Last updated on 2022-02-10 08:49:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.47 | 18.17 | 157.90 | 176.07 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.47 | 15.55 | 119.82 | 135.37 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.47 | 225.40 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.47 | 198.01 | ERROR | |||
| r-devel-windows-x86_64-new-UL | 1.47 | 76.00 | 171.00 | 247.00 | ERROR | |
| r-devel-windows-x86_64-new-TK | 1.47 | ERROR | ||||
| r-patched-linux-x86_64 | 1.47 | 18.40 | 146.51 | 164.91 | ERROR | |
| r-release-linux-x86_64 | 1.47 | 15.42 | 147.19 | 162.61 | ERROR | |
| r-release-macos-arm64 | 1.47 | NOTE | ||||
| r-release-macos-x86_64 | 1.47 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.47 | 39.00 | 167.00 | 206.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.47 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.47 | 39.00 | 171.00 | 210.00 | ERROR |
Version: 1.47
Check: examples
Result: ERROR
Running examples in 'tidyMicro-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alpha_div
> ### Title: Alpha Diversity Calculations for tidy_micro
> ### Aliases: alpha_div
>
> ### ** Examples
>
> data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
> otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
+ Order = bpd_ord, Family = bpd_fam)
>
> set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
+ filter(day == 7) ## Only including the first week
Error:
! Can't subset `.data` outside of a data mask context.
Backtrace:
x
1. +-tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>% ...
2. +-dplyr::filter(., day == 7)
3. +-tidyMicro::tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin)
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(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.47
Check: tests
Result: ERROR
Running 'testthat.R' [20s/23s]
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 1.2.0 v stringr 1.4.0
v readr 2.1.2 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.47
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'tidy_micro_vignette.Rmd' using rmarkdown
Quitting from lines 88-93 (tidy_micro_vignette.Rmd)
Error: processing vignette 'tidy_micro_vignette.Rmd' failed with diagnostics:
Can't subset `.data` outside of a data mask context.
--- failed re-building 'tidy_micro_vignette.Rmd'
SUMMARY: processing the following file failed:
'tidy_micro_vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.47
Check: examples
Result: ERROR
Running examples in ‘tidyMicro-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alpha_div
> ### Title: Alpha Diversity Calculations for tidy_micro
> ### Aliases: alpha_div
>
> ### ** Examples
>
> data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
> otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
+ Order = bpd_ord, Family = bpd_fam)
>
> set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
+ filter(day == 7) ## Only including the first week
Error in `dplyr::select()`:
! Can't subset `.data` outside of a data mask context.
Backtrace:
▆
1. ├─tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>% ...
2. ├─dplyr::filter(., day == 7)
3. ├─tidyMicro::tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin)
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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.47
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/25s]
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 1.0.8
✔ 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 in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_beta_heatmap.R:7:3): beta_heat map breaks with more than 1 variable ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_chisq_rank_sum.R:6:3): micro_chisq only takes correct modsum ────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_heatmap.R:7:3): cor_heatmap takes numeric values only ───────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_heatmap.R:20:3): cor_heatmap takes numeric values only ──────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_rocky_mtn.R:7:3): cor_rocky_mtn takes numeric values only ───
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_rocky_mtn.R:21:3): cor_rocky_mtn takes numeric values only ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_forest.R:6:3): micro_forest needs correct modsum ──────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_heatmap.R:6:3): micro_heatmap needs correct modsum ────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_pca.R:6:3): micro_pca needs grp_var ───────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_pca.R:17:3): micro_pca distance matrix ────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_rocky_mtn.R:6:3): micro_rocky_mtn requires specified covariate ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_rocky_mtn.R:19:3): micro_rocky_mtn requires nb_ or bb_mods ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_otu_filters.R:9:5): filter limits work ──────────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_pca_3d.R:6:3): warning message pops ─────────────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
24. │ │ └─base::withCallingHandlers(...)
25. │ └─tidyselect::eval_select(expr(c(...)), .data)
26. │ └─tidyselect:::eval_select_impl(...)
