Last updated on 2025-12-20 09:49:50 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 3.20 | 90.59 | 93.79 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 2.21 | 53.61 | 55.82 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 145.08 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 6.00 | 165.74 | 171.74 | NOTE | |
| r-devel-windows-x86_64 | 0.1.0 | 5.00 | 105.00 | 110.00 | NOTE | |
| r-patched-linux-x86_64 | 0.1.0 | 3.37 | 83.91 | 87.28 | NOTE | |
| r-release-linux-x86_64 | 0.1.0 | 3.03 | 84.33 | 87.36 | NOTE | |
| r-release-macos-arm64 | 0.1.0 | NOTE | ||||
| r-release-macos-x86_64 | 0.1.0 | 2.00 | 94.00 | 96.00 | NOTE | |
| r-release-windows-x86_64 | 0.1.0 | 5.00 | 103.00 | 108.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.1.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.1.0 | 2.00 | 76.00 | 78.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.1.0 | 7.00 | 126.00 | 133.00 | NOTE |
Version: 0.1.0
Check: Rd files
Result: NOTE
checkRd: (-1) SSE_GIA.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SSE_GIA.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SSE_GIA.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boot_GIA.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boot_GIA.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boot_GIA.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boot_GIA.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) boot_GIA.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) boot_GIA.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cyrpa_ripr.Rd:17: Lost braces
17 | \item{exp{x}{y}rep{z}}{the results from experiment x, sub item y, repetition z}
| ^
checkRd: (-1) cyrpa_ripr.Rd:17: Lost braces
17 | \item{exp{x}{y}rep{z}}{the results from experiment x, sub item y, repetition z}
| ^
checkRd: (-1) cyrpa_ripr.Rd:17: Lost braces
17 | \item{exp{x}{y}rep{z}}{the results from experiment x, sub item y, repetition z}
| ^
checkRd: (-1) estimate_params.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_params.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_params.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_params.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_params.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_params.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_params.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rh5_ama1ron2.Rd:12: Lost braces
12 | \item{exp{x}{y}rep{z}}{the results from experiment x, sub item y, repetition z}
| ^
checkRd: (-1) rh5_ama1ron2.Rd:12: Lost braces
12 | \item{exp{x}{y}rep{z}}{the results from experiment x, sub item y, repetition z}
| ^
checkRd: (-1) rh5_ama1ron2.Rd:12: Lost braces
12 | \item{exp{x}{y}rep{z}}{the results from experiment x, sub item y, repetition z}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, 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
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘loewesadditivity-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_surface
> ### Title: Plot the surface and observations
> ### Aliases: plot_surface
>
> ### ** Examples
>
> df <- loewesadditivity::cyrpa_ripr
> df$dose_A <- df$CyRPA
> df$dose_B <- df$RIPR
> data <- fortify_gia_data(df)
> model_params <- c("beta_A" = .5, "beta_B" = .5,
+ "gamma_A" = .5, "gamma_B" = .5,
+ "tau_1" = 0, "tau_2" = 0)
> n_boot <- 10
> GIA_fn <- base_GIA
> S_fn <- calc_S_base
> fn_list <- NULL
> alpha <- .05
> verbose <- FALSE
> out <- estimate_params(data = data,
+ init_params = model_params,
+ n_boot = n_boot,
+ GIA_fn = GIA_fn,
+ S_fn = S_fn,
+ fn_list = fn_list,
+ alpha = alpha,
+ verbose = verbose)
> plot_surface(out)
Error in `metR::geom_text_contour()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─loewesadditivity::plot_surface(out)
2. │ ├─base::print(g)
3. │ └─ggplot2 (local) `print.ggplot2::ggplot`(g)
4. │ ├─ggplot2::ggplot_gtable(data)
5. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
6. │ └─ggplot2:::by_layer(...)
7. │ ├─rlang::try_fetch(...)
8. │ │ ├─base::tryCatch(...)
9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
12. │ │ └─base::withCallingHandlers(...)
13. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
14. │ └─l$draw_geom(d, layout)
15. │ └─ggplot2 (local) draw_geom(..., self = self)
16. │ └─self$geom$draw_layer(...)
17. │ └─ggplot2 (local) draw_layer(..., self = self)
18. │ └─base::lapply(...)
19. │ └─ggplot2 (local) FUN(X[[i]], ...)
20. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
21. │ └─self$draw_panel(...)
22. │ └─metR (local) draw_panel(...)
23. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
24. │ └─data.table:::`[.data.table`(...)
25. └─base::.handleSimpleError(...)
26. └─rlang (local) h(simpleError(msg, call))
27. └─handlers[[1L]](cnd)
28. └─cli::cli_abort(...)
29. └─rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(loewesadditivity)
>
> test_check("loewesadditivity")
library(loewesadditivity)
levels_A <- c(0, 0.0625, 0.125, 0.25, 0.5, 1, 2, 4)
levels_B <- c(0, 0.125, 0.25, 0.5, 1, 2, 4, 8)
par <- c( 'beta_A' = 1,
'beta_B' = 2,
'gamma_A' = 0.5,
'gamma_B' = 0.5,
'tau_1' = 3,
'tau_2' = 0.05)
my_grid <- design_grid(levels_A = levels_A,
levels_B = levels_B,
n_rep = 2)
## SIMULATE COVERAGE
sim_results <- simulate_coverage(n_sims = 100,
n_boot = 100,
experimental_grid = my_grid,
model_par = par,
alpha = .05,
noise_par = c('a0' = 3,
'a1' = 0.01))
## LOOK AT RESULTS
sim_results
## Uncomment below to write the grid to a .csv file you can open in Excel or google spreadsheets
#write.csv(sim_results, 'coverage_results.csv')Saving _problems/test-plot-32.R
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 20 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot.R:32:3'): plot_surface ────────────────────────────────────
Error in `metR::geom_text_contour(data = df_grid, ggplot2::aes(x = .data$dose_A/beta_A, y = .data$dose_B/beta_B, z = .data$GIA))`: Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─loewesadditivity::plot_surface(out_surface) at test-plot.R:32:3
2. │ ├─base::print(g)
3. │ └─ggplot2 (local) `print.ggplot2::ggplot`(g)
4. │ ├─ggplot2::ggplot_gtable(data)
5. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
6. │ └─ggplot2:::by_layer(...)
7. │ ├─rlang::try_fetch(...)
8. │ │ ├─base::tryCatch(...)
9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
12. │ │ └─base::withCallingHandlers(...)
13. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
14. │ └─l$draw_geom(d, layout)
15. │ └─ggplot2 (local) draw_geom(..., self = self)
16. │ └─self$geom$draw_layer(...)
17. │ └─ggplot2 (local) draw_layer(..., self = self)
18. │ └─base::lapply(...)
19. │ └─ggplot2 (local) FUN(X[[i]], ...)
20. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
21. │ └─self$draw_panel(...)
22. │ └─metR (local) draw_panel(...)
23. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
24. │ └─data.table:::`[.data.table`(...)
25. └─base::.handleSimpleError(...)
26. └─rlang (local) h(simpleError(msg, call))
27. └─handlers[[1L]](cnd)
28. └─cli::cli_abort(...)
29. └─rlang::abort(...)
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 20 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from quickstart.Rmd:157-160 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
--- failed re-building ‘quickstart.Rmd’
SUMMARY: processing the following file failed:
‘quickstart.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc