Running ‘testthat.R’ [14s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyMicro)
  Loading required package: tidyverse
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
  ✔ ggplot2 3.3.5     ✔ purrr   0.3.4
  ✔ tibble  3.1.6     ✔ dplyr   1.0.7
  ✔ tidyr   1.2.0     ✔ stringr 1.4.0
  ✔ readr   2.1.2     ✔ forcats 0.5.1
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  > 
  > test_check("tidyMicro")
  [ FAIL 18 | WARN 0 | SKIP 2 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_bb_bars.R:7:3): bb_bars knows it is a bb_mod ────────────────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_bb_bars.R:7:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_beta_heatmap.R:7:3): beta_heat map breaks with more than 1 variable ──
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_beta_heatmap.R:7:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_chisq_rank_sum.R:6:3): micro_chisq only takes correct modsum ────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_chisq_rank_sum.R:6:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_cor_heatmap.R:7:3): cor_heatmap takes numeric values only ───────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_cor_heatmap.R:7:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_cor_heatmap.R:20:3): cor_heatmap takes numeric values only ──────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_cor_heatmap.R:20:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_cor_rocky_mtn.R:7:3): cor_rocky_mtn takes numeric values only ───
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_cor_rocky_mtn.R:7:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_cor_rocky_mtn.R:21:3): cor_rocky_mtn takes numeric values only ──
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_cor_rocky_mtn.R:21:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_micro_forest.R:6:3): micro_forest needs correct modsum ──────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_micro_forest.R:6:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_micro_heatmap.R:6:3): micro_heatmap needs correct modsum ────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_micro_heatmap.R:6:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_micro_pca.R:6:3): micro_pca needs grp_var ───────────────────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_micro_pca.R:6:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_micro_pca.R:17:3): micro_pca distance matrix ────────────────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_micro_pca.R:17:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_micro_rocky_mtn.R:6:3): micro_rocky_mtn requires specified covariate ──
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_micro_rocky_mtn.R:6:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_micro_rocky_mtn.R:19:3): micro_rocky_mtn requires nb_ or bb_mods ──
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_micro_rocky_mtn.R:19:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_otu_filters.R:9:5): filter limits work ──────────────────────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_otu_filters.R:9:4
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_pca_3d.R:6:3): warning message pops ─────────────────────────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test_pca_3d.R:6:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─... %>% ...
    7. ├─tidyMicro::pca_3d(., table = "P", time_var = day, subject = study_id)
    8. │ ├─table %nin% unique(micro_set$Table)
    9. │ │ └─base f(...)
   10. │ └─base::unique(micro_set$Table)
   11. ├─tidyMicro::tidy_micro(...)
   12. │ ├─base::suppressWarnings(...)
   13. │ │ └─base::withCallingHandlers(...)
   14. │ └─otu_tabs %>% ...
   15. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
   16. │ └─plyr::llply(...)
   17. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   18. │   └─base::lapply(pieces, .fun, ...)
   19. │     └─tidyMicro FUN(X[[i]], ...)
   20. │       └─... %>% ...
   21. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   22. ├─dplyr:::select.data.frame(...)
   23. │ └─tidyselect::eval_select(expr(c(...)), .data)
   24. │   └─tidyselect:::eval_select_impl(...)
   25. │     ├─tidyselect:::with_subscript_errors(...)
   26. │     │ ├─base::tryCatch(...)
   27. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   28. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   29. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   30. │     │ └─tidyselect:::instrument_base_errors(expr)
   31. │     │   └─base::withCallingHandlers(...)
   32. │     └─tidyselect:::vars_select_eval(...)
   33. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   34. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   35. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   36. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   37. │               └─tidyselect:::eval_context(expr, context_mask)
   38. │                 └─rlang::eval_tidy(expr, context_mask)
   39. ├─rlang::.data$Lib
   40. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   41.   └─rlang:::stop_fake_data_subset(call)
   42.     └─rlang::abort(...)
  ── Error (test_pca_3d.R:17:3): Requires 'time_var' and 'subject' ───────────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─tidyMicro::tidy_micro(...) at test_pca_3d.R:17:2
    2. │ ├─base::suppressWarnings(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ └─otu_tabs %>% ...
    5. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    6. │ └─plyr::llply(...)
    7. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
    8. │   └─base::lapply(pieces, .fun, ...)
    9. │     └─tidyMicro FUN(X[[i]], ...)
   10. │       └─... %>% ...
   11. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   12. ├─dplyr:::select.data.frame(...)
   13. │ └─tidyselect::eval_select(expr(c(...)), .data)
   14. │   └─tidyselect:::eval_select_impl(...)
   15. │     ├─tidyselect:::with_subscript_errors(...)
   16. │     │ ├─base::tryCatch(...)
   17. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   18. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   19. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   20. │     │ └─tidyselect:::instrument_base_errors(expr)
   21. │     │   └─base::withCallingHandlers(...)
   22. │     └─tidyselect:::vars_select_eval(...)
   23. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   24. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   25. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   26. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   27. │               └─tidyselect:::eval_context(expr, context_mask)
   28. │                 └─rlang::eval_tidy(expr, context_mask)
   29. ├─rlang::.data$Lib
   30. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   31.   └─rlang:::stop_fake_data_subset(call)
   32.     └─rlang::abort(...)
  ── Error (test_ra_bars.R:6:3): ra_bars can't have both top_taxa and RA ─────────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─... %>% filter(day == 7) at test_ra_bars.R:6:2
    2. ├─dplyr::filter(., day == 7)
    3. ├─tidyMicro::tidy_micro(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ └─otu_tabs %>% ...
    7. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    8. │ └─plyr::llply(...)
    9. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   10. │   └─base::lapply(pieces, .fun, ...)
   11. │     └─tidyMicro FUN(X[[i]], ...)
   12. │       └─... %>% ...
   13. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   14. ├─dplyr:::select.data.frame(...)
   15. │ └─tidyselect::eval_select(expr(c(...)), .data)
   16. │   └─tidyselect:::eval_select_impl(...)
   17. │     ├─tidyselect:::with_subscript_errors(...)
   18. │     │ ├─base::tryCatch(...)
   19. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   20. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   22. │     │ └─tidyselect:::instrument_base_errors(expr)
   23. │     │   └─base::withCallingHandlers(...)
   24. │     └─tidyselect:::vars_select_eval(...)
   25. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   26. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   27. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   28. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   29. │               └─tidyselect:::eval_context(expr, context_mask)
   30. │                 └─rlang::eval_tidy(expr, context_mask)
   31. ├─rlang::.data$Lib
   32. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   33.   └─rlang:::stop_fake_data_subset(call)
   34.     └─rlang::abort(...)
  ── Error (test_tidyMicro.R:20:3): Named lists and lists give same result ───────
  Error: Can't subset `.data` outside of a data mask context.
  Backtrace:
       ▆
    1. ├─tidyMicro::tidy_micro(...) at test_tidyMicro.R:20:2
    2. │ ├─base::suppressWarnings(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ └─otu_tabs %>% ...
    5. ├─plyr::ldply(., mul_otu_long, .meta = clinical, .id = "Table")
    6. │ └─plyr::llply(...)
    7. │   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
    8. │   └─base::lapply(pieces, .fun, ...)
    9. │     └─tidyMicro FUN(X[[i]], ...)
   10. │       └─... %>% ...
   11. ├─dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())
   12. ├─dplyr:::select.data.frame(...)
   13. │ └─tidyselect::eval_select(expr(c(...)), .data)
   14. │   └─tidyselect:::eval_select_impl(...)
   15. │     ├─tidyselect:::with_subscript_errors(...)
   16. │     │ ├─base::tryCatch(...)
   17. │     │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
   18. │     │ │   └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   19. │     │ │     └─base doTryCatch(return(expr), name, parentenv, handler)
   20. │     │ └─tidyselect:::instrument_base_errors(expr)
   21. │     │   └─base::withCallingHandlers(...)
   22. │     └─tidyselect:::vars_select_eval(...)
   23. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   24. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
   25. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   26. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
   27. │               └─tidyselect:::eval_context(expr, context_mask)
   28. │                 └─rlang::eval_tidy(expr, context_mask)
   29. ├─rlang::.data$Lib
   30. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
   31.   └─rlang:::stop_fake_data_subset(call)
   32.     └─rlang::abort(...)
  
  [ FAIL 18 | WARN 0 | SKIP 2 | PASS 2 ]
  Error: Test failures
  Execution halted