• using R Under development (unstable) (2025-02-21 r87787)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc2     flang version 20.1.0-rc2
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘dataquieR/DESCRIPTION’ ... OK
• this is package ‘dataquieR’ version ‘2.5.0’
• package encoding: UTF-8
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘dataquieR’ can be installed ... [126s/169s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... 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 ... [295s/351s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [59s/32s] ERROR   Running ‘testthat.R’ [59s/32s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # options("testthat.default_reporter" = testthat::RStudioReporter)   > library(dataquieR)   > testthat::test_check("dataquieR")   Starting 2 test processes   [ FAIL 2 | WARN 0 | SKIP 231 | PASS 20 ]      ══ Skipped tests (231) ═════════════════════════════════════════════════════════   • On CRAN (231): 'test-dq_report2.R:2:3', 'test-dq_report_by_sm.R:7:3',     'test-dq_report_by_arguments.R:7:3', 'test-dq_report_by_s.R:3:3',     'test-dq_report_by_pipesymbol_list.R:3:3', 'test-int_encoding_errors.R:2:3',     'test-int_encoding_errors.R:80:3', 'test-dq_report_by_m.R:3:3',     'test-plots.R:2:3', 'test-plots.R:33:3', 'test-plots.R:102:3',     'test-plots.R:144:3', 'test-plots.R:167:3', 'test-plots.R:185:3',     'test-plots.R:210:3', 'test-plots.R:271:3', 'test-plots.R:301:3',     'test-plots.R:400:3', 'test-plots.R:453:3', 'test-plots.R:483:3',     'test-com_item_missingness.R:2:3', 'test-dq_report_by_na.R:3:3',     'test-acc_loess.R:2:3', 'test-acc_loess.R:273:3', 'test-acc_loess.R:438:3',     'test-acc_loess.R:521:3', 'test-acc_loess.R:565:3', 'test-acc_loess.R:681:3',     'test-acc_loess.R:886:3', 'test-acc_loess.R:949:3', 'test-acc_loess.R:993:3',     'test-acc_loess.R:1037:3', 'test-acc_loess.R:1083:3',     'test-acc_loess.R:1116:3', 'test-acc_loess.R:1149:3',     'test-acc_loess.R:1207:3', 'test-dq_report_by_directories.R:3:3',     'test-con_contradictions_redcap.R:2:3',     'test-con_contradictions_redcap.R:59:3',     'test-con_contradictions_redcap.R:108:3',     'test-con_contradictions_redcap.R:182:3',     'test-com_segment_missingness.R:2:3', 'test-com_segment_missingness.R:221:3',     'test-util_correct_variable_use.R:2:3', 'test-000_globs.R:3:3',     'test-acc_cat_distributions.R:2:3', 'test-con_limit_deviations.R:2:3',     'test-con_limit_deviations.R:47:3', 'test-con_limit_deviations.R:101:3',     'test-con_limit_deviations.R:160:3', 'test-con_limit_deviations.R:240:3',     'test-con_limit_deviations.R:288:3', 'test-con_limit_deviations.R:336:3',     'test-con_limit_deviations.R:384:3', 'test-con_limit_deviations.R:440:3',     'test-con_limit_deviations.R:531:3', 'test-con_limit_deviations.R:567:3',     'test-con_limit_deviations.R:602:3', 'test-con_limit_deviations.R:642:3',     'test-acc_distributions_ecdf.R:2:3', 'test-acc_distributions.R:2:3',     'test-acc_distributions.R:93:3', 'test-acc_distributions.R:114:3',     'test-acc_distributions.R:138:3', 'test-acc_margins.R:2:3',     'test-acc_margins.R:248:3', 'test-acc_end_digits.R:2:3',     'test-acc_end_digits.R:45:3', 'test-acc_end_digits.R:81:3',     