Last updated on 2025-01-30 04:48:57 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.2 | 8.70 | 141.55 | 150.25 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.2.2 | 6.37 | 70.25 | 76.62 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.2 | 251.02 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.2 | 254.58 | NOTE | |||
| r-devel-windows-x86_64 | 1.2.2 | 13.00 | 126.00 | 139.00 | NOTE | |
| r-patched-linux-x86_64 | 1.2.2 | 14.27 | 128.47 | 142.74 | OK | |
| r-release-linux-x86_64 | 1.2.2 | 8.16 | 128.15 | 136.31 | OK | |
| r-release-macos-arm64 | 1.2.2 | 68.00 | NOTE | |||
| r-release-macos-x86_64 | 1.2.2 | 116.00 | NOTE | |||
| r-release-windows-x86_64 | 1.2.2 | 12.00 | 128.00 | 140.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.2.2 | 70.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.2.2 | 119.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.2.2 | 12.00 | 156.00 | 168.00 | NOTE |
Version: 1.2.2
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
plot_kinetics.Rd: bind_rows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘HaDeX-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_stat_dependency
> ### Title: Calculates confidence limits
> ### Aliases: add_stat_dependency
>
> ### ** Examples
>
> #load example data
> dat <- read_hdx(system.file(package = "HaDeX",
+ "HaDeX/data/KD_180110_CD160_HVEM.csv"))
>
> # prepate dataset for states `CD160` and `CD160_HVEM` in given time parameters
> calc_dat <- prepare_dataset(dat,
+ in_state_first = "CD160_0.001",
+ chosen_state_first = "CD160_1",
+ out_state_first = "CD160_1440",
+ in_state_second = "CD160_HVEM_0.001",
+ chosen_state_second = "CD160_HVEM_1",
+ out_state_second = "CD160_HVEM_1440")
Error in `summarize()`:
ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─HaDeX::prepare_dataset(...)
2. │ └─... %>% arrange(Start, End)
3. ├─dplyr::arrange(., Start, End)
4. ├─dplyr::select(...)
5. ├─dplyr::ungroup(.)
6. ├─dplyr::mutate(...)
7. ├─dplyr::summarize(...)
8. ├─dplyr:::summarise.grouped_df(...)
9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
12. │ └─base::lapply(.x, .f, ...)
13. │ └─dplyr (local) FUN(X[[i]], ...)
14. │ └─mask$eval_all_summarise(quo)
15. │ └─dplyr (local) eval()
16. ├─base::mean(CD160_0.001, na.rm = TRUE)
17. └─base::.handleSimpleError(...)
18. └─dplyr (local) h(simpleError(msg, call))
19. └─dplyr (local) handler(cnd)
20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(HaDeX)
>
> test_check("HaDeX")
[ FAIL 27 | WARN 0 | SKIP 0 | PASS 6 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_add_stat_dependency.R:7:1'): (code run outside of `test_that()`) ──
Error in `summarize(., in_time_mean_1 = mean(!!sym(in_state_first), na.rm = TRUE),
err_in_time_mean_1 = coalesce(sd(!!sym(in_state_first), na.rm = TRUE)/sqrt(length(!!sym(in_state_first))),
0), chosen_time_mean_1 = mean(!!sym(chosen_state_first),
na.rm = TRUE), err_chosen_time_mean_1 = sd(!!sym(chosen_state_first),
na.rm = TRUE)/sqrt(length(!!sym(chosen_state_first))),
out_time_mean_1 = mean(!!sym(out_state_first), na.rm = TRUE),
err_out_time_mean_1 = sd(!!sym(out_state_first), na.rm = TRUE)/sqrt(length(!!sym(out_state_first))),
in_time_mean_2 = mean(!!sym(in_state_second), na.rm = TRUE),
err_in_time_mean_2 = coalesce(sd(!!sym(in_state_second),
na.rm = TRUE)/sqrt(length(!!sym(in_state_second))), 0),
chosen_time_mean_2 = mean(!!sym(chosen_state_second), na.rm = TRUE),
err_chosen_time_mean_2 = sd(!!sym(chosen_state_second), na.rm = TRUE)/sqrt(length(!!sym(chosen_state_second))),
out_time_mean_2 = mean(!!sym(out_state_second), na.rm = TRUE),
err_out_time_mean_2 = sd(!!sym(out_state_second), na.rm = TRUE)/sqrt(length(!!sym(out_state_second))))`: ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─HaDeX::prepare_dataset(...) at test_add_stat_dependency.R:7:1
2. │ └─... %>% arrange(Start, End)
3. ├─dplyr::arrange(., Start, End)
4. ├─dplyr::select(...)
