* using log directory 'd:/RCompile/CRANincoming/R-devel/chevron.Rcheck' * using R Under development (unstable) (2025-04-13 r88141 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'chevron/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'chevron' version '0.2.11' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [15s] OK * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .devcontainer These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. CRAN-pack does not know about .devcontainer * checking for portable file names ... OK * checking whether package 'chevron' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [24s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'chevron-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: aet01_main > ### Title: 'AET01' Table 1 (Default) Overview of Deaths and Adverse Events > ### Summary Table 1. > ### Aliases: aet01_main aet01_pre aet01_post aet01 > ### Keywords: datasets > > ### ** Examples > > run(aet01, syn_data, arm_var = "ARM") Error in aet01_lyt(arm_var = arm_var, lbl_overall = lbl_overall, anl_vars = anl_vars, : non-interactive browser() -- left over from debugging? Calls: run ... run -> do_call -> do.call -> -> aet01_lyt Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [109s] ERROR Running 'testthat.R' [109s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(checkmate) > library(chevron) > > test_check("chevron") [ FAIL 8 | WARN 9 | SKIP 236 | PASS 151 ] ══ Skipped tests (236) ═════════════════════════════════════════════════════════ • On CRAN (62): 'test-ael01_nollt.R:7:3', 'test-ael02.R:9:3', 'test-ael03.R:9:3', 'test-aet01_aesi.R:17:3', 'test-aet03.R:10:3', 'test-aet04.R:10:3', 'test-aet05.R:7:3', 'test-aet05_all.R:7:3', 'test-aet10.R:10:3', 'test-chevron_tlg-methods.R:8:3', 'test-chevron_tlg-methods.R:99:3', 'test-chevron_tlg-methods.R:117:3', 'test-chevron_tlg-methods.R:137:3', 'test-chevron_tlg-methods.R:334:3', 'test-chevron_tlg-methods.R:338:3', 'test-cml02a_gl.R:5:3', 'test-coxt01.R:6:3', 'test-coxt02.R:5:3', 'test-default_tlg.R:5:3', 'test-default_tlg.R:19:3', 'test-default_tlg.R:33:3', 'test-default_tlg.R:40:3', 'test-default_tlg.R:47:3', 'test-default_tlg.R:54:3', 'test-default_tlg.R:61:3', 'test-default_tlg.R:78:3', 'test-default_tlg.R:86:3', 'test-default_tlg.R:93:3', 'test-default_tlg.R:100:3', 'test-default_tlg.R:107:3', 'test-dmt01.R:8:3', 'test-dst01.R:11:3', 'test-dtht01.R:12:3', 'test-egt01.R:7:3', 'test-egt02.R:7:3', 'test-egt03.R:7:3', 'test-egt05_qtcat.R:7:3', 'test-ext01.R:7:3', 'test-ext01.R:61:3', 'test-lbt01.R:11:3', 'test-lbt04.R:7:3', 'test-lbt05.R:7:3', 'test-lbt07.R:7:3', 'test-lbt14.R:11:3', 'test-lbt15.R:7:3', 'test-mng01.R:10:5', 'test-pdt01.R:7:3', 'test-pdt02.R:7:3', 'test-rmpt01.R:7:3', 'test-rmpt03.R:10:3', 'test-rmpt04.R:7:3', 'test-rmpt05.R:7:3', 'test-rmpt06.R:8:3', 'test-rspt01.R:5:3', 'test-ttet01.R:10:3', 'test-unwrap.R:8:3', 'test-unwrap.R:60:3', 'test-unwrap.R:101:3', 'test-unwrap.R:125:3', 'test-utils.R:76:1', 'test-vst01.R:11:3', 'test-vst02.R:7:3' • On Windows (174): 'test-ael01_nollt.R:12:3', 