'test-acc_end_digits.R:109:3', 'test-acc_shape_or_scale.R:2:3',     'test-acc_shape_or_scale.R:243:3', 'test-acc_multivariate_outlier.R:2:3',     'test-acc_multivariate_outlier.R:60:3',     'test-acc_multivariate_outlier.R:127:3', 'test-acc_univariate_outlier.R:2:3',     'test-acc_univariate_outlier.R:135:3', 'test-acc_varcomp2.R:2:3',     'test-acc_varcomp.R:2:3', 'test-acc_varcomp.R:52:3',     'test-acc_varcomp.R:88:3', 'test-acc_varcomp.R:134:3',     'test-acc_varcomp.R:174:3', 'test-com_qualified_item_missingness.R:2:3',     'test-com_qualified_segment_missingness.R:2:3',     'test-com_qualified_segment_missingness.R:32:3',     'test-com_unit_missingness.R:2:3', 'test-con_contradictions.R:2:3',     'test-con_inadmissible_categorical.R:2:3', 'test-dataquieR_resultset.R:2:3',     'test-des_summary.R:7:3', 'test-dataquieR_resultset2.R:2:3',     'test-dq_report_by_respvars.R:3:3', 'test-dq_report_by_sb.R:7:3',     'test-dq_report_by_storr.R:2:3', 'test-get_internal_api.R:2:3',     'test-function_arguments.R:2:3', 'test-function_arguments.R:61:3',     'test-function_arguments.R:88:3', 'test-int_datatype_matrix.R:2:3',     'test-int_sts_element_dataframe.R:2:3', 'test-int_unexp_elements.R:2:3',     'test-int_unexp_records.R:2:3', 'test-int_unexp_records_set.R:2:3',     'test-meta_data_env.R:2:3', 'test-nres.R:2:3',     'test-prep_acc_distributions_with_ecdf.R:2:3', 'test-prep_add_to_meta.R:2:3',     'test-prep_apply_coding.R:2:3', 'test-prep_check_meta_names.R:2:3',     'test-prep_clean_labels.R:2:3', 'test-prep_combine_report_summaries.R:2:3',     'test-prep_compare_meta_with_study.R:2:3', 'test-prep_create_meta.R:2:3',     'test-prep_create_meta_data_file.R:2:3',     'test-prep_datatype_from_data.R:2:3', 'test-prep_datatype_from_data.R:39:3',     'test-prep_dq_data_type_of.R:2:3', 'test-prep_get_data_frame.R:2:3',     'test-prep_get_study_data_segment.R:2:3',     'test-prep_load_folder_with_metadata.R:2:3', 'test-prep_map_labels.R:2:3',     'test-prep_min_obs_level.R:2:3', 'test-prep_pmap.R:2:3',     'test-prep_render_pie_charts.R:2:3', 'test-prep_prepare_dataframes.R:2:3',     'test-prep_save_report.R:2:3', 'test-prep_title_escape.R:2:3',     'test-prep_study2meta.R:2:3', 'test-prep_study2meta.R:57:3',     'test-prep_study2meta.R:132:3', 'test-prep_undisclose.R:2:3',     'test-prep_valuelabels_from_data.R:2:3',     'test-pro_applicability_matrix.R:2:3', 'test-print.R:2:3',     'test-print.R:14:3', 'test-print.R:170:3', 'test-print.R:213:3',     'test-rbind.R:2:3', 'test-reflection.R:2:3', 'test-util_acc_loess_bin.R:2:3',     'test-util_app_cd.R:2:3', 'test-util_app_dc.R:2:3', 'test-util_app_dl.R:2:3',     'test-util_app_ed.R:2:3', 'test-util_app_hl.R:2:3',     'test-util_app_iac.R:2:3', 'test-util_app_iav.R:2:3',     'test-util_app_im.R:2:3', 'test-util_app_loess.R:2:3',     'test-util_app_mol.R:2:3', 'test-util_app_mar.R:2:3',     'test-util_app_ol.R:2:3', 'test-util_app_sl.R:2:3', 'test-util_app_sm.R:2:3',     'test-util_app_sos.R:2:3', 'test-util_app_vc.R:2:3',     'test-util_as_numeric.R:2:3', 'test-util_assign_levlabs.R:2:3',     'test-util_check_data_type.R:2:3', 'test-util_backtickQuote.R:2:3',     'test-util_check_group_levels.R:2:3',     