5. ├─dplyr::ungroup(.)
6. ├─dplyr::mutate(...)
7. ├─dplyr::summarize(...)
8. ├─dplyr:::summarise.grouped_df(...)
9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
12. │ └─base::lapply(.x, .f, ...)
13. │ └─dplyr (local) FUN(X[[i]], ...)
14. │ └─mask$eval_all_summarise(quo)
15. │ └─dplyr (local) eval()
16. ├─base::mean(CD160_0.001, na.rm = TRUE)
17. └─base::.handleSimpleError(...)
18. └─dplyr (local) h(simpleError(msg, call))
19. └─dplyr (local) handler(cnd)
20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test_calculate_confidence_limit_values.R:7:1'): (code run outside of `test_that()`) ──
Error in `summarize(., in_time_mean_1 = mean(!!sym(in_state_first), na.rm = TRUE),
err_in_time_mean_1 = coalesce(sd(!!sym(in_state_first), na.rm = TRUE)/sqrt(length(!!sym(in_state_first))),
0), chosen_time_mean_1 = mean(!!sym(chosen_state_first),
na.rm = TRUE), err_chosen_time_mean_1 = sd(!!sym(chosen_state_first),
na.rm = TRUE)/sqrt(length(!!sym(chosen_state_first))),
out_time_mean_1 = mean(!!sym(out_state_first), na.rm = TRUE),
err_out_time_mean_1 = sd(!!sym(out_state_first), na.rm = TRUE)/sqrt(length(!!sym(out_state_first))),
in_time_mean_2 = mean(!!sym(in_state_second), na.rm = TRUE),
err_in_time_mean_2 = coalesce(sd(!!sym(in_state_second),
na.rm = TRUE)/sqrt(length(!!sym(in_state_second))), 0),
chosen_time_mean_2 = mean(!!sym(chosen_state_second), na.rm = TRUE),
err_chosen_time_mean_2 = sd(!!sym(chosen_state_second), na.rm = TRUE)/sqrt(length(!!sym(chosen_state_second))),
out_time_mean_2 = mean(!!sym(out_state_second), na.rm = TRUE),
err_out_time_mean_2 = sd(!!sym(out_state_second), na.rm = TRUE)/sqrt(length(!!sym(out_state_second))))`: ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─HaDeX::prepare_dataset(...) at test_calculate_confidence_limit_values.R:7:1
2. │ └─... %>% arrange(Start, End)
3. ├─dplyr::arrange(., Start, End)
4. ├─dplyr::select(...)
5. ├─dplyr::ungroup(.)
6. ├─dplyr::mutate(...)
7. ├─dplyr::summarize(...)
8. ├─dplyr:::summarise.grouped_df(...)
9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
12. │ └─base::lapply(.x, .f, ...)
13. │ └─dplyr (local) FUN(X[[i]], ...)
14. │ └─mask$eval_all_summarise(quo)
15. │ └─dplyr (local) eval()
16. ├─base::mean(CD160_0.001, na.rm = TRUE)
17. └─base::.handleSimpleError(...)
18. └─dplyr (local) h(simpleError(msg, call))
19. └─dplyr (local) handler(cnd)
20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Failure ('test_calculate_state_deuteration.R:36:3'): frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:36:3'): frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:36:3'): frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:36:3'): frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:36:3'): frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:53:3'): err_frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:53:3'): err_frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:53:3'): err_frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:53:3'): err_frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:53:3'): err_frac_deut_uptake is right ──
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_frac_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:70:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:70:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:70:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:70:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:70:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:87:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:87:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:87:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:87:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Failure ('test_calculate_state_deuteration.R:87:3'): deut_uptake is right ───
... %>% .[[1]] not equal to ref_dat[ref_dat[["Exposure"]] == chosen_time, ]["err_deut_uptake"][[1]].
Lengths differ: 0 is not 1
── Error ('test_comparison_plot.R:9:1'): (code run outside of `test_that()`) ───
Error in `summarize(., in_time_mean_1 = mean(!!sym(in_state_first), na.rm = TRUE),
err_in_time_mean_1 = coalesce(sd(!!sym(in_state_first), na.rm = TRUE)/sqrt(length(!!sym(in_state_first))),
0), chosen_time_mean_1 = mean(!!sym(chosen_state_first),
na.rm = TRUE), err_chosen_time_mean_1 = sd(!!sym(chosen_state_first),
na.rm = TRUE)/sqrt(length(!!sym(chosen_state_first))),
out_time_mean_1 = mean(!!sym(out_state_first), na.rm = TRUE),
err_out_time_mean_1 = sd(!!sym(out_state_first), na.rm = TRUE)/sqrt(length(!!sym(out_state_first))),
in_time_mean_2 = mean(!!sym(in_state_second), na.rm = TRUE),
err_in_time_mean_2 = coalesce(sd(!!sym(in_state_second),
na.rm = TRUE)/sqrt(length(!!sym(in_state_second))), 0),
chosen_time_mean_2 = mean(!!sym(chosen_state_second), na.rm = TRUE),
err_chosen_time_mean_2 = sd(!!sym(chosen_state_second), na.rm = TRUE)/sqrt(length(!!sym(chosen_state_second))),
out_time_mean_2 = mean(!!sym(out_state_second), na.rm = TRUE),
err_out_time_mean_2 = sd(!!sym(out_state_second), na.rm = TRUE)/sqrt(length(!!sym(out_state_second))))`: ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─HaDeX::prepare_dataset(...) at test_comparison_plot.R:9:1
2. │ └─... %>% arrange(Start, End)
3. ├─dplyr::arrange(., Start, End)
4. ├─dplyr::select(...)
5. ├─dplyr::ungroup(.)
6. ├─dplyr::mutate(...)
7. ├─dplyr::summarize(...)
8. ├─dplyr:::summarise.grouped_df(...)
9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
12. │ └─base::lapply(.x, .f, ...)
13. │ └─dplyr (local) FUN(X[[i]], ...)
14. │ └─mask$eval_all_summarise(quo)
15. │ └─dplyr (local) eval()
16. ├─base::mean(CD160_0.001, na.rm = TRUE)
17. └─base::.handleSimpleError(...)
18. └─dplyr (local) h(simpleError(msg, call))
19. └─dplyr (local) handler(cnd)
20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test_plot_coverage.R:9:1'): class is right ──────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., ID = 1L:nrow(.))`: ℹ In argument: `ID = 1L:nrow(.)`.
Caused by error:
! `ID` must be size 0 or 1, not 2.
Backtrace:
▆
1. ├─testthat::expect_is(...)
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─HaDeX::plot_coverage(dat, chosen_state = "CD160_HVEM")
5. │ └─... %>% ggplot(aes(x = value, y = ID, group = ID))
6. ├─ggplot2::ggplot(., aes(x = value, y = ID, group = ID))
7. ├─reshape2::melt(., id.vars = "ID")
8. ├─dplyr::mutate(., ID = 1L:nrow(.))
9. ├─dplyr:::mutate.data.frame(., ID = 1L:nrow(.))
10. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
11. │ ├─base::withCallingHandlers(...)
12. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. └─dplyr (local) `<fn>`(`<dpl:::__>`)
20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test_quality_control.R:8:1'): class is right ────────────────────────
Error in `summarize(., in_time_mean_1 = mean(!!sym(in_state_first), na.rm = TRUE),
err_in_time_mean_1 = coalesce(sd(!!sym(in_state_first), na.rm = TRUE)/sqrt(length(!!sym(in_state_first))),
0), chosen_time_mean_1 = mean(!!sym(chosen_state_first),
na.rm = TRUE), err_chosen_time_mean_1 = sd(!!sym(chosen_state_first),
na.rm = TRUE)/sqrt(length(!!sym(chosen_state_first))),
out_time_mean_1 = mean(!!sym(out_state_first), na.rm = TRUE),
err_out_time_mean_1 = sd(!!sym(out_state_first), na.rm = TRUE)/sqrt(length(!!sym(out_state_first))),
in_time_mean_2 = mean(!!sym(in_state_second), na.rm = TRUE),
err_in_time_mean_2 = coalesce(sd(!!sym(in_state_second),
na.rm = TRUE)/sqrt(length(!!sym(in_state_second))), 0),
chosen_time_mean_2 = mean(!!sym(chosen_state_second), na.rm = TRUE),
err_chosen_time_mean_2 = sd(!!sym(chosen_state_second), na.rm = TRUE)/sqrt(length(!!sym(chosen_state_second))),
out_time_mean_2 = mean(!!sym(out_state_second), na.rm = TRUE),
err_out_time_mean_2 = sd(!!sym(out_state_second), na.rm = TRUE)/sqrt(length(!!sym(out_state_second))))`: ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─testthat::expect_is(...)
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─HaDeX::quality_control(...)
5. │ └─base::lapply(...)
6. │ └─HaDeX (local) FUN(X[[i]], ...)
7. │ └─HaDeX::prepare_dataset(...)
8. │ └─... %>% arrange(Start, End)
9. ├─dplyr::arrange(., Start, End)
10. ├─dplyr::select(...)
11. ├─dplyr::ungroup(.)
12. ├─dplyr::mutate(...)
13. ├─dplyr::summarize(...)
14. ├─dplyr:::summarise.grouped_df(...)
15. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
16. │ ├─base::withCallingHandlers(...)
17. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
18. │ └─base::lapply(.x, .f, ...)
19. │ └─dplyr (local) FUN(X[[i]], ...)
20. │ └─mask$eval_all_summarise(quo)
21. │ └─dplyr (local) eval()
22. ├─base::mean(CD160_0.001, na.rm = TRUE)
23. └─base::.handleSimpleError(...)
24. └─dplyr (local) h(simpleError(msg, call))
25. └─dplyr (local) handler(cnd)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test_quality_control.R:16:1'): size is right ────────────────────────
Error in `summarize(., in_time_mean_1 = mean(!!sym(in_state_first), na.rm = TRUE),
err_in_time_mean_1 = coalesce(sd(!!sym(in_state_first), na.rm = TRUE)/sqrt(length(!!sym(in_state_first))),
0), chosen_time_mean_1 = mean(!!sym(chosen_state_first),
na.rm = TRUE), err_chosen_time_mean_1 = sd(!!sym(chosen_state_first),
na.rm = TRUE)/sqrt(length(!!sym(chosen_state_first))),
out_time_mean_1 = mean(!!sym(out_state_first), na.rm = TRUE),
err_out_time_mean_1 = sd(!!sym(out_state_first), na.rm = TRUE)/sqrt(length(!!sym(out_state_first))),
in_time_mean_2 = mean(!!sym(in_state_second), na.rm = TRUE),
err_in_time_mean_2 = coalesce(sd(!!sym(in_state_second),
na.rm = TRUE)/sqrt(length(!!sym(in_state_second))), 0),
chosen_time_mean_2 = mean(!!sym(chosen_state_second), na.rm = TRUE),
err_chosen_time_mean_2 = sd(!!sym(chosen_state_second), na.rm = TRUE)/sqrt(length(!!sym(chosen_state_second))),
out_time_mean_2 = mean(!!sym(out_state_second), na.rm = TRUE),
err_out_time_mean_2 = sd(!!sym(out_state_second), na.rm = TRUE)/sqrt(length(!!sym(out_state_second))))`: ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...)