27. │ ├─tidyselect:::with_subscript_errors(...)
28. │ │ ├─base::tryCatch(...)
29. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
30. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
31. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
32. │ │ └─tidyselect:::instrument_base_errors(expr)
33. │ │ └─base::withCallingHandlers(...)
34. │ └─tidyselect:::vars_select_eval(...)
35. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
36. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
37. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
38. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
39. │ └─tidyselect:::eval_context(expr, context_mask)
40. │ └─rlang::eval_tidy(expr, context_mask)
41. ├─rlang::.data$Lib
42. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
43. └─rlang:::stop_fake_data_subset(call)
44. └─rlang::abort(...)
── Error (test_pca_3d.R:17:3): Requires 'time_var' and 'subject' ───────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
14. │ │ └─base::withCallingHandlers(...)
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_ra_bars.R:6:3): ra_bars can't have both top_taxa and RA ─────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_tidyMicro.R:20:3): Named lists and lists give same result ───────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
14. │ │ └─base::withCallingHandlers(...)
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(...)
[ FAIL 18 | WARN 0 | SKIP 2 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.47
Check: package dependencies
Result: NOTE
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.47
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
‘png’ ‘shapes’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.47
Check: examples
Result: ERROR
Running examples in ‘tidyMicro-Ex.R’ failed
The error most likely occurred in:
> ### Name: alpha_div
> ### Title: Alpha Diversity Calculations for tidy_micro
> ### Aliases: alpha_div
>
> ### ** Examples
>
> data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
> otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
+ Order = bpd_ord, Family = bpd_fam)
>
> set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
+ filter(day == 7) ## Only including the first week
Error:
! Can't subset `.data` outside of a data mask context.
Backtrace:
▆
1. ├─tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>% ...
2. ├─dplyr::filter(., day == 7)
3. ├─tidyMicro::tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin)
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(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK
Version: 1.47
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/30s]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.47
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘tidy_micro_vignette.Rmd’ using rmarkdown
Quitting from lines 88-93 (tidy_micro_vignette.Rmd)
Error: processing vignette 'tidy_micro_vignette.Rmd' failed with diagnostics:
Can't subset `.data` outside of a data mask context.
--- failed re-building ‘tidy_micro_vignette.Rmd’
SUMMARY: processing the following file failed:
‘tidy_micro_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.47
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/27s]
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.47
Check: tests
Result: ERROR
Running 'testthat.R' [20s]
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
Flavor: r-devel-windows-x86_64-new-UL
Version: 1.47
Check: tests
Result: ERROR
Running 'testthat.R'
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
Flavor: r-devel-windows-x86_64-new-TK
Version: 1.47
Check: examples
Result: ERROR
Running examples in ‘tidyMicro-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alpha_div
> ### Title: Alpha Diversity Calculations for tidy_micro
> ### Aliases: alpha_div
>
> ### ** Examples
>
> data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
> otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
+ Order = bpd_ord, Family = bpd_fam)
>
> set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
+ filter(day == 7) ## Only including the first week
Error:
! Can't subset `.data` outside of a data mask context.
Backtrace:
▆
1. ├─tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>% ...
2. ├─dplyr::filter(., day == 7)
3. ├─tidyMicro::tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin)
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(...)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.47
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/21s]
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
Flavor: r-patched-linux-x86_64
Version: 1.47
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/22s]
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 1.0.8
✔ 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 in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_beta_heatmap.R:7:3): beta_heat map breaks with more than 1 variable ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_chisq_rank_sum.R:6:3): micro_chisq only takes correct modsum ────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_heatmap.R:7:3): cor_heatmap takes numeric values only ───────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_heatmap.R:20:3): cor_heatmap takes numeric values only ──────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_rocky_mtn.R:7:3): cor_rocky_mtn takes numeric values only ───
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_cor_rocky_mtn.R:21:3): cor_rocky_mtn takes numeric values only ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_forest.R:6:3): micro_forest needs correct modsum ──────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_heatmap.R:6:3): micro_heatmap needs correct modsum ────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_pca.R:6:3): micro_pca needs grp_var ───────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_pca.R:17:3): micro_pca distance matrix ────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_rocky_mtn.R:6:3): micro_rocky_mtn requires specified covariate ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_micro_rocky_mtn.R:19:3): micro_rocky_mtn requires nb_ or bb_mods ──
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_otu_filters.R:9:5): filter limits work ──────────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_pca_3d.R:6:3): warning message pops ─────────────────────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
24. │ │ └─base::withCallingHandlers(...)
