Package check result: OK Changes to worse in reverse depends: Package: autoslider.core Check: examples New result: ERROR Running examples in ‘autoslider.core-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: t_dd_slide > ### Title: Death table > ### Aliases: t_dd_slide > > ### ** 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 > adsl <- eg_adsl %>% preprocess_t_dd() > out1 <- t_dd_slide(adsl, "TRT01A") Error in format_value(rawvalues(x), format = format, output = output, : Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Calls: t_dd_slide ... mapply -> -> format_rcell -> format_value Execution halted Package: autoslider.core Check: tests New result: ERROR Running ‘testthat.R’ [152s/153s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "autoslider.core" > library(testthat) > test_check(pkg_name, reporter = ParallelProgressReporter$new()) Loading required package: autoslider.core Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Attaching package: 'rtables' The following object is masked from 'package:utils': str Attaching package: 'purrr' The following object is masked from 'package:magrittr': set_names The following object is masked from 'package:formatters': %||% The following object is masked from 'package:testthat': is_null Loading required package: ggplot2 ✔ | F W S OK | Context ⠋ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] Starting up... ✔ | 1 | bad_filters ✔ | 1 0 | data_snapshot [[1]] [[1]] [[2]] Loading required namespace: rsvg ✔ | 8 | decorate [1.1s] ✔ | 1 0 | filter_spec-verbose ✔ | 6 | formats ✔ | 5 9 | g_mean_slides [2.5s] ✔ | 1 1 | helper_functions Loading required package: tibble Attaching package: 'tibble' The following object is masked from 'package:assertthat': has_name ✔ | 1 0 | l_ae_slide [10.1s] v Total number of success 100/100 v Total number of success 99/100 x Total number of failures 1/100 ✔ | 2 | log [1] "test title" [1] "test title" [1] "test title" [1] "test title" [1] "test title" ✔ | 5 | output-table-format [4.0s] ✔ | 1 | save_output ✔ | 1 1 | slides_preview v 27/50 outputs matched the filter condition `program %in% c("t_ds_slide", "t_ds_trt_slide", "t_dd_slide", `. v 27/50 outputs matched the filter condition ` "t_ae_slide", "t_ae_sae_slide", "t_ae_pt_slide", "t_ae_pt_soc_slide", `. v 27/50 outputs matched the filter condition ` "t_ae_pt_diff_slide", "t_ae_pt_diff_soc_slide", "t_pop_slide", `. v 27/50 outputs matched the filter condition ` "t_dor_slide", "t_orr_dor_slide", "t_tte_slide", "t_orr_slide", `. v 27/50 outputs matched the filter condition ` "g_vs_slide", "g_lab_slide", "g_eg_slide", "t_dm_slide", `. v 27/50 outputs matched the filter condition ` "t_vs_slide", "t_ae_summ_slide", "t_ex_slide", "l_ae_slide")`. > Running program `t_pop_slide` with suffix 'FAS'. ! Error: object 't_pop_slide' of mode 'function' was not found > Running program `t_ds_slide` with suffix 'FAS'. Filter 'FAS' matched target ADSL. 400/400 records matched the filter condition `FASFL == 'Y'`. > Running program `t_ds_trt_slide` with suffix 'SE'. ! Error: object 't_ds_trt_slide' of mode 'function' was not found > Running program `t_dm_slide` with suffix 'FAS'. Filter 'FAS' matched target ADSL. 400/400 records matched the filter condition `FASFL == 'Y'`. > Running program `t_dm_slide` with suffix 'FAS'. Filter 'FAS' matched target ADSL. 400/400 records matched the filter condition `FASFL == 'Y'`. > Running program `t_tte_slide` with suffix 'PFSINV_FAS'. ! Error: object 't_tte_slide' of mode 'function' was not found > Running program `t_tte_slide` with suffix 'PFSINV_FAS'. ! Error: object 't_tte_slide' of mode 'function' was not found > Running program `t_tte_slide` with suffix 'OS_FAS'. ! Error: object 't_tte_slide' of mode 'function' was not found > Running program `t_orr_slide` with suffix 'INVET'. ! Error: object 't_orr_slide' of mode 'function' was not found > Running program `t_orr_slide` with suffix 'INVET'. ! Error: object 't_orr_slide' of mode 'function' was not found > Running program `t_orr_dor_slide` with suffix 'INVET_PFSINV'. ! Error: object 't_orr_dor_slide' of mode 'function' was not found > Running program `t_orr_dor_slide` with suffix 'PFSINV_INVET_SE'. ! Error: object 't_orr_dor_slide' of mode 'function' was not found > Running program `t_dor_slide` with suffix 'PFSINV_SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. Filter 'PFSINV' matched target ADTTE. 400/2000 records matched the filter condition `PARAMCD == 'PFS'`. > Running program `t_ex_slide` with suffix 'SE'. ! Error: object 't_ex_slide' of mode 'function' was not found > Running program `t_ae_summ_slide` with suffix 'SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. > Running program `t_ae_pt_slide` with suffix 'X10PER_SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. Filter 'X10PER' matched target ADAE. 1934/1934 records matched the filter condition `1 == 1`. > Running program `t_ae_pt_slide` with suffix 'G34_X2PER_SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. Filters 'G34', 'X2PER' matched target ADAE. 560/1934 records matched the filter condition `AETOXGR %in% c('3', '4') & 1 == 1`. > Running program `t_ae_pt_soc_slide` with suffix 'X10PER_SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. Filter 'X10PER' matched target ADAE. 1934/1934 records matched the filter condition `1 == 1`. > Running program `t_ae_pt_soc_slide` with suffix 'G34_X2PER_SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. Filters 'G34', 'X2PER' matched target ADAE. 560/1934 records matched the filter condition `AETOXGR %in% c('3', '4') & 1 == 1`. > Running program `t_dd_slide` with suffix 'SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. ! Error: Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). > Running program `t_vs_slide` with suffix 'FAS'. ! Error: object 't_vs_slide' of mode 'function' was not found > Running program `g_vs_slide` with suffix 'FAS_SYSBP'. Filter 'FAS' matched target ADSL. 400/400 records matched the filter condition `FASFL == 'Y'`. Filter 'SYSBP' matched target ADVS. 2800/16800 records matched the filter condition `PARAMCD == 'SYSBP'`. > Running program `g_eg_slide` with suffix 'FAS_EGHR'. Filter 'FAS' matched target ADSL. 400/400 records matched the filter condition `FASFL == 'Y'`. Filter 'EGHR' matched target ADEG. 3600/13600 records matched the filter condition `PARAMCD == 'HR'`. > Running program `l_ae_slide` with suffix 'SE'. Filter 'SE' matched target ADSL. 400/400 records matched the filter condition `SAFFL == 'Y'`. > Running program `t_ae_sae_slide` with suffix 'SE'. ! Error: object 't_ae_sae_slide' of mode 'function' was not found > Running program `g_vs_slide` with suffix 'ADSL_SYSBP'. Filter 'ADSL' matched target ADSL. 400/400 records matched the filter condition `1 == 1`. Filter 'SYSBP' matched target ADVS. 2800/16800 records matched the filter condition `PARAMCD == 'SYSBP'`. > Running program `g_eg_slide` with suffix 'ADSL_HR'. Filter 'ADSL' matched target ADSL. 400/400 records matched the filter condition `1 == 1`. Filter 'HR' matched target ADEG. 3600/13600 records matched the filter condition `PARAMCD == 'HR'`. object 't_pop_slide' of mode 'function' was not found object 't_ds_trt_slide' of mode 'function' was not found object 't_tte_slide' of mode 'function' was not found object 't_tte_slide' of mode 'function' was not found object 't_tte_slide' of mode 'function' was