CRAN Package Check Results for Package tern.gee

Last updated on 2025-12-11 07:49:55 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.1.5	15.08	140.53	155.61	OK
r-devel-linux-x86_64-debian-gcc	0.1.5	10.76	100.37	111.13	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.5	37.00	195.89	232.89	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.5	57.00	194.83	251.83	ERROR
r-devel-windows-x86_64	0.1.5	18.00	130.00	148.00	OK
r-patched-linux-x86_64	0.1.5	13.23	131.18	144.41	ERROR
r-release-linux-x86_64	0.1.5	12.91	132.28	145.19	OK
r-release-macos-arm64	0.1.5				OK
r-release-macos-x86_64	0.1.5	9.00	100.00	109.00	OK
r-release-windows-x86_64	0.1.5	16.00	131.00	147.00	OK
r-oldrel-macos-arm64	0.1.5				OK
r-oldrel-macos-x86_64	0.1.5	19.00	147.00	166.00	OK
r-oldrel-windows-x86_64	0.1.5	24.00	177.00	201.00	OK

Check Details

Version: 0.1.5
Check: examples
Result: ERROR Running examples in ‘tern.gee-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: tabulate_gee > ### Title: Tabulation of a GEE Model > ### Aliases: tabulate_gee as.rtable.tern_gee s_lsmeans_logistic > ### a_lsmeans_logistic summarize_gee_logistic > > ### ** Examples > > 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 > > df <- fev_data %>% + mutate(AVAL = as.integer(fev_data$FEV1 > 30)) > df_counts <- df %>% + select(USUBJID, ARMCD) %>% + unique() > > lsmeans_df <- lsmeans(fit_gee(vars = vars_gee(arm = "ARMCD"), data = df)) > > s_lsmeans_logistic(lsmeans_df[1, ], .in_ref_col = TRUE) $n [1] 420 $adj_prop_se [1] 0.88390403 0.01948562 $adj_prop_ci [1] 0.8398239 0.9170515 attr(,"label") [1] "95% CI" $odds_ratio_est character(0) $odds_ratio_ci character(0) attr(,"label") [1] "95% CI" $log_odds_ratio_est character(0) $log_odds_ratio_ci character(0) attr(,"label") [1] "95% CI" > > s_lsmeans_logistic(lsmeans_df[2, ], .in_ref_col = FALSE) $n [1] 380 $adj_prop_se [1] 0.94325891 0.01386798 $adj_prop_ci [1] 0.9090296 0.9651032 attr(,"label") [1] "95% CI" $odds_ratio_est [1] 2.18346 $odds_ratio_ci [1] 1.161678 4.103974 attr(,"label") [1] "95% CI" $log_odds_ratio_est [1] 0.7809108 $log_odds_ratio_ci [1] 0.1498659 1.4119557 attr(,"label") [1] "95% CI" > basic_table() %>% + split_cols_by("ARMCD") %>% + add_colcounts() %>% + summarize_gee_logistic( + .in_ref_col = FALSE + ) %>% + build_table(lsmeans_df, alt_counts_df = df_counts) Error in match.arg(round_type) : 'arg' must be of length 1 Calls: %>% ... <Anonymous> -> format_rcell -> format_value -> match.arg Execution halted Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/8s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not Saving _problems/test-tabulate_gee-32.R Saving _problems/test-tabulate_gee-71.R Saving _problems/test-tabulate_gee-96.R [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-tabulate_gee.R:32:3'): h_gee_cov works as expected ───────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toString': 'arg' must be of length 1 Backtrace: ▆ 1. ├─testthat::expect_snapshot(result) at test-tabulate_gee.R:32:3 2. │ └─testthat:::expect_snapshot_(...) 3. │ ├─testthat:::with_is_snapshotting(...) 4. │ └─testthat:::verify_exec(quo_get_expr(x), quo_get_env(x), replay) 5. │ └─evaluate::evaluate(source, envir = env, new_device = FALSE, output_handler = handler) 6. │ ├─base::withRestarts(...) 7. │ │ └─base (local) withRestartList(expr, restarts) 8. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 9. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 10. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 11. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 12. │ │ └─base (local) doWithOneRestart(return(expr), restart) 13. │ ├─evaluate:::with_handlers(...) 14. │ │ ├─base::eval(call) 15. │ │ │ └─base::eval(call) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─watcher$print_value(ev$value, ev$visible, envir) 18. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 19. │ └─evaluate:::handle_value(handler, value, visible, envir) 20. │ ├─handler$value(value) 21. │ └─testthat:::testthat_print.default(value) 22. │ ├─base::print(x) 23. │ └─base::print.default(x) 24. │ ├─methods (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 25. │ └─rtables (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 26. │ ├─base::cat(toString(object)) 27. │ ├─base::toString(object) 28. │ └─rtables::toString(object) 29. │ └─rtables (local) .local(x, ...) 