'test-util_check_one_unique_value.R:2:3',     'test-util_combine_missing_lists.R:2:3',     'test-util_compare_meta_with_study.R:2:3', 'test-util_detect_cores.R:2:3',     'test-util_dichotomize.R:2:3', 'test-util_dichotomize.R:49:3',     'test-util_dist_selection.R:2:3', 'test-util_ds1_eval_env.R:2:3',     'test-util_contradiction_rules.R:32:3',     'test-util_contradiction_rules.R:41:3',     'test-util_contradiction_rules.R:72:3',     'test-util_contradiction_rules.R:107:3',     'test-util_contradiction_rules.R:142:3',     'test-util_contradiction_rules.R:189:3',     'test-util_contradiction_rules.R:204:3',     'test-util_contradiction_rules.R:223:3',     'test-util_contradiction_rules.R:235:3',     'test-util_contradiction_rules.R:247:3', 'test-util_empty.R:2:3',     'test-util_ensure_character.R:2:3', 'test-util_ensure_suggested.R:2:3',     'test-util_error.R:2:3', 'test-util_finalize_sizing_hints.R:2:3',     'test-util_find_first_externally_called_functions_in_stacktrace.R:2:3',     'test-util_find_external_functions_in_stacktrace.R:2:3',     'test-util_find_external_functions_in_stacktrace.R:26:3',     'test-util_find_free_missing_code.R:2:3', 'test-util_get_code_list.R:2:3',     'test-util_get_code_list.R:88:3', 'test-util_get_code_list.R:117:3',     'test-util_has_no_group_vars.R:2:3', 'test-util_heatmap_1th.R:2:3',     'test-util_html_attr_quote_escape.R:2:3',     'test-util_is_valid_missing_codes.R:2:3',     'test-util_looks_like_missing.R:2:3', 'test-util_interpret_limits.R:2:3',     'test-util_map_all.R:2:3', 'test-util_map_by_largest_prefix.R:2:3',     'test-util_map_labels.R:2:3', 'test-util_no_value_labels.R:2:3',     'test-util_observations_in_subgroups.R:2:3', 'test-util_par_pmap.R:2:3',     'test-util_parallel_futures.R:4:3', 'test-util_parse_assignments.R:2:3',     'test-util_parse_assignments.R:18:3', 'test-util_parse_redcap_rule.R:2:3',     'test-util_plot_categorical_vars.R:2:3',     'test-util_plot_categorical_vars.R:55:3',     'test-util_plot_figure_no_plotly.R:2:3',     'test-util_plot_figure_plotly.R:2:3', 'test-util_queue_cluster.R:2:3',     'test-util_remove_empty_rows.R:2:3', 'test-util_remove_na_records.R:2:3',     'test-util_render_table_dataquieR_summary.R:7:3',     'test-util_replace_codes_by_na.R:2:3', 'test-util_set_doublequotes.R:2:3',     'test-util_set_singlequotes.R:2:3', 'test-util_split_val_tab.R:2:3',     'test-util_split_val_tab.R:68:3', 'test-util_set_size.R:2:3',     'test-util_standardise_ordinal_codes.R:2:3',     'test-util_startsWith_prefix._or_equals_prefix.R:2:3',     'test-util_user_hint.R:2:3', 'test-util_unit2baseunit.R:2:3',     'test-util_validate_known_meta.R:2:3', 'test-util_varcomp_robust.R:2:3',     'test-util_warn_unordered.R:3:3', 'test-util_warning.R:2:3',     'test-util_warning.R:48:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-prep_add_missing_codes.R:8:4'): prep_add_missing_codes works ───   Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean   Backtrace:        ▆     1. └─dataquieR::prep_add_missing_codes(...) at test-prep_add_missing_codes.R:8:4     2. └─dataquieR::prep_prepare_dataframes(...)     3. └─dataquieR:::util_validate_known_meta(meta_data)     4. ├─base::suppressMessages(...)     