25. │ └─tidyselect::eval_select(expr(c(...)), .data)
26. │ └─tidyselect:::eval_select_impl(...)
27. │ ├─tidyselect:::with_subscript_errors(...)
28. │ │ ├─base::tryCatch(...)
29. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
30. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
31. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
32. │ │ └─tidyselect:::instrument_base_errors(expr)
33. │ │ └─base::withCallingHandlers(...)
34. │ └─tidyselect:::vars_select_eval(...)
35. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
36. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
37. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
38. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
39. │ └─tidyselect:::eval_context(expr, context_mask)
40. │ └─rlang::eval_tidy(expr, context_mask)
41. ├─rlang::.data$Lib
42. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
43. └─rlang:::stop_fake_data_subset(call)
44. └─rlang::abort(...)
── Error (test_pca_3d.R:17:3): Requires 'time_var' and 'subject' ───────────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
14. │ │ └─base::withCallingHandlers(...)
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_ra_bars.R:6:3): ra_bars can't have both top_taxa and RA ─────────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─tidyselect::eval_select(expr(c(...)), .data)
18. │ └─tidyselect:::eval_select_impl(...)
19. │ ├─tidyselect:::with_subscript_errors(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─tidyselect:::instrument_base_errors(expr)
25. │ │ └─base::withCallingHandlers(...)
26. │ └─tidyselect:::vars_select_eval(...)
27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
31. │ └─tidyselect:::eval_context(expr, context_mask)
32. │ └─rlang::eval_tidy(expr, context_mask)
33. ├─rlang::.data$Lib
34. └─rlang:::`$.rlang_fake_data_pronoun`(rlang::.data, Lib)
35. └─rlang:::stop_fake_data_subset(call)
36. └─rlang::abort(...)
── Error (test_tidyMicro.R:20:3): Named lists and lists give same result ───────
Error in `dplyr::select(., rlang::.data$Lib, rlang::.data$Taxa, dplyr::everything())`: 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. │ ├─dplyr:::tidyselect_fix_call(...)
14. │ │ └─base::withCallingHandlers(...)
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(...)
[ FAIL 18 | WARN 0 | SKIP 2 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.47
Check: examples
Result: ERROR
Running examples in 'tidyMicro-Ex.R' failed
The error most likely occurred in:
> ### Name: alpha_div
> ### Title: Alpha Diversity Calculations for tidy_micro
> ### Aliases: alpha_div
>
> ### ** Examples
>
> data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
> otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
+ Order = bpd_ord, Family = bpd_fam)
>
> set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
+ filter(day == 7) ## Only including the first week
Error:
! Can't subset `.data` outside of a data mask context.
Backtrace:
x
1. +-tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>% ...
2. +-dplyr::filter(., day == 7)
3. +-tidyMicro::tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin)
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(...)
Execution halted
Flavors: r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.47
Check: tests
Result: ERROR
Running 'testthat.R' [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 --
v ggplot2 3.3.5 v purrr 0.3.4
v tibble 3.1.6 v dplyr 1.0.7
v tidyr 1.2.0 v stringr 1.4.0
v readr 2.1.2 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
Flavor: r-release-windows-ix86+x86_64
Version: 1.47
Check: tests
Result: ERROR
Running 'testthat.R' [25s]
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 1.2.0 v stringr 1.4.0
v readr 2.1.2 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
Flavor: r-oldrel-windows-ix86+x86_64