CRAN Package Check Results for Maintainer ‘Shannon Gallagher <skgallagher19 at gmail.com>’

Last updated on 2025-12-28 03:52:18 CET.

Package	ERROR	NOTE
loewesadditivity	1	12

Package loewesadditivity

Current CRAN status: ERROR: 1, NOTE: 12

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: > ### 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-windows-x86_64

Version: 0.1.0
Check: tests
Result: ERROR Running 'testthat.R' [14s] 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-windows-x86_64

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] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> 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, xlab = "RH5", ylab = "AMA1RON2") 2. ├─base::print(g) at loewesadditivity/R/plot.R:114:3 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`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-windows-x86_64