Running 'testthat.R' [26s/32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyMicro)
  Loading required package: tidyverse
  -- Attaching packages --------------------------------------- tidyverse 1.3.1 --
  v ggplot2 3.3.5     v purrr   0.3.4
  v tibble  3.1.6     v dplyr   1.0.7
  v tidyr   1.1.4     v stringr 1.4.0
  v readr   2.1.1     v forcats 0.5.1
  -- Conflicts ------------------------------------------ tidyverse_conflicts() --
  x readr::edition_get()   masks testthat::edition_get()
  x dplyr::filter()        masks stats::filter()
  x purrr::is_null()       masks testthat::is_null()
  x dplyr::lag()           masks stats::lag()
  x readr::local_edition() masks testthat::local_edition()
  x 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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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:
       x
    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