* using log directory 'd:/Rcompile/CRANpkg/local/4.3/MiscMetabar.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MiscMetabar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MiscMetabar' version '0.9.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MiscMetabar' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [18s] OK
* checking whether the package can be loaded with stated dependencies ... [17s] OK
* checking whether the package can be unloaded cleanly ... [18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s] OK
* checking whether the namespace can be unloaded cleanly ... [18s] OK
* checking loading without being on the library search path ... [19s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [54s] OK
* checking Rd files ... [3s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [10s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [204s] 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [82s] 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [31s] OK
* checking PDF version of manual ... [25s] OK
* checking HTML version of manual ... [26s] OK
* DONE
Status: 2 ERRORs