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::colnames(...)
5. │ └─base::is.data.frame(x)
6. ├─HaDeX::quality_control(...)
7. │ └─base::lapply(...)
8. │ └─HaDeX (local) FUN(X[[i]], ...)
9. │ └─HaDeX::prepare_dataset(...)
10. │ └─... %>% arrange(Start, End)
11. ├─dplyr::arrange(., Start, End)
12. ├─dplyr::select(...)
13. ├─dplyr::ungroup(.)
14. ├─dplyr::mutate(...)
15. ├─dplyr::summarize(...)
16. ├─dplyr:::summarise.grouped_df(...)
17. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
18. │ ├─base::withCallingHandlers(...)
19. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
20. │ └─base::lapply(.x, .f, ...)
21. │ └─dplyr (local) FUN(X[[i]], ...)
22. │ └─mask$eval_all_summarise(quo)
23. │ └─dplyr (local) eval()
24. ├─base::mean(CD160_0.001, na.rm = TRUE)
25. └─base::.handleSimpleError(...)
26. └─dplyr (local) h(simpleError(msg, call))
27. └─dplyr (local) handler(cnd)
28. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test_woods_plot.R:9:1'): (code run outside of `test_that()`) ────────
Error in `summarize(., in_time_mean_1 = mean(!!sym(in_state_first), na.rm = TRUE),
err_in_time_mean_1 = coalesce(sd(!!sym(in_state_first), na.rm = TRUE)/sqrt(length(!!sym(in_state_first))),
0), chosen_time_mean_1 = mean(!!sym(chosen_state_first),
na.rm = TRUE), err_chosen_time_mean_1 = sd(!!sym(chosen_state_first),
na.rm = TRUE)/sqrt(length(!!sym(chosen_state_first))),
out_time_mean_1 = mean(!!sym(out_state_first), na.rm = TRUE),
err_out_time_mean_1 = sd(!!sym(out_state_first), na.rm = TRUE)/sqrt(length(!!sym(out_state_first))),
in_time_mean_2 = mean(!!sym(in_state_second), na.rm = TRUE),
err_in_time_mean_2 = coalesce(sd(!!sym(in_state_second),
na.rm = TRUE)/sqrt(length(!!sym(in_state_second))), 0),
chosen_time_mean_2 = mean(!!sym(chosen_state_second), na.rm = TRUE),
err_chosen_time_mean_2 = sd(!!sym(chosen_state_second), na.rm = TRUE)/sqrt(length(!!sym(chosen_state_second))),
out_time_mean_2 = mean(!!sym(out_state_second), na.rm = TRUE),
err_out_time_mean_2 = sd(!!sym(out_state_second), na.rm = TRUE)/sqrt(length(!!sym(out_state_second))))`: ℹ In argument: `in_time_mean_1 = mean(CD160_0.001, na.rm = TRUE)`.
ℹ In group 1: `Sequence = "ARSQKSGIRLQGHF"`, `Start = 88`, `End = 101`,
`MaxUptake = 13`, `MHP = 1584.872`.
Caused by error:
! object 'CD160_0.001' not found
Backtrace:
▆
1. ├─HaDeX::prepare_dataset(...) at test_woods_plot.R:9:1
2. │ └─... %>% arrange(Start, End)
3. ├─dplyr::arrange(., Start, End)
4. ├─dplyr::select(...)