'test-ael01_nollt.R:25:3', 'test-ael01_nollt.R:39:3', 'test-ael01_nollt.R:55:3', 'test-ael01_nollt.R:71:3', 'test-ael02.R:13:3', 'test-ael02.R:31:3', 'test-ael03.R:13:3', 'test-ael03.R:31:3', 'test-aet01.R:18:3', 'test-aet01.R:34:3', 'test-aet01.R:41:3', 'test-aet01.R:54:3', 'test-aet01.R:73:3', 'test-aet01_aesi.R:23:3', 'test-aet01_aesi.R:35:3', 'test-aet01_aesi.R:42:3', 'test-aet02.R:18:3', 'test-aet02.R:29:3', 'test-aet03.R:14:3', 'test-aet04.R:29:3', 'test-aet05.R:11:3', 'test-aet05_all.R:11:3', 'test-aet10.R:14:3', 'test-cfbt01.R:4:3', 'test-cfbt01.R:14:3', 'test-chevron_tlg-methods.R:12:3', 'test-chevron_tlg-methods.R:21:3', 'test-chevron_tlg-methods.R:29:3', 'test-chevron_tlg-methods.R:37:3', 'test-chevron_tlg-methods.R:56:3', 'test-chevron_tlg-methods.R:63:3', 'test-chevron_tlg-methods.R:143:3', 'test-chevron_tlg-methods.R:150:3', 'test-chevron_tlg-methods.R:162:3', 'test-chevron_tlg-methods.R:182:3', 'test-chevron_tlg-methods.R:189:3', 'test-chevron_tlg-methods.R:199:3', 'test-chevron_tlg-methods.R:212:3', 'test-chevron_tlg-methods.R:219:3', 'test-chevron_tlg-methods.R:227:3', 'test-chevron_tlg-methods.R:238:3', 'test-chevron_tlg-methods.R:244:3', 'test-chevron_tlg-methods.R:252:3', 'test-chevron_tlg-methods.R:263:3', 'test-chevron_tlg-methods.R:269:3', 'test-chevron_tlg-methods.R:276:3', 'test-chevron_tlg-methods.R:286:3', 'test-chevron_tlg-methods.R:293:3', 'test-chevron_tlg-methods.R:300:3', 'test-chevron_tlg-methods.R:325:3', 'test-cml02a_gl.R:9:3', 'test-cml02a_gl.R:19:3', 'test-cmt01a.R:11:3', 'test-cmt01a.R:26:3', 'test-cmt01a.R:39:3', 'test-cmt02_pt.R:13:3', 'test-coxt01.R:19:3', 'test-coxt02.R:18:3', 'test-dmt01.R:12:3', 'test-dmt01.R:20:3', 'test-dmt01.R:35:3', 'test-dmt01.R:41:3', 'test-dmt01.R:47:3', 'test-dmt01.R:53:3', 'test-dmt01.R:61:3', 'test-dmt01.R:75:3', 'test-dmt01.R:89:3', 'test-dst01.R:15:3', 'test-dst01.R:27:3', 'test-dst01.R:35:3', 'test-dst01.R:46:3', 'test-dst01.R:52:3', 'test-dst01.R:58:3', 'test-dtht01.R:16:3', 'test-dtht01.R:26:3', 'test-egt01.R:13:3', 'test-egt02.R:11:3', 'test-egt03.R:13:3', 'test-egt03.R:25:3', 'test-egt03.R:34:3', 'test-egt05_qtcat.R:13:3', 'test-egt05_qtcat.R:24:3', 'test-empty_report.R:18:3', 'test-ext01.R:11:3', 'test-ext01.R:22:3', 'test-ext01.R:34:3', 'test-ext01.R:45:3', 'test-ext01.R:65:3', 'test-ext01.R:77:3', 'test-fstg01.R:13:3', 'test-fstg01.R:24:3', 'test-fstg01.R:38:3', 'test-fstg02.R:13:3', 'test-fstg02.R:24:3', 'test-fstg02.R:38:3', 'test-fstg02.R:49:3', 'test-kmg01.R:15:3', 'test-kmg01.R:32:3', 'test-kmg01.R:47:3', 'test-kmg01.R:60:3', 'test-lbt01.R:17:3', 'test-lbt01.R:27:3', 'test-lbt04.R:13:3', 'test-lbt04.R:25:3', 'test-lbt04.R:37:3', 'test-lbt04.R:46:3', 'test-lbt05.R:16:3', 'test-lbt05.R:28:3', 'test-lbt05.R:42:3', 'test-lbt05.R:50:3', 'test-lbt05.R:59:3', 'test-lbt05.R:66:3', 'test-lbt05.R:73:3', 'test-lbt06.R:15:3', 'test-lbt06.R:25:3', 'test-lbt07.R:13:3', 'test-lbt07.R:27:3', 'test-lbt14.R:15:3', 'test-lbt14.R:23:3', 'test-lbt14.R:31:3', 'test-lbt14.R:40:3', 'test-lbt14.R:53:3', 'test-lbt14.R:73:3', 'test-lbt14.R:83:3', 