', 'test_figures_taxo.R:30:3', 'test_figures_taxo.R:45:3',
'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
'test_figures_taxo.R:379:3', 'test_phyloseq_class.R:10:3',
'test_phyloseq_class.R:51:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:34:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:101:3',
'test_targets.R:111:3', 'test_tuckey.R:5:3', 'test_tuckey.R:17:3',
'test_tuckey.R:26:3', 'test_misc.R:11:3', 'test_misc.R:30:3',
'test_misc.R:97:3'
• On Windows (13): 'test_figures_misc.R:10:3', 'test_figures_misc.R:18:3',
'test_figures_beta_div.R:208:3', 'test_figures_beta_div.R:401:3',
'test_figures_beta_div.R:413:3', 'test_figures_taxo.R:14:3',
'test_figures_taxo.R:413:3', 'test_phyloseq_class.R:92:3', 'test_rw.R:38:3',
'test_table_functions.R:5:3', 'test_table_functions.R:18:3',
'test_targets.R:83:3', 'test_targets.R:128:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]],
.envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
▆
1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
5. │ └─tbl %>% gtsummary::tbl_summary(...)
6. ├─gtsummary::tbl_summary(., ...)
7. │ ├─base::structure(...)
8. │ ├─base::append(...)
9. │ └─gtsummary::brdg_summary(...)
10. │ ├─dplyr::left_join(...)
11. │ ├─dplyr:::left_join.data.frame(...)
12. │ │ └─dplyr::auto_copy(x, y, copy = copy)
13. │ │ ├─dplyr::same_src(x, y)
14. │ │ └─dplyr:::same_src.data.frame(x, y)
15. │ │ └─base::is.data.frame(y)
16. │ ├─dplyr::bind_rows(...)
17. │ │ └─rlang::list2(...)
18. │ └─gtsummary::pier_summary_continuous(...)
19. │ ├─... %>% ...
20. │ ├─dplyr::bind_rows(...)
21. │ │ └─rlang::list2(...)
22. │ ├─dplyr::group_map(...)
23. │ └─dplyr:::group_map.data.frame(...)
24. │ └─dplyr:::map2(chunks, group_keys, .f, ...)
25. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
26. │ └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
27. │ ├─dplyr::mutate(...)
28. │ └─dplyr:::mutate.data.frame(...)
29. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
30. │ ├─base::withCallingHandlers(...)
31. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
32. │ └─mask$eval_all_mutate(quo)
33. │ └─dplyr (local) eval()
34. ├─dplyr::left_join(...)
35. ├─dplyr:::left_join.data.frame(...)
36. │ └─dplyr::auto_copy(x, y, copy = copy)
37. │ ├─dplyr::same_src(x, y)
38. │ └─dplyr:::same_src.data.frame(x, y)
39. │ └─base::is.data.frame(y)
40. ├─glue::glue(...)
41. │ └─glue::glue_data(...)
42. │ └─base::stopifnot(is.environment(.envir))
43. │ └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
44. └─dplyr (local) `<fn>`(`<smplErrr>`)
45. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 1 | WARN 0 | SKIP 77 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64