5. ├─dplyr::ungroup(.)
6. ├─dplyr::mutate(...)
7. ├─dplyr::summarize(...)
8. ├─dplyr:::summarise.grouped_df(...)
9. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
12. │ └─base::lapply(.x, .f, ...)
13. │ └─dplyr (local) FUN(X[[i]], ...)
14. │ └─mask$eval_all_summarise(quo)
15. │ └─dplyr (local) eval()
16. ├─base::mean(CD160_0.001, na.rm = TRUE)
17. └─base::.handleSimpleError(...)
18. └─dplyr (local) h(simpleError(msg, call))
19. └─dplyr (local) handler(cnd)
20. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 27 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘HaDeX.Rmd’ using rmarkdown
Quitting from lines 265-272 [unnamed-chunk-6] (HaDeX.Rmd)
Error: processing vignette 'HaDeX.Rmd' failed with diagnostics:
ℹ In argument: `in_time_mean_1 = mean(gg_Nucb2_EDTA_0.001, na.rm =
TRUE)`.
ℹ In group 1: `Sequence = "DELKRQEVARL"`, `Start = 96`, `End = 106`, `MaxUptake
= 10`, `MHP = 1356.759`.
Caused by error:
! object 'gg_Nucb2_EDTA_0.001' not found
--- failed re-building ‘HaDeX.Rmd’
--- re-building ‘datafiles.Rmd’ using rmarkdown
--- finished re-building ‘datafiles.Rmd’
--- re-building ‘mass_comparison.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HaDeX.Rcheck/vign_test/HaDeX/vignettes/mass_comparison_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 40322 bytes
Input file size = 40445 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20040
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19959
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 18832
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 18712
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 18712
Output IDAT size = 18712 bytes (21610 bytes decrease)
Output file size = 18783 bytes (21662 bytes = 53.56% decrease)
--- finished re-building ‘mass_comparison.Rmd’
--- re-building ‘transformation.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HaDeX.Rcheck/vign_test/HaDeX/vignettes/transformation_files/figure-html/unnamed-chunk-3-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 22126 bytes
Input file size = 22225 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9976
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 9936
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 9936
Output IDAT size = 9936 bytes (12190 bytes decrease)
Output file size = 10007 bytes (12218 bytes = 54.97% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HaDeX.Rcheck/vign_test/HaDeX/vignettes/transformation_files/figure-html/unnamed-chunk-4-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17885 bytes
Input file size = 17984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7132
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7107
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7107
Output IDAT size = 7107 bytes (10778 bytes decrease)
Output file size = 7178 bytes (10806 bytes = 60.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HaDeX.Rcheck/vign_test/HaDeX/vignettes/transformation_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17885 bytes
Input file size = 17984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7132
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7107
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7107
Output IDAT size = 7107 bytes (10778 bytes decrease)
Output file size = 7178 bytes (10806 bytes = 60.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HaDeX.Rcheck/vign_test/HaDeX/vignettes/transformation_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17885 bytes
Input file size = 17984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7132
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7107
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7107
Output IDAT size = 7107 bytes (10778 bytes decrease)
Output file size = 7178 bytes (10806 bytes = 60.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HaDeX.Rcheck/vign_test/HaDeX/vignettes/transformation_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 27195 bytes
Input file size = 27306 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11551
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11504
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11504
Output IDAT size = 11504 bytes (15691 bytes decrease)
Output file size = 11575 bytes (15731 bytes = 57.61% decrease)
--- finished re-building ‘transformation.Rmd’
SUMMARY: processing the following file failed:
‘HaDeX.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘DT’ ‘gsubfn’ ‘stringr’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.2
Check: installed package size
Result: NOTE
installed size is 8.2Mb
sub-directories of 1Mb or more:
HaDeX 4.0Mb
doc 4.0Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64