'test-lbt14.R:94:3', 'test-lbt14.R:108:3', 'test-lbt14.R:128:3', 'test-lbt14.R:139:3', 'test-lbt15.R:13:3', 'test-lbt15.R:25:3', 'test-lbt15.R:37:3', 'test-lbt15.R:49:3', 'test-lbt15.R:58:3', 'test-lbt15.R:67:3', 'test-mht01.R:13:3', 'test-mht01.R:20:3', 'test-mht01.R:27:3', 'test-mng01.R:15:3', 'test-mng01.R:54:3', 'test-mng01.R:76:3', 'test-mng01.R:98:3', 'test-mng01.R:110:3', 'test-mng01.R:128:3', 'test-mng01.R:149:3', 'test-pdt01.R:13:3', 'test-pdt01.R:26:3', 'test-pdt02.R:13:3', 'test-pdt02.R:26:3', 'test-rmpt01.R:13:3', 'test-rmpt01.R:25:3', 'test-rmpt01.R:40:3', 'test-rmpt03.R:16:3', 'test-rmpt03.R:30:3', 'test-rmpt03.R:47:3', 'test-rmpt04.R:13:3', 'test-rmpt04.R:25:3', 'test-rmpt04.R:47:3', 'test-rmpt05.R:13:3', 'test-rmpt05.R:25:3', 'test-rmpt05.R:47:3', 'test-rmpt06.R:12:3', 'test-rmpt06.R:21:3', 'test-rspt01.R:9:3', 'test-rspt01.R:30:3', 'test-rspt01.R:49:3', 'test-rspt01.R:70:3', 'test-rspt01.R:91:3', 'test-rspt01.R:121:3', 'test-ttet01.R:26:3', 'test-ttet01.R:48:3', 'test-ttet01.R:71:3', 'test-vst01.R:17:3', 'test-vst02.R:11:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-aet01.R:11:3'): aet01 can handle all NA values ───────────────── Error in `aet01_lyt(arm_var = arm_var, lbl_overall = lbl_overall, anl_vars = anl_vars, anl_lbls = anl_lbls, lbl_vars = lbl_vars)`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. ├─testthat::expect_silent(run(aet01, proc_data)) at test-aet01.R:11:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─chevron::run(aet01, proc_data) 10. ├─chevron::run(aet01, proc_data) 11. │ └─chevron:::do_call(object@main, c(proc_data, user_args)) 12. │ └─base::do.call(what, new_args, envir = args_env) 13. └─chevron (local) ``(adam_db = adam_db) 14. └─chevron:::aet01_lyt(...) ── Error ('test-chevron_tlg-methods.R:84:3'): run print internal functions when unwrap is TRUE ── Error in `(function (adam_db, arm_var = "ACTARM", row_split_var = "AEBODSYS", lbl_overall = NULL, summary_labels = list(all = aet02_label, TOTAL = c(nonunique = "Overall total number of events")), ...) { assert_all_tablenames(adam_db, "adsl", "adae") assert_string(arm_var) assert_character(row_split_var, null.ok = TRUE) assert_string(lbl_overall, null.ok = TRUE) assert_valid_variable(adam_db$adsl, c("USUBJID", arm_var), types = list(c("character", "factor"))) assert_valid_variable(adam_db$adae, c(arm_var, row_split_var, "AEDECOD"), types = list(c("character", "factor"))) assert_valid_variable(adam_db$adae, "USUBJID", empty_ok = TRUE, types = list(c("character", "factor"))) assert_valid_var_pair(adam_db$adsl, adam_db$adae, arm_var) assert_list(summary_labels, null.ok = TRUE) assert_subset(names(summary_labels), c("all", "TOTAL", row_split_var)) assert_subset(unique(unlist(lapply(summary_labels, names))), c("unique", "nonunique", "unique_count")) summary_labels <- expand_list(summary_labels, c("TOTAL", row_split_var)) lbl_overall <- render_safe(lbl_overall) lbl_row_split <- var_labels_for(adam_db$adae, row_split_var) lbl_aedecod <- var_labels_for(adam_db$adae, "AEDECOD") browser() lyt <- occurrence_lyt(arm_var = arm_var, lbl_overall = lbl_overall, row_split_var = row_split_var, lbl_row_split = lbl_row_split, medname_var = "AEDECOD", lbl_medname_var = lbl_aedecod, summary_labels = summary_labels, count_by = NULL) tbl <- build_table(lyt, adam_db$adae, alt_counts_df = adam_db$adsl) tbl })(adam_db = adam_db, prune_0 = prune_0)`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. ├─testthat::capture_output(...) at test-chevron_tlg-methods.R:84:3 2. │ └─testthat::capture_output_lines(code, print, width = width) 3. │ └─testthat:::eval_with_output(code, print = print, width = width) 4. │ ├─withr::with_output_sink(path, withVisible(code)) 5. │ │ └─base::force(code) 6. │ └─base::withVisible(code) 7. ├─chevron::run(...) 8. ├─chevron::run(...) 9. │ └─chevron:::do_call(object@main, c(proc_data, user_args)) 10. │ └─base::do.call(what, new_args, envir = args_env) 11. └─chevron (local) ``(adam_db = adam_db, prune_0 = prune_0) ── Error ('test-cmt01a.R:5:3'): cmt01a functions with default argument value return expected result with test data ── Error in `occurrence_lyt(arm_var = arm_var, lbl_overall = lbl_overall, row_split_var = row_split_var, lbl_row_split = lbl_row_split, medname_var = medname_var, lbl_medname_var = lbl_medname_var, summary_labels = summary_labels, count_by = "CMSEQ")`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. └─chevron::cmt01a_main(pre_data) at test-cmt01a.R:5:3 2. └─chevron:::occurrence_lyt(...) ── Error ('test-cmt02_pt.R:8:3'): cmt02_pt can handle all NA values ──────────── Error in `occurrence_lyt(arm_var = arm_var, lbl_overall = lbl_overall, row_split_var = row_split_var, lbl_row_split = lbl_row_split, medname_var = medname_var, lbl_medname_var = lbl_medname_var, summary_labels = summary_labels, count_by = "CMSEQ")`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. ├─testthat::expect_silent(run(cmt02_pt, proc_data)) at test-cmt02_pt.R:8:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─chevron::run(cmt02_pt, proc_data) 10. ├─chevron::run(cmt02_pt, proc_data) 11. │ └─chevron:::do_call(object@main, c(proc_data, user_args)) 12. │ └─base::do.call(what, new_args, envir = args_env) 13. └─chevron (local) ``(adam_db = adam_db) 14. └─chevron:::occurrence_lyt(...) ── Error ('test-default_tlg.R:10:3'): aet01 function with default argument value return expected result with test data ── Error in `aet01_lyt(arm_var = arm_var, lbl_overall = lbl_overall, anl_vars = anl_vars, anl_lbls = anl_lbls, lbl_vars = lbl_vars)`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. └─chevron::aet01_main(pre_data) at test-default_tlg.R:10:3 2. └─chevron:::aet01_lyt(...) ── Error ('test-default_tlg.R:24:3'): aet02 functions with default argument value return expected result with test data ── Error in `aet02_main(pre_data)`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. └─chevron::aet02_main(pre_data) at test-default_tlg.R:24:3 ── Error ('test-default_tlg.R:66:3'): cmt02_pt functions with default argument value return expected result with test data ── Error in `occurrence_lyt(arm_var = arm_var, lbl_overall = lbl_overall, row_split_var = row_split_var, lbl_row_split = lbl_row_split, medname_var = medname_var, lbl_medname_var = lbl_medname_var, summary_labels = summary_labels, count_by = "CMSEQ")`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. └─chevron::cmt02_pt_main(pre_data) at test-default_tlg.R:66:3 2. └─chevron:::occurrence_lyt(...) ── Error ('test-mht01.R:5:3'): mht01 functions with default argument value return expected result with test data ── Error in `occurrence_lyt(arm_var = arm_var, lbl_overall = lbl_overall, row_split_var = row_split_var, lbl_row_split = lbl_row_split, medname_var = "MHDECOD", lbl_medname_var = lbl_mhdecod, summary_labels = summary_labels, count_by = "MHSEQ")`: non-interactive browser() -- left over from debugging? Backtrace: ▆ 1. └─chevron::mht01_main(pre_data) at test-mht01.R:5:3 2. └─chevron:::occurrence_lyt(...) [ FAIL 8 | WARN 9 | SKIP 236 | PASS 151 ] Deleting unused snapshots: • mng01/mng01-with-custom-theme.svg • mng01/run-mng01-with-combination-of-x-variables.svg • mng01/run-mng01-with-custom-color-set.svg • mng01/run-mng01-with-custom-line-type-set.svg • mng01/run-mng01-with-custom-unnamed-color-set.svg • mng01/run-mng01-with-custom-unnamed-line-type-set.svg • mng01/run-mng01-with-jitter.svg • mng01/run-mng01-with-numeric-x-variables.svg • mng01/run-mng01-without-table.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'chevron.Rmd' using rmarkdown Quitting from chevron.Rmd:84-86 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! non-interactive browser() -- left over from debugging? --- Backtrace: ▆ 1. ├─chevron::run(aet02, syn_data) 2. ├─chevron::run(aet02, syn_data) 3. │ └─chevron:::do_call(object@main, c(proc_data, user_args)) 4. │ └─base::do.call(what, new_args, envir = args_env) 5. └─chevron (local) ``(adam_db = adam_db) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'chevron.Rmd' failed with diagnostics: non-interactive browser() -- left over from debugging? --- failed re-building 'chevron.Rmd' --- re-building 'chevron_catalog.rmd' using rmarkdown Quitting from chevron_catalog.rmd:109-111 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `aet01_lyt()`: ! non-interactive browser() -- left over from debugging? --- Backtrace: ▆ 1. ├─chevron::run(aet01, syn_data, arm_var = "ARM") 2. ├─chevron::run(aet01, syn_data, arm_var = "ARM") 3. │ └─chevron:::do_call(object@main, c(proc_data, user_args)) 4. │ └─base::do.call(what, new_args, envir = args_env) 5. └─chevron (local) ``(adam_db = adam_db, arm_var = arm_var) 6. └─chevron:::aet01_lyt(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'chevron_catalog.rmd' failed with diagnostics: non-interactive browser() -- left over from debugging? --- failed re-building 'chevron_catalog.rmd' --- re-building 'script_generator.Rmd' using rmarkdown --- finished re-building 'script_generator.Rmd' SUMMARY: processing the following files failed: 'chevron.Rmd' 'chevron_catalog.rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [26s] OK * checking HTML version of manual ... [26s] OK * DONE Status: 3 ERRORs, 1 NOTE