30. │ ├─base::toString(...) 31. │ ├─formatters::matrix_form(...) 32. │ └─rtables::matrix_form(...) 33. │ └─rtables:::.tbl_header_mat(obj) 34. │ ├─base::matrix(...) 35. │ └─base::rapply(...) 36. │ └─rtables (local) `<fn>`(X, ...) 37. │ ├─rtables::get_formatted_cells(x) 38. │ └─rtables::get_formatted_cells(x) 39. │ ├─base::matrix(...) 40. │ ├─base::unlist(...) 41. │ └─base::Map(...) 42. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 43. │ └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 44. │ └─rtables::format_rcell(...) 45. │ └─formatters::format_value(...) 46. │ └─base::match.arg(round_type) 47. │ └─base::stop(gettextf("'%s' must be of length 1", "arg"), domain = NA) 48. └─base::.handleSimpleError(...) 49. └─base (local) h(simpleError(msg, call)) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘tern-gee.Rmd’ using rmarkdown Quitting from tern-gee.Rmd:122-133 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `match.arg()`: ! 'arg' must be of length 1 --- Backtrace: ▆ 1. ├─... %>% build_table(fev_lsmeans, alt_counts_df = fev_counts) 2. └─rtables::build_table(., fev_lsmeans, alt_counts_df = fev_counts) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tern-gee.Rmd' failed with diagnostics: 'arg' must be of length 1 --- failed re-building ‘tern-gee.Rmd’ SUMMARY: processing the following file failed: ‘tern-gee.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 0.1.5
Check: examples
Result: ERROR Running examples in ‘tern.gee-Ex.R’ failed The error most likely occurred in: > ### Name: tabulate_gee > ### Title: Tabulation of a GEE Model > ### Aliases: tabulate_gee as.rtable.tern_gee s_lsmeans_logistic > ### a_lsmeans_logistic summarize_gee_logistic > > ### ** Examples > > 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 > > df <- fev_data %>% + mutate(AVAL = as.integer(fev_data$FEV1 > 30)) > df_counts <- df %>% + select(USUBJID, ARMCD) %>% + unique() > > lsmeans_df <- lsmeans(fit_gee(vars = vars_gee(arm = "ARMCD"), data = df)) > > s_lsmeans_logistic(lsmeans_df[1, ], .in_ref_col = TRUE) $n [1] 420 $adj_prop_se [1] 0.88390403 0.01948562 $adj_prop_ci [1] 0.8398239 0.9170515 attr(,"label") [1] "95% CI" $odds_ratio_est character(0) $odds_ratio_ci character(0) attr(,"label") [1] "95% CI" $log_odds_ratio_est character(0) $log_odds_ratio_ci character(0) attr(,"label") [1] "95% CI" > > s_lsmeans_logistic(lsmeans_df[2, ], .in_ref_col = FALSE) $n [1] 380 $adj_prop_se [1] 0.94325891 0.01386798 $adj_prop_ci [1] 0.9090296 0.9651032 attr(,"label") [1] "95% CI" $odds_ratio_est [1] 2.18346 $odds_ratio_ci [1] 1.161678 4.103974 attr(,"label") [1] "95% CI" $log_odds_ratio_est [1] 0.7809108 $log_odds_ratio_ci [1] 0.1498659 1.4119557 attr(,"label") [1] "95% CI" > basic_table() %>% + split_cols_by("ARMCD") %>% + add_colcounts() %>% + summarize_gee_logistic( + .in_ref_col = FALSE + ) %>% + build_table(lsmeans_df, alt_counts_df = df_counts) Error in match.arg(round_type) : 'arg' must be of length 1 Calls: %>% ... <Anonymous> -> format_rcell -> format_value -> match.arg Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [14s/15s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not Saving _problems/test-tabulate_gee-32.R Saving _problems/test-tabulate_gee-71.R Saving _problems/test-tabulate_gee-96.R [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-tabulate_gee.R:32:3'): h_gee_cov works as expected ───────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toString': 'arg' must be of length 1 Backtrace: ▆ 1. ├─testthat::expect_snapshot(result) at test-tabulate_gee.R:32:3 2. │ └─testthat:::expect_snapshot_(...) 3. │ ├─testthat:::with_is_snapshotting(...) 4. │ └─testthat:::verify_exec(quo_get_expr(x), quo_get_env(x), replay) 5. │ └─evaluate::evaluate(source, envir = env, new_device = FALSE, output_handler = handler) 6. │ ├─base::withRestarts(...) 7. │ │ └─base (local) withRestartList(expr, restarts) 8. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 9. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 10. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 11. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 12. │ │ └─base (local) doWithOneRestart(return(expr), restart) 13. │ ├─evaluate:::with_handlers(...) 