5. │ └─base::withCallingHandlers(...)     6. ├─base::suppressWarnings(...)     7. │ └─base::withCallingHandlers(...)     8. ├─base::withCallingHandlers(...)     9. └─dataquieR:::util_interpret_limits(mdata = meta_data)    10. ├─base::cbind.data.frame(...)    11. │ └─base::data.frame(..., check.names = FALSE)    12. ├─base::t(apply(as.data.frame(X[[lv[i]]]), 1, myfun1))    13. └─base::apply(as.data.frame(X[[lv[i]]]), 1, myfun1)    14. └─dataquieR (local) FUN(newX[, i], ...)    15. ├─base::trimws(unlist(strsplit(as.character(x), split = ";"), "both"))    16. │ ├─base (local) mysub(...)    17. │ │ └─base::sub(re, "", x, perl = TRUE)    18. │ │ └─base::is.factor(x)    19. │ └─base (local) mysub(paste0("^", whitespace, "+"), x)    20. │ └─base::sub(re, "", x, perl = TRUE)    21. │ └─base::is.factor(x)    22. └─base::unlist(strsplit(as.character(x), split = ";"), "both")   ── Error ('test-util_interpret_limits.R:45:3'): util_interpret_limits works ────   Error in `islistfactor(x, recursive)`: NA in coercion to Rboolean   Backtrace:        ▆     1. └─dataquieR:::util_interpret_limits(meta) at test-util_interpret_limits.R:45:3     2. ├─base::cbind.data.frame(...)     3. │ └─base::data.frame(..., check.names = FALSE)     4. ├─base::t(apply(as.data.frame(X[[lv[i]]]), 1, myfun1))     5. └─base::apply(as.data.frame(X[[lv[i]]]), 1, myfun1)     6. └─dataquieR (local) FUN(newX[, i], ...)     7. ├─base::trimws(unlist(strsplit(as.character(x), split = ";"), "both"))     8. │ ├─base (local) mysub(...)     9. │ │ └─base::sub(re, "", x, perl = TRUE)    10. │ │ └─base::is.factor(x)    11. │ └─base (local) mysub(paste0("^", whitespace, "+"), x)    12. │ └─base::sub(re, "", x, perl = TRUE)    13. │ └─base::is.factor(x)    14. └─base::unlist(strsplit(as.character(x), split = ";"), "both")      [ FAIL 2 | WARN 0 | SKIP 231 | PASS 20 ]   Deleting unused snapshots:   • R4.3/acc_cat_distributions/acc-cat-distributions-education-1.svg   • R4.3/acc_distributions/empty-cat5.svg   • R4.3/acc_distributions/few-float-values.svg   • R4.3/acc_distributions/non-consecutive-codes-work.svg   • R4.3/acc_end_digits/enddigits-plot-for-crp-0-ok.svg   • R4.3/acc_loess/loess-combined-plot-for-crp-0-both-ok.svg   • R4.3/acc_loess/loess-combined-plot-for-crp-0-combined-ok.svg   • R4.3/acc_loess/loess-combined-plot-for-crp-0-ok.svg   • R4.3/acc_loess/loess-combined-plot-for-crp-0-with-covars-ok.svg   • R4.3/acc_loess/loess-facets-plot-for-crp-0-both-ok.svg   • R4.3/acc_loess/loess-facets-plot-for-crp-0-facets-ok.svg   • R4.3/acc_loess/loess-facets-plot-for-crp-0-ok.svg   • R4.3/acc_loess/loess-facets-plot-for-crp-0-with-covars-ok.svg   • R4.3/acc_loess/loess-plot-for-crp-0-auto1-ok.svg   • R4.3/acc_loess/loess-plot-for-crp-0-auto2-ok.svg   • R4.3/acc_margins/margins-plot-for-crp-0-ok.svg   • R4.3/acc_multivariate_outlier/acc-mv-outliercrp0globheava0.svg   • R4.3/acc_shape_or_scale/shape-or-scale-plot-for-crp-0-ok.svg   • R4.3/com_item_missingness/item-missingness-no-labels.svg   • R4.3/com_item_missingness/item-missingness-w-labels.svg   • R4.3/com_segment_missingness/segment-missingness-plot-ok.svg   • R4.3/com_segment_missingness/segment-missingness-plot-r1-ok.svg   • R4.3/com_segment_missingness/segment-missingness-plot-r2-ok.svg   • R4.3/com_segment_missingness/segment-missingness-plot-r3-ok.svg   • R4.3/con_contradictions/one-cat-contradiction-plot-ok.svg   • R4.3/con_contradictions/summary-contradiction-plot-ok.svg   • R4.3/con_contradictions_redcap/one-cat-contradiction-plot-ok.svg   • R4.3/con_contradictions_redcap/summary-contradiction-plot-ok.svg   • R4.3/con_limit_deviations/con-limit-deviations-4-hists-1-val.svg   • R4.3/con_limit_deviations/con-limit-deviations-for-reverted.svg   • R4.3/con_limit_deviations/con-limit-deviations-histgrms-misscds.svg   • R4.3/con_limit_deviations/con-limit-deviations-nothing-within.svg   • R4.3/con_limit_deviations/con-limit-deviations-reverse-w-1-0-max.svg   • R4.3/int_datatype_matrix/intdtpart-interview.svg   • R4.3/int_datatype_matrix/intdtpart-lab.svg   • R4.3/int_datatype_matrix/intdtpart-phys-exam.svg   • R4.3/int_datatype_matrix/intdtpart-questionnaire.svg   • R4.3/int_datatype_matrix/intdtpart-study.svg   • R4.3/int_datatype_matrix/integrity-datatype.svg   • R4.3/plots/acc-distributions-def-edu0.svg   • R4.3/plots/acc-distributions-gr-dbp0.svg   • R4.3/plots/acc-multivariate-outlier-test-1.svg   • R4.3/plots/acc-univariate-outlier-r-dbp-0.svg   • R4.3/plots/con-contradictions-all-checks.svg   • R4.3/plots/con-contradictions-by-tag.svg   • R4.3/plots/con-contradictions-logical-age-checks-only.svg   • R4.3/plots/con-contradictions-rc-all-checks.svg   • R4.3/plots/con-contradictions-rc-by-tag.svg   • R4.3/plots/con-contradictions-rc-logical-checks-only.svg   • R4.3/plots/con-limit-deviations-all-item.svg   • R4.3/plots/con-limit-deviations-all-quest-dt.svg   • R4.3/plots/con-limit-deviations-all-sbp-0.svg   • R4.3/plots/con-limit-deviations-low-item.svg   • R4.3/plots/con-limit-deviations-low-quest-dt.svg   • R4.3/plots/con-limit-deviations-low-sbp-0.svg   • R4.3/plots/con-limit-deviations-upp-item.svg   • R4.3/plots/con-limit-deviations-upp-quest-dt.svg   • R4.3/plots/con-limit-deviations-upp-sbp-0.svg   • R4.3/plots/empty-reportsummarytable.svg   • R4.3/plots/heatmap-with-1-cat-var.svg   • R4.3/plots/heatmap-with-2-cat-vars-but-w-o-strata-vars.svg   • R4.3/plots/heatmap-with-2-cat-vars-but-w-strata-vars.svg   • R4.3/plots/int-datatype-matrix-reportsummarytable.svg   • R4.3/plots/int-datatype-matrix-segment-v50000.svg   • R4.3/plots/int-datatype-matrix.svg   • R4.3/plots/loess-def-dbp0.svg   • R4.3/plots/loess-def-edu0.svg   • 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R4.5/plots/shape-or-scale-dbp0.svg   • R4.5/prep_render_pie_charts/acc-varcomp-observer.svg   • R4.5/prep_render_pie_charts/com-item-missingness.svg   • R4.5/print/app-ex-repsumtab.svg   • R4.5/print/im-empty-repsumtab.svg   • R4.5/print/im-ex1-repsumtab.svg   • R4.5/print/im-ex2-repsumtab.svg   • R4.5/pro_applicability_matrix/appmatrix-plot-ok.svg   • R4.5/pro_applicability_matrix/appmatrix-segment-v10000.svg   • R4.5/util_heatmap_1th/util-heatmap-1th-1.svg   • R4.5/util_heatmap_1th/util-heatmap-1th-2.svg   • R4.5/util_heatmap_1th/util-heatmap-1th-3.svg   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... OK
• checking PDF version of manual ... [23s/23s] OK
• checking HTML version of manual ... [18s/18s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR