Package check result: OK Changes to worse in reverse depends: Package: autoReg Check: examples New result: ERROR Running examples in ‘autoReg-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: autoReg > ### Title: Perform univariable and multivariable regression and stepwise > ### backward regression automatically > ### Aliases: autoReg autoReg.lm autoReg.glm autoReg.coxph autoReg.survreg > > ### ** Examples > > data(cancer,package="survival") > fit=glm(status~rx+sex+age+obstruct+nodes,data=colon,family="binomial") > autoReg(fit) —————————————————————————————————————————————————————————————————————————————————— Dependent: status 0 (N=925) 1 (N=897) OR (multivariable) —————————————————————————————————————————————————————————————————————————————————— rx Obs 282 (30.5%) 342 (38.1%) Lev 285 (30.8%) 323 (36%) 0.94 (0.74-1.18, p=.576) Lev+5FU 358 (38.7%) 232 (25.9%) 0.53 (0.42-0.68, p<.001) sex Mean ± SD 0.5 ± 0.5 0.5 ± 0.5 0.95 (0.78-1.15, p=.589) age Mean ± SD 60.1 ± 11.5 59.5 ± 12.3 1.00 (0.99-1.01, p=.583) obstruct Mean ± SD 0.2 ± 0.4 0.2 ± 0.4 1.34 (1.05-1.72, p=.018) nodes Mean ± SD 2.7 ± 2.4 4.6 ± 4.2 1.21 (1.17-1.25, p<.001) —————————————————————————————————————————————————————————————————————————————————— > autoReg(fit,uni=FALSE,final=TRUE) ———————————————————————————————————————————————————————————————————————————————————————————————————————————— Dependent: status 0 (N=925) 1 (N=897) OR (multivariable) OR (final) ———————————————————————————————————————————————————————————————————————————————————————————————————————————— rx Obs 282 (30.5%) 342 (38.1%) Lev 285 (30.8%) 323 (36%) 0.94 (0.74-1.18, p=.576) 0.94 (0.74-1.18, p=.575) Lev+5FU 358 (38.7%) 232 (25.9%) 0.53 (0.42-0.68, p<.001) 0.54 (0.42-0.68, p<.001) sex Mean ± SD 0.5 ± 0.5 0.5 ± 0.5 0.95 (0.78-1.15, p=.589) age Mean ± SD 60.1 ± 11.5 59.5 ± 12.3 1.00 (0.99-1.01, p=.583) obstruct Mean ± SD 0.2 ± 0.4 0.2 ± 0.4 1.34 (1.05-1.72, p=.018) 1.34 (1.05-1.71, p=.019) nodes Mean ± SD 2.7 ± 2.4 4.6 ± 4.2 1.21 (1.17-1.25, p<.001) 1.21 (1.17-1.25, p<.001) ———————————————————————————————————————————————————————————————————————————————————————————————————————————— > autoReg(fit,uni=FALSE,imputed=TRUE) Error in `mutate()`: ℹ In argument: `lower = exp(.data$`2.5 %`)`. Caused by error in `` .data$`2.5 %` ``: ! Column `2.5 %` not found in `.data`. Backtrace: ▆ 1. ├─autoReg::autoReg(fit, uni = FALSE, imputed = TRUE) 2. ├─autoReg:::autoReg.glm(fit, uni = FALSE, imputed = TRUE) 3. │ └─autoReg::autoReg_sub(fit = x, ...) 4. │ └─autoReg::imputedReg(fit2, data = data1, ...) 5. │ └─... %>% ... 6. ├─dplyr::mutate(...) 7. ├─dplyr:::mutate.data.frame(...) 8. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 9. │ ├─base::withCallingHandlers(...) 10. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 11. │ └─mask$eval_all_mutate(quo) 12. │ └─dplyr (local) eval() 13. ├─2.5 % 14. ├─rlang:::`$.rlang_data_pronoun`(.data, `2.5 %`) 15. │ └─rlang:::data_pronoun_get(...) 16. └─rlang:::abort_data_pronoun(x, call = y) 17. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call) Execution halted Package: autoReg Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Automatic_Regression_Modeling.Rmd’ using rmarkdown Quitting from lines 134-137 [unnamed-chunk-14] (Automatic_Regression_Modeling.Rmd) Error: processing vignette 'Automatic_Regression_Modeling.Rmd' failed with diagnostics: ℹ In argument: `lower = .data$`2.5 %``. Caused by error in `` .data$`2.5 %` ``: ! Column `2.5 %` not found in `.data`. --- failed re-building ‘Automatic_Regression_Modeling.Rmd’ --- re-building ‘Bootstrap_Prediction.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Bootstrap_Prediction_files/figure-html/unnamed-chunk-5-1.png 768x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11530 bytes Input file size = 12400 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9956 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 9938 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 = 9938 Output IDAT size = 9938 bytes (1592 bytes decrease) Output file size = 10016 bytes (2384 bytes = 19.23% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Bootstrap_Prediction_files/figure-html/unnamed-chunk-8-1.png 768x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 47071 bytes Input file size = 47209 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 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 = 44818 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 = 0 f = 5 IDAT size = 44818 Output IDAT size = 44818 bytes (2253 bytes decrease) Output file size = 44896 bytes (2313 bytes = 4.90% decrease) --- finished re-building ‘Bootstrap_Prediction.Rmd’ --- re-building ‘Getting_started.Rmd’ using rmarkdown Quitting from lines 169-170 [unnamed-chunk-19] (Getting_started.Rmd) Error: processing vignette 'Getting_started.Rmd' failed with diagnostics: ℹ In argument: `lower = exp(.data$`2.5 %`)`. Caused by error in `` .data$`2.5 %` ``: ! Column `2.5 %` not found in `.data`. --- failed re-building ‘Getting_started.Rmd’ --- re-building ‘Statiastical_test_in_gaze.Rmd’ using rmarkdown --- finished re-building ‘Statiastical_test_in_gaze.Rmd’ --- re-building ‘Survival.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Survival_files/figure-html/unnamed-chunk-9-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17395 bytes Input file size = 17497 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13251 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 13251 Output IDAT size = 13251 bytes (4144 bytes decrease) Output file size = 13329 bytes (4168 bytes = 23.82% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Survival_files/figure-html/unnamed-chunk-13-1.png 768x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14753 bytes Input file size = 15623 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13587 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 13587 Output IDAT size = 13587 bytes (1166 bytes decrease) Output file size = 13665 bytes (1958 bytes = 12.53% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Survival_files/figure-html/unnamed-chunk-16-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 78477 bytes Input file size = 78663 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60598 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 60598 Output IDAT size = 60598 bytes (17879 bytes decrease) Output file size = 60676 bytes (17987 bytes = 22.87% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Survival_files/figure-html/unnamed-chunk-20-1.png 768x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16200 bytes Input file size = 16290 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14256 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 14256 Output IDAT size = 14256 bytes (1944 bytes decrease) Output file size = 14334 bytes (1956 bytes = 12.01% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/autoReg.Rcheck/vign_test/autoReg/vignettes/Survival_files/figure-html/unnamed-chunk-21-1.png 768x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19030 bytes Input file size = 19132 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16588 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 16588 Output IDAT size = 16588 bytes (2442 bytes decrease) Output file size = 16666 bytes (2466 bytes = 12.89% decrease) --- finished re-building ‘Survival.Rmd’ SUMMARY: processing the following files failed: ‘Automatic_Regression_Modeling.Rmd’ ‘Getting_started.Rmd’ Error: Vignette re-building failed. Execution halted Package: finalfit Check: examples New result: ERROR Running examples in ‘finalfit-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: missing_predictorMatrix > ### Title: Create predictorMatrix for use with mice > ### Aliases: missing_predictorMatrix > > ### ** Examples > > library(mice) Attaching package: ‘mice’ The following object is masked from ‘package:stats’: filter The following objects are masked from ‘package:base’: cbind, rbind > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > > # Create some extra missing data > ## Smoking missing completely at random > set.seed(1) > colon_s$smoking_mcar = + sample(c("Smoker", "Non-smoker", NA), + dim(colon_s)[1], replace=TRUE, + prob = c(0.2, 0.7, 0.1)) %>% + factor() %>% + ff_label("Smoking (MCAR)") > > ## Make smoking missing conditional on patient sex > colon_s$smoking_mar[colon_s$sex.factor == "Female"] = + sample(c("Smoker", "Non-smoker", NA), + sum(colon_s$sex.factor == "Female"), + replace = TRUE, prob = c(0.1, 0.5, 0.4)) > > colon_s$smoking_mar[colon_s$sex.factor == "Male"] = + sample(c("Smoker", "Non-smoker", NA), + sum(colon_s$sex.factor == "Male"), + replace=TRUE, prob = c(0.15, 0.75, 0.1)) > colon_s$smoking_mar = factor(colon_s$smoking_mar)%>% + ff_label("Smoking (MAR)") > > explanatory = c("age", "sex.factor", + "nodes", "obstruct.factor", "smoking_mar") > dependent = "mort_5yr" > > colon_s %>% + select(dependent, explanatory) %>% + missing_predictorMatrix(drop_from_imputed = + c("obstruct.factor", "mort_5yr")) -> predM Warning: Using an external vector in selections was deprecated in tidyselect 1.1.0. ℹ Please use `all_of()` or `any_of()` instead. # Was: data %>% select(dependent) # Now: data %>% select(all_of(dependent)) See . Warning: Using an external vector in selections was deprecated in tidyselect 1.1.0. ℹ Please use `all_of()` or `any_of()` instead. # Was: data %>% select(explanatory) # Now: data %>% select(all_of(explanatory)) See . > > colon_s %>% + select(dependent, explanatory) %>% + mice(m = 2, predictorMatrix = predM) %>% # e.g. m=10 when for real + # Run logistic regression on each imputed set + with(glm(formula(ff_formula(dependent, explanatory)), + family="binomial")) %>% + pool() %>% + summary(conf.int = TRUE, exponentiate = TRUE) %>% + # Jiggle into finalfit format + mutate(explanatory_name = rownames(.)) %>% + select(explanatory_name, estimate, `2.5 %`, `97.5 %`, p.value) %>% + condense_fit(estimate_suffix = " (multiple imputation)") %>% + remove_intercept() -> fit_imputed iter imp variable 1 1 mort_5yr nodes obstruct.factor smoking_mar 1 2 mort_5yr nodes obstruct.factor smoking_mar 2 1 mort_5yr nodes obstruct.factor smoking_mar 2 2 mort_5yr nodes obstruct.factor smoking_mar 3 1 mort_5yr nodes obstruct.factor smoking_mar 3 2 mort_5yr nodes obstruct.factor smoking_mar 4 1 mort_5yr nodes obstruct.factor smoking_mar 4 2 mort_5yr nodes obstruct.factor smoking_mar 5 1 mort_5yr nodes obstruct.factor smoking_mar 5 2 mort_5yr nodes obstruct.factor smoking_mar Error in `select()`: ! Can't select columns that don't exist. ✖ Column `2.5 %` doesn't exist. Backtrace: ▆ 1. ├─... %>% remove_intercept() 2. ├─finalfit::remove_intercept(.) 3. │ └─.data %>% ... 4. ├─dplyr::filter_at(., .vars = 1, dplyr::any_vars(. != intercept_name)) 5. │ └─dplyr:::tbl_at_syms(.tbl, .vars, .include_group_vars = TRUE) 6. │ └─dplyr:::tbl_at_vars(...) 7. │ └─dplyr::tbl_vars(tbl) 8. │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x)) 9. │ │ └─base::structure(...) 10. │ └─dplyr:::tbl_vars_dispatch(x) 11. ├─finalfit::condense_fit(., estimate_suffix = " (multiple imputation)") 12. ├─dplyr::select(...) 13. ├─dplyr:::select.data.frame(., explanatory_name, estimate, `2.5 %`, `97.5 %`, p.value) 14. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call) 15. │ └─tidyselect:::eval_select_impl(...) 16. │ ├─tidyselect:::with_subscript_errors(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ └─tidyselect:::vars_select_eval(...) 19. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask) 20. │ └─tidyselect:::eval_c(expr, data_mask, context_mask) 21. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) 22. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask) 23. │ └─tidyselect:::as_indices_sel_impl(...) 24. │ └─tidyselect:::as_indices_impl(...) 25. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg) 26. │ └─vctrs::vec_as_location(...) 27. └─vctrs (local) ``() 28. └─vctrs:::stop_subscript_oob(...) 29. └─vctrs:::stop_subscript(...) 30. └─rlang::abort(...) Execution halted Package: finalfit Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘all_plots_examples.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-2-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35285 bytes Input file size = 35411 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28275 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28275 Output IDAT size = 28275 bytes (7010 bytes decrease) Output file size = 28353 bytes (7058 bytes = 19.93% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-4-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34893 bytes Input file size = 35019 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27914 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 27914 Output IDAT size = 27914 bytes (6979 bytes decrease) Output file size = 27992 bytes (7027 bytes = 20.07% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-5-1.png 864x192 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21103 bytes Input file size = 21205 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16631 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 16631 Output IDAT size = 16631 bytes (4472 bytes decrease) Output file size = 16709 bytes (4496 bytes = 21.20% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-6-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34885 bytes Input file size = 35011 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27901 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 27901 Output IDAT size = 27901 bytes (6984 bytes decrease) Output file size = 27979 bytes (7032 bytes = 20.09% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-7-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35699 bytes Input file size = 35825 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28568 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28568 Output IDAT size = 28568 bytes (7131 bytes decrease) Output file size = 28646 bytes (7179 bytes = 20.04% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-8-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33586 bytes Input file size = 33712 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26471 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 26471 Output IDAT size = 26471 bytes (7115 bytes decrease) Output file size = 26549 bytes (7163 bytes = 21.25% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-9-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35785 bytes Input file size = 35911 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28742 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28742 Output IDAT size = 28742 bytes (7043 bytes decrease) Output file size = 28820 bytes (7091 bytes = 19.75% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-10-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35276 bytes Input file size = 35402 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28301 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28301 Output IDAT size = 28301 bytes (6975 bytes decrease) Output file size = 28379 bytes (7023 bytes = 19.84% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-11-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35040 bytes Input file size = 35166 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28115 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28115 Output IDAT size = 28115 bytes (6925 bytes decrease) Output file size = 28193 bytes (6973 bytes = 19.83% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-12-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35707 bytes Input file size = 35833 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28674 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28674 Output IDAT size = 28674 bytes (7033 bytes decrease) Output file size = 28752 bytes (7081 bytes = 19.76% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-13-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32652 bytes Input file size = 32766 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26312 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 26312 Output IDAT size = 26312 bytes (6340 bytes decrease) Output file size = 26390 bytes (6376 bytes = 19.46% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-14-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28794 bytes Input file size = 28908 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22941 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 22941 Output IDAT size = 22941 bytes (5853 bytes decrease) Output file size = 23019 bytes (5889 bytes = 20.37% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-15-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35527 bytes Input file size = 35653 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28256 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 28256 Output IDAT size = 28256 bytes (7271 bytes decrease) Output file size = 28334 bytes (7319 bytes = 20.53% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-16-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33701 bytes Input file size = 33827 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 26881 Output IDAT size = 26881 bytes (6820 bytes decrease) Output file size = 26959 bytes (6868 bytes = 20.30% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-17-1.png 960x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38441 bytes Input file size = 38567 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30838 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 30838 Output IDAT size = 30838 bytes (7603 bytes decrease) Output file size = 30916 bytes (7651 bytes = 19.84% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-19-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33336 bytes Input file size = 33462 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26851 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 26851 Output IDAT size = 26851 bytes (6485 bytes decrease) Output file size = 26929 bytes (6533 bytes = 19.52% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-21-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33418 bytes Input file size = 33544 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26893 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 26893 Output IDAT size = 26893 bytes (6525 bytes decrease) Output file size = 26971 bytes (6573 bytes = 19.60% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-22-1.png 864x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33418 bytes Input file size = 33544 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26893 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 26893 Output IDAT size = 26893 bytes (6525 bytes decrease) Output file size = 26971 bytes (6573 bytes = 19.60% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-23-1.png 576x432 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26886 bytes Input file size = 27000 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21107 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 21107 Output IDAT size = 21107 bytes (5779 bytes decrease) Output file size = 21185 bytes (5815 bytes = 21.54% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/all_plots_examples_files/figure-html/unnamed-chunk-24-1.png 576x432 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27561 bytes Input file size = 27675 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21530 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 21530 Output IDAT size = 21530 bytes (6031 bytes decrease) Output file size = 21608 bytes (6067 bytes = 21.92% decrease) --- finished re-building ‘all_plots_examples.Rmd’ --- re-building ‘all_tables_examples.Rmd’ using rmarkdown --- finished re-building ‘all_tables_examples.Rmd’ --- re-building ‘bootstrap.Rmd’ using rmarkdown --- finished re-building ‘bootstrap.Rmd’ --- re-building ‘data_prep.Rmd’ using rmarkdown --- finished re-building ‘data_prep.Rmd’ --- re-building ‘export.Rmd’ using rmarkdown --- finished re-building ‘export.Rmd’ --- re-building ‘finalfit.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/finalfit_files/figure-html/unnamed-chunk-15-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12974 bytes Input file size = 13064 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9570 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 9570 Output IDAT size = 9570 bytes (3404 bytes decrease) Output file size = 9648 bytes (3416 bytes = 26.15% decrease) --- finished re-building ‘finalfit.Rmd’ --- re-building ‘missing.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/missing_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13889 bytes Input file size = 13979 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10028 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 10028 Output IDAT size = 10028 bytes (3861 bytes decrease) Output file size = 10106 bytes (3873 bytes = 27.71% decrease) Quitting from lines 324-406 [unnamed-chunk-14] (missing.Rmd) Error: processing vignette 'missing.Rmd' failed with diagnostics: Can't select columns that don't exist. ✖ Column `2.5 %` doesn't exist. --- failed re-building ‘missing.Rmd’ --- re-building ‘survival.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/survival_files/figure-html/unnamed-chunk-8-1.png 480x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22187 bytes Input file size = 22289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17207 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 17207 Output IDAT size = 17207 bytes (4980 bytes decrease) Output file size = 17285 bytes (5004 bytes = 22.45% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/survival_files/figure-html/unnamed-chunk-12-1.png 480x384 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 12732 bytes Input file size = 13602 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11742 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11684 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 = 11684 Output IDAT size = 11684 bytes (1048 bytes decrease) Output file size = 11762 bytes (1840 bytes = 13.53% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/finalfit.Rcheck/vign_test/finalfit/vignettes/survival_files/figure-html/unnamed-chunk-17-1.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27049 bytes Input file size = 27163 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21182 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 21182 Output IDAT size = 21182 bytes (5867 bytes decrease) Output file size = 21260 bytes (5903 bytes = 21.73% decrease) --- finished re-building ‘survival.Rmd’ SUMMARY: processing the following file failed: ‘missing.Rmd’ Error: Vignette re-building failed. Execution halted Package: smdi Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a_data_generation.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/a_data_generation_files/figure-html/pr_treatment_assignment-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51549 bytes Input file size = 51699 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45598 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 45598 Output IDAT size = 45598 bytes (5951 bytes decrease) Output file size = 45676 bytes (6023 bytes = 11.65% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/a_data_generation_files/figure-html/unnamed-chunk-2-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 52927 bytes Input file size = 53077 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39175 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 39175 Output IDAT size = 39175 bytes (13752 bytes decrease) Output file size = 39253 bytes (13824 bytes = 26.05% decrease) --- finished re-building ‘a_data_generation.Rmd’ --- re-building ‘b_routine_diagnostics.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-5-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22104 bytes Input file size = 22206 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20281 zc = 9 zm = 8 zs = 1 f = 0 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 = 19651 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 = 0 f = 5 IDAT size = 19651 Output IDAT size = 19651 bytes (2453 bytes decrease) Output file size = 19729 bytes (2477 bytes = 11.15% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-6-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 39424 bytes Input file size = 39550 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34520 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 34520 Output IDAT size = 34520 bytes (4904 bytes decrease) Output file size = 34598 bytes (4952 bytes = 12.52% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-7-1.png 900x675 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10795 bytes Input file size = 11665 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8693 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 8693 Output IDAT size = 8693 bytes (2102 bytes decrease) Output file size = 8771 bytes (2894 bytes = 24.81% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-11-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 54591 bytes Input file size = 54741 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44682 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 44682 Output IDAT size = 44682 bytes (9909 bytes decrease) Output file size = 44760 bytes (9981 bytes = 18.23% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-17-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51345 bytes Input file size = 51495 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41754 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 41754 Output IDAT size = 41754 bytes (9591 bytes decrease) Output file size = 41832 bytes (9663 bytes = 18.76% decrease) --- finished re-building ‘b_routine_diagnostics.Rmd’ --- re-building ‘c_multivariate_missingness.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/c_multivariate_missingness_files/figure-html/unnamed-chunk-4-1.png 900x675 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8063 bytes Input file size = 8918 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6444 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 6444 Output IDAT size = 6444 bytes (1619 bytes decrease) Output file size = 6522 bytes (2396 bytes = 26.87% decrease) --- finished re-building ‘c_multivariate_missingness.Rmd’ --- re-building ‘d_narfcs_sensitivity_analysis.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/smdi.Rcheck/vign_test/smdi/vignettes/d_narfcs_sensitivity_analysis_files/figure-html/unnamed-chunk-3-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49906 bytes Input file size = 50056 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39816 zc = 9 zm = 8 zs = 1 f = 0 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 = 0 f = 0 IDAT size = 39816 Output IDAT size = 39816 bytes (10090 bytes decrease) Output file size = 39894 bytes (10162 bytes = 20.30% decrease) Quitting from lines 153-197 [unnamed-chunk-6] (d_narfcs_sensitivity_analysis.Rmd) Error: processing vignette 'd_narfcs_sensitivity_analysis.Rmd' failed with diagnostics: Can't select columns that don't exist. ✖ Column `2.5 %` doesn't exist. --- failed re-building ‘d_narfcs_sensitivity_analysis.Rmd’ --- re-building ‘smdi.Rmd’ using rmarkdown --- finished re-building ‘smdi.Rmd’ SUMMARY: processing the following file failed: ‘d_narfcs_sensitivity_analysis.Rmd’ Error: Vignette re-building failed. Execution halted