14. │ │ ├─base::eval(call) 15. │ │ │ └─base::eval(call) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─watcher$print_value(ev$value, ev$visible, envir) 18. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 19. │ └─evaluate:::handle_value(handler, value, visible, envir) 20. │ ├─handler$value(value) 21. │ └─testthat:::testthat_print.default(value) 22. │ ├─base::print(x) 23. │ └─base::print.default(x) 24. │ ├─methods (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 25. │ └─rtables (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 26. │ ├─base::cat(toString(object)) 27. │ ├─base::toString(object) 28. │ └─rtables::toString(object) 29. │ └─rtables (local) .local(x, ...) 30. │ ├─base::toString(...) 31. │ ├─formatters::matrix_form(...) 32. │ └─rtables::matrix_form(...) 33. │ └─rtables:::.tbl_header_mat(obj) 34. │ ├─base::matrix(...) 35. │ └─base::rapply(...) 36. │ └─rtables (local) `<fn>`(X, ...) 37. │ ├─rtables::get_formatted_cells(x) 38. │ └─rtables::get_formatted_cells(x) 39. │ ├─base::matrix(...) 40. │ ├─base::unlist(...) 41. │ └─base::Map(...) 42. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 43. │ └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 44. │ └─rtables::format_rcell(...) 45. │ └─formatters::format_value(...) 46. │ └─base::match.arg(round_type) 47. │ └─base::stop(gettextf("'%s' must be of length 1", "arg"), domain = NA) 48. └─base::.handleSimpleError(...) 49. └─base (local) h(simpleError(msg, call)) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘tern-gee.Rmd’ using rmarkdown Quitting from tern-gee.Rmd:122-133 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `match.arg()`: ! 'arg' must be of length 1 --- Backtrace: ▆ 1. ├─... %>% build_table(fev_lsmeans, alt_counts_df = fev_counts) 2. └─rtables::build_table(., fev_lsmeans, alt_counts_df = fev_counts) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tern-gee.Rmd' failed with diagnostics: 'arg' must be of length 1 --- failed re-building ‘tern-gee.Rmd’ SUMMARY: processing the following file failed: ‘tern-gee.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [17s/21s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not Saving _problems/test-tabulate_gee-32.R Saving _problems/test-tabulate_gee-71.R Saving _problems/test-tabulate_gee-96.R [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-tabulate_gee.R:32:3'): h_gee_cov works as expected ───────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toString': 'arg' must be of length 1 Backtrace: ▆ 1. ├─testthat::expect_snapshot(result) at test-tabulate_gee.R:32:3 2. │ └─testthat:::expect_snapshot_(...) 3. │ ├─testthat:::with_is_snapshotting(...) 4. │ └─testthat:::verify_exec(quo_get_expr(x), quo_get_env(x), replay) 5. │ └─evaluate::evaluate(source, envir = env, new_device = FALSE, output_handler = handler) 6. │ ├─base::withRestarts(...) 7. │ │ └─base (local) withRestartList(expr, restarts) 8. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 9. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 10. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 11. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 12. │ │ └─base (local) doWithOneRestart(return(expr), restart) 13. │ ├─evaluate:::with_handlers(...) 14. │ │ ├─base::eval(call) 15. │ │ │ └─base::eval(call) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─watcher$print_value(ev$value, ev$visible, envir) 18. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 19. │ └─evaluate:::handle_value(handler, value, visible, envir) 20. │ ├─handler$value(value) 21. │ └─testthat:::testthat_print.default(value) 22. │ ├─base::print(x) 23. │ └─base::print.default(x) 24. │ ├─methods (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 25. │ └─rtables (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 26. │ ├─base::cat(toString(object)) 27. │ ├─base::toString(object) 28. │ └─rtables::toString(object) 29. │ └─rtables (local) .local(x, ...) 30. │ ├─base::toString(...) 31. │ ├─formatters::matrix_form(...) 32. │ └─rtables::matrix_form(...) 33. │ └─rtables:::.tbl_header_mat(obj) 34. │ ├─base::matrix(...) 35. │ └─base::rapply(...) 36. │ └─rtables (local) `<fn>`(X, ...) 