not found object 't_orr_slide' of mode 'function' was not found object 't_orr_slide' of mode 'function' was not found object 't_orr_dor_slide' of mode 'function' was not found object 't_orr_dor_slide' of mode 'function' was not found object 't_ex_slide' of mode 'function' was not found Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). object 't_vs_slide' of mode 'function' was not found object 't_ae_sae_slide' of mode 'function' was not found x Saving output t_pop_slide_FAS failed in step filter dataset with error message: object 't_pop_slide' of mode 'function' was not found v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_ds_slide_FAS x Saving output t_ds_trt_slide_SE failed in step filter dataset with error message: object 't_ds_trt_slide' of mode 'function' was not found v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_dm_slide_FAS v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_dm_slide_FAS x Saving output t_tte_slide_PFSINV_FAS failed in step filter dataset with error message: object 't_tte_slide' of mode 'function' was not found x Saving output t_tte_slide_PFSINV_FAS failed in step filter dataset with error message: object 't_tte_slide' of mode 'function' was not found x Saving output t_tte_slide_OS_FAS failed in step filter dataset with error message: object 't_tte_slide' of mode 'function' was not found x Saving output t_orr_slide_INVET failed in step filter dataset with error message: object 't_orr_slide' of mode 'function' was not found x Saving output t_orr_slide_INVET failed in step filter dataset with error message: object 't_orr_slide' of mode 'function' was not found x Saving output t_orr_dor_slide_INVET_PFSINV failed in step filter dataset with error message: object 't_orr_dor_slide' of mode 'function' was not found x Saving output t_orr_dor_slide_PFSINV_INVET_SE failed in step filter dataset with error message: object 't_orr_dor_slide' of mode 'function' was not found v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_dor_slide_PFSINV_SE x Saving output t_ex_slide_SE failed in step filter dataset with error message: object 't_ex_slide' of mode 'function' was not found v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_ae_summ_slide_SE v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_ae_pt_slide_X10PER_SE v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_ae_pt_slide_G34_X2PER_SE v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_ae_pt_soc_slide_X10PER_SE v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/t_ae_pt_soc_slide_G34_X2PER_SE x Saving output t_dd_slide_SE failed in step user program with error message: Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). x Saving output t_vs_slide_FAS failed in step filter dataset with error message: object 't_vs_slide' of mode 'function' was not found v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/g_vs_slide_FAS_SYSBP v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/g_eg_slide_FAS_EGHR v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/l_ae_slide_SE x Saving output t_ae_sae_slide_SE failed in step filter dataset with error message: object 't_ae_sae_slide' of mode 'function' was not found v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/g_vs_slide_ADSL_SYSBP v Output saved in path /home/hornik/tmp/scratch/RtmptTSEJN/g_eg_slide_ADSL_HR v Total number of success 14/27 x Total number of failures 13/27 ✔ | 1 2 | srep_outputs [116.0s] ──────────────────────────────────────────────────────────────────────────────── Warning ('test-srep_outputs.R:13:3'): Listing print correctly Non-unique sibling analysis table names. Using Labels instead. Use the table_names argument to analyze to avoid this when analyzing the same variable multiple times. occured at (row) path: root Backtrace: ▆ 1. ├─... %>% ... at test-srep_outputs.R:13:3 2. ├─autoslider.core::decorate_outputs(., version_label = NULL, for_test = TRUE) 3. │ └─base::lapply(...) 4. └─autoslider.core::generate_outputs(., datasets = testdata) 5. └─base::lapply(...) 6. └─autoslider.core (local) FUN(X[[i]], ...) 7. └─autoslider.core::fastDoCall(generate_output, args) 8. └─base::eval(call, envir = args, enclos = envir) 9. └─base::eval(call, envir = args, enclos = envir) 10. └─autoslider.core::generate_output(...) 11. ├─base::tryCatch(...) 12. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. └─autoslider.core (local) func(...) 16. └─autoslider.core::fastDoCall(...) 17. └─base::eval(call, envir = args, enclos = envir) 18. └─base::eval(call, envir = args, enclos = envir) 19. └─autoslider.core (local) func(...) 20. └─rtables::build_table(lyt, df = anl, alt_counts_df = adsl) 21. └─base::lapply(...) 22. └─rtables (local) FUN(X[[i]], ...) 23. └─rtables:::recursive_applysplit(...) 24. ├─rtables:::.make_split_kids(...) 25. └─rtables:::.make_split_kids(...) 26. └─rtables (local) .local(spl, have_controws, make_lrow, ...) ──────────────────────────────────────────────────────────────────────────────── ✔ | 7 1 | t_ae_pt_diff_slide [2.8s] ✔ | 6 0 | t_ae_pt_slide [2.0s] ✔ | 4 1 | t_ae_pt_soc_diff_slide [2.5s] ✔ | 2 0 | t_ae_slide ✔ | 3 0 | t_ae_summary_slide ✔ | 3 2 | t_aesi_slide [1.7s] ✖ | 3 2 0 | t_dd_slide ──────────────────────────────────────────────────────────────────────────────── Error ('test-t_dd_slide.R:2:3'): Test table creation of t_dd_slide (death table) Error in `format_value(rawvalues(x), format = format, output = output, na_str = na_str)`: Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Backtrace: ▆ 1. └─testthat::expect_snapshot(t_dd_slide(testdata$adsl, "TRT01A")) at test-t_dd_slide.R:2:3 2. └─rlang::cnd_signal(state$error) Error ('test-t_dd_slide.R:15:3'): Test table creation of t_dd_slide (death table) Error in `format_value(rawvalues(x), format = format, output = output, na_str = na_str)`: Cell contents <12> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-t_dd_slide.R:15:3 2. └─rlang::cnd_signal(state$error) Error ('test-t_dd_slide.R:20:3'): Test table creation of t_dd_slide (death table) Error in `format_value(rawvalues(x), format = format, output = output, na_str = na_str)`: Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-t_dd_slide.R:20:3 2. └─rlang::cnd_signal(state$error) ──────────────────────────────────────────────────────────────────────────────── ✔ | 1 0 | t_dm_slide ✔ | 2 0 | t_dor_slide ✔ | 4 0 | t_ds_slide [1.4s] fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). ✔ | 3 15 | util ──────────────────────────────────────────────────────────────────────────────── Warning ('test-util.R:12:3'): Test some functions in util.R running command 'git remote -v' had status 128 Backtrace: ▆ 1. ├─testthat::expect_no_error(get_remote_url()) at test-util.R:12:3 2. │ └─testthat:::expect_no_(...) 3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─rlang::try_fetch(...) 6. │ │ ├─base::tryCatch(...) 7. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. │ │ └─base::withCallingHandlers(...) 11. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 12. └─autoslider.core:::get_remote_url() 13. └─base::system("git remote -v", intern = TRUE) Warning ('test-util.R:13:3'): Test some functions in util.R running command 'git rev-parse HEAD' had status 128 Backtrace: ▆ 1. ├─testthat::expect_no_error(get_last_gitcommit_sha()) at test-util.R:13:3 2. │ └─testthat:::expect_no_(...) 3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─rlang::try_fetch(...) 6. │ │ ├─base::tryCatch(...) 7. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. │ │ └─base::withCallingHandlers(...) 11. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 12. └─autoslider.core:::get_last_gitcommit_sha() 13. └─base::system("git rev-parse HEAD", intern = TRUE) Warning ('test-util.R:14:3'): Test some functions in util.R running command 'git rev-parse --abbrev-ref HEAD' had status 128 Backtrace: ▆ 1. ├─testthat::expect_no_error(get_repo_head_name()) at test-util.R:14:3 2. │ └─testthat:::expect_no_(...) 3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─rlang::try_fetch(...) 6. │ │ ├─base::tryCatch(...) 7. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. │ │ └─base::withCallingHandlers(...) 11. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 12. └─autoslider.core:::get_repo_head_name() 13. └─base::system("git rev-parse --abbrev-ref HEAD", intern = TRUE) ──────────────────────────────────────────────────────────────────────────────── ✔ | 1 0 | format_date ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 148.8 s ── Skipped tests (45) ────────────────────────────────────────────────────────── • On CRAN (45): 'test-data_snapshot.R:6:5', 'test-filter_spec-verbose.R:12:3', 'test-g_mean_slides.R:21:3', 'test-g_mean_slides.R:38:3', 'test-g_mean_slides.R:55:3', 'test-g_mean_slides.R:73:3', 'test-g_mean_slides.R:95:3', 'test-helper_functions.R:3:3', 'test-l_ae_slide.R:7:3', 'test-slides_preview.R:5:3', 'test-t_ae_pt_diff_slide.R:2:3', 'test-t_ae_pt_diff_slide.R:6:3', 'test-t_ae_pt_diff_slide.R:11:3', 'test-t_ae_pt_diff_slide.R:17:3', 'test-t_ae_pt_diff_slide.R:25:3', 'test-t_ae_pt_diff_slide.R:43:3', 'test-t_ae_pt_diff_slide.R:57:3', 'test-t_ae_pt_slide.R:2:3', 'test-t_ae_pt_slide.R:6:3', 'test-t_ae_pt_slide.R:10:3', 'test-t_ae_pt_slide.R:15:3', 'test-t_ae_pt_slide.R:19:3', 'test-t_ae_pt_slide.R:23:3', 'test-t_ae_pt_soc_diff_slide.R:2:3', 'test-t_ae_pt_soc_diff_slide.R:6:3', 'test-t_ae_pt_soc_diff_slide.R:10:3', 'test-t_ae_pt_soc_diff_slide.R:16:3', 'test-t_ae_slide.R:10:3', 'test-t_ae_slide.R:24:3', 'test-t_ae_summary_slide.R:2:3', 'test-t_ae_summary_slide.R:23:3', 'test-t_ae_summary_slide.R:35:3', 'test-t_aesi_slide.R:2:3', 'test-t_aesi_slide.R:10:3', 'test-t_aesi_slide.R:21:3', 'test-t_dd_slide.R:6:3', 'test-t_dd_slide.R:10:3', 'test-t_dm_slide.R:3:3', 'test-t_dor_slide.R:8:3', 'test-t_dor_slide.R:19:3', 'test-t_ds_slide.R:2:3', 'test-t_ds_slide.R:6:3', 'test-t_ds_slide.R:10:3', 'test-t_ds_slide.R:14:3', 'test_format_date.R:2:3' ── Failed tests ──────────────────────────────────────────────────────────────── Error ('test-t_dd_slide.R:2:3'): Test table creation of t_dd_slide (death table) Error in `format_value(rawvalues(x), format = format, output = output, na_str = na_str)`: Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Backtrace: ▆ 1. └─testthat::expect_snapshot(t_dd_slide(testdata$adsl, "TRT01A")) at test-t_dd_slide.R:2:3 2. └─rlang::cnd_signal(state$error) Error ('test-t_dd_slide.R:15:3'): Test table creation of t_dd_slide (death table) Error in `format_value(rawvalues(x), format = format, output = output, na_str = na_str)`: Cell contents <12> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-t_dd_slide.R:15:3 2. └─rlang::cnd_signal(state$error) Error ('test-t_dd_slide.R:20:3'): Test table creation of t_dd_slide (death table) Error in `format_value(rawvalues(x), format = format, output = output, na_str = na_str)`: Cell contents <25> and format 'xx (xx.xx%)' are of different lengths (1 vs 2). Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-t_dd_slide.R:20:3 2. └─rlang::cnd_signal(state$error) [ FAIL 3 | WARN 4 | SKIP 45 | PASS 55 ] Error: Test failures Execution halted