37. │ ├─rtables::get_formatted_cells(x) 38. │ └─rtables::get_formatted_cells(x) 39. │ ├─base::matrix(...) 40. │ ├─base::unlist(...) 41. │ └─base::Map(...) 42. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 43. │ └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 44. │ └─rtables::format_rcell(...) 45. │ └─formatters::format_value(...) 46. │ └─base::match.arg(round_type) 47. │ └─base::stop(gettextf("'%s' must be of length 1", "arg"), domain = NA) 48. └─base::.handleSimpleError(...) 49. └─base (local) h(simpleError(msg, call)) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not Saving _problems/test-tabulate_gee-32.R Saving _problems/test-tabulate_gee-71.R Saving _problems/test-tabulate_gee-96.R [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-tabulate_gee.R:32:3'): h_gee_cov works as expected ───────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toString': 'arg' must be of length 1 Backtrace: ▆ 1. ├─testthat::expect_snapshot(result) at test-tabulate_gee.R:32:3 2. │ └─testthat:::expect_snapshot_(...) 3. │ ├─testthat:::with_is_snapshotting(...) 4. │ └─testthat:::verify_exec(quo_get_expr(x), quo_get_env(x), replay) 5. │ └─evaluate::evaluate(source, envir = env, new_device = FALSE, output_handler = handler) 6. │ ├─base::withRestarts(...) 7. │ │ └─base (local) withRestartList(expr, restarts) 8. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 9. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 10. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 11. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 12. │ │ └─base (local) doWithOneRestart(return(expr), restart) 13. │ ├─evaluate:::with_handlers(...) 14. │ │ ├─base::eval(call) 15. │ │ │ └─base::eval(call) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─watcher$print_value(ev$value, ev$visible, envir) 18. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 19. │ └─evaluate:::handle_value(handler, value, visible, envir) 20. │ ├─handler$value(value) 21. │ └─testthat:::testthat_print.default(value) 22. │ ├─base::print(x) 23. │ └─base::print.default(x) 24. │ ├─methods (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 25. │ └─rtables (local) `<stndrdGn>`(`<ElmntryT[,4]>`) 26. │ ├─base::cat(toString(object)) 27. │ ├─base::toString(object) 28. │ └─rtables::toString(object) 29. │ └─rtables (local) .local(x, ...) 30. │ ├─base::toString(...) 31. │ ├─formatters::matrix_form(...) 32. │ └─rtables::matrix_form(...) 33. │ └─rtables:::.tbl_header_mat(obj) 34. │ ├─base::matrix(...) 35. │ └─base::rapply(...) 36. │ └─rtables (local) `<fn>`(X, ...) 37. │ ├─rtables::get_formatted_cells(x) 38. │ └─rtables::get_formatted_cells(x) 39. │ ├─base::matrix(...) 40. │ ├─base::unlist(...) 41. │ └─base::Map(...) 42. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 43. │ └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 44. │ └─rtables::format_rcell(...) 45. │ └─formatters::format_value(...) 46. │ └─base::match.arg(round_type) 47. │ └─base::stop(gettextf("'%s' must be of length 1", "arg"), domain = NA) 48. └─base::.handleSimpleError(...) 49. └─base (local) h(simpleError(msg, call)) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in `match.arg(round_type)`: 'arg' must be of length 1 Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. └─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. └─rtables::update_ref_indexing(tab) 4. ├─formatters::make_row_df(tt) 5. └─rtables::make_row_df(tt) 6. └─rtables (local) .local(...) 7. ├─formatters::make_row_df(...) 8. └─rtables::make_row_df(...) 9. └─rtables (local) .local(...) 10. ├─formatters::pagdfrow(...) 11. │ └─base::data.frame(...) 12. ├─formatters::nlines(...) 13. └─rtables::nlines(...) 14. ├─base::as.vector(get_formatted_cells(x)) 15. ├─rtables::get_formatted_cells(x) 16. └─rtables::get_formatted_cells(x) 17. ├─base::matrix(...) 18. ├─base::unlist(...) 19. └─base::Map(...) 20. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 21. └─rtables (local) `<fn>`(val = dots[[1L]][[1L]], spn = dots[[2L]][[1L]], shelli = dots[[3L]][[1L]]) 22. └─rtables::format_rcell(...) 23. └─formatters::format_value(...) 24. └─base::match.arg(round_type) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ] Error: ! Test failures. Execution halted Flavor: r-patched-linux-x86_64