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Last updated on 2026-10-13 05:51:36 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.6 | 24.31 | 601.07 | 625.38 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.6 | 17.21 | 388.37 | 405.58 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.6 | 19.00 | 359.39 | 378.39 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.6 | 18.00 | 369.71 | 387.71 | ERROR | |
| r-devel-windows-x86_64 | 0.1.6 | 34.00 | 709.00 | 743.00 | OK | |
| r-patched-linux-x86_64 | 0.1.6 | 27.75 | 570.35 | 598.10 | ERROR | |
| r-release-linux-x86_64 | 0.1.6 | 25.13 | 575.78 | 600.91 | ERROR | |
| r-release-macos-arm64 | 0.1.6 | 6.00 | 141.00 | 147.00 | OK | |
| r-release-macos-x86_64 | 0.1.6 | 18.00 | 461.00 | 479.00 | OK | |
| r-release-windows-x86_64 | 0.1.6 | 31.00 | 658.00 | 689.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.6 | 6.00 | 141.00 | 147.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.6 | 18.00 | 426.00 | 444.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.6 | 41.00 | 760.00 | 801.00 | ERROR |
Version: 0.1.6
Check: examples
Result: ERROR
Running examples in ‘junco-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: a_freq_j
> ### Title: Analysis/statistical function for count and percentage in core
> ### columns and (optional) relative risk columns
> ### Aliases: a_freq_j s_freq_j a_freq_j_with_exclude
>
> ### ** 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 <- ex_adsl |> select("USUBJID", "SEX", "ARM")
> adae <- ex_adae |> select("USUBJID", "AEBODSYS", "AEDECOD")
> adae[["TRTEMFL"]] <- "Y"
>
> trtvar <- "ARM"
> ctrl_grp <- "B: Placebo"
> adsl$colspan_trt <- factor(ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"),
+ levels = c("Active Study Agent", " ")
+ )
>
> adsl$rrisk_header <- "Risk Difference (%) (95% CI)"
> adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp))
>
> adae <- adae |> left_join(adsl)
Joining with `by = join_by(USUBJID)`
>
> colspan_trt_map <- create_colspan_map(adsl,
+ non_active_grp = "B: Placebo",
+ non_active_grp_span_lbl = " ",
+ active_grp_span_lbl = "Active Study Agent",
+ colspan_var = "colspan_trt",
+ trt_var = trtvar
+ )
>
> ref_path <- c("colspan_trt", " ", trtvar, ctrl_grp)
>
> lyt <- basic_table(show_colcounts = TRUE) |>
+ split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map)) |>
+ split_cols_by(trtvar) |>
+ split_cols_by("rrisk_header", nested = FALSE) |>
+ split_cols_by(trtvar, labels_var = "rrisk_label", split_fun = remove_split_levels(ctrl_grp))
>
> lyt1 <- lyt |>
+ analyze("TRTEMFL",
+ show_labels = "hidden",
+ afun = a_freq_j,
+ extra_args = list(
+ method = "wald",
+ .stats = c("count_unique_denom_fraction"),
+ ref_path = ref_path
+ )
+ )
>
> result1 <- build_table(lyt1, adae, alt_counts_df = adsl)
>
> result1
Active Study Agent Risk Difference (%) (95% CI)
A: Drug X C: Combination B: Placebo A: Drug X vs B: Placebo C: Combination vs B: Placebo
(N=134) (N=132) (N=134) (N=134) (N=132)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Y 122/134 (91.0%) 120/132 (90.9%) 123/134 (91.8%) -0.7 (-7.5, 6.0) -0.9 (-7.6, 5.9)
>
> x_drug_x <- list(length(unique(subset(adae, adae[[trtvar]] == "A: Drug X")[["USUBJID"]])))
> N_x_drug_x <- length(unique(subset(adsl, adsl[[trtvar]] == "A: Drug X")[["USUBJID"]]))
> y_placebo <- list(length(unique(subset(adae, adae[[trtvar]] == ctrl_grp)[["USUBJID"]])))
> N_y_placebo <- length(unique(subset(adsl, adsl[[trtvar]] == ctrl_grp)[["USUBJID"]]))
>
> tern::stat_propdiff_ci(
+ x = x_drug_x,
+ N_x = N_x_drug_x,
+ y = y_placebo,
+ N_y = N_y_placebo
+ )
[[1]]
[1] -0.7462687 -7.4525893 5.9600520
>
> x_combo <- list(length(unique(subset(adae, adae[[trtvar]] == "C: Combination")[["USUBJID"]])))
> N_x_combo <- length(unique(subset(adsl, adsl[[trtvar]] == "C: Combination")[["USUBJID"]]))
>
> tern::stat_propdiff_ci(
+ x = x_combo,
+ N_x = N_x_combo,
+ y = y_placebo,
+ N_y = N_y_placebo
+ )
[[1]]
[1] -0.8819539 -7.6386167 5.8747089
>
>
> extra_args_rr <- list(
+ denom = "n_altdf",
+ denom_by = "SEX",
+ riskdiff = FALSE,
+ .stats = c("count_unique")
+ )
>
> extra_args_rr2 <- list(
+ denom = "n_altdf",
+ denom_by = "SEX",
+ riskdiff = TRUE,
+ ref_path = ref_path,
+ method = "wald",
+ .stats = c("count_unique_denom_fraction"),
+ na_str = rep("NA", 3)
+ )
>
> lyt2 <- basic_table(
+ top_level_section_div = " ",
+ colcount_format = "N=xx"
+ ) |>
+ split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map)) |>
+ split_cols_by(trtvar, show_colcounts = TRUE) |>
+ split_cols_by("rrisk_header", nested = FALSE) |>
+ split_cols_by(trtvar,
+ labels_var = "rrisk_label", split_fun = remove_split_levels("B: Placebo"),
+ show_colcounts = FALSE
+ ) |>
+ split_rows_by("SEX", split_fun = drop_split_levels) |>
+ summarize_row_groups("SEX",
+ cfun = a_freq_j,
+ extra_args = append(extra_args_rr, list(label_fstr = "Gender: %s"))
+ ) |>
+ split_rows_by("TRTEMFL",
+ split_fun = keep_split_levels("Y"),
+ indent_mod = -1L,
+ section_div = c(" ")
+ ) |>
+ summarize_row_groups("TRTEMFL",
+ cfun = a_freq_j,
+ extra_args = append(extra_args_rr2, list(
+ label =
+ "Subjects with >=1 AE", extrablankline = TRUE
+ ))
+ ) |>
+ split_rows_by("AEBODSYS",
+ split_label = "System Organ Class",
+ split_fun = trim_levels_in_group("AEDECOD"),
+ label_pos = "topleft",
+ section_div = c(" "),
+ nested = TRUE
+ ) |>
+ summarize_row_groups("AEBODSYS",
+ cfun = a_freq_j,
+ extra_args = extra_args_rr2
+ ) |>
+ analyze("AEDECOD",
+ afun = a_freq_j,
+ extra_args = extra_args_rr2
+ )
>
> result2 <- build_table(lyt2, adae, alt_counts_df = adsl)
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]->TRTEMFL[Y]
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [274s/368s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ancova_combined.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘ancova_combined.Rmd’
--- re-building ‘auto_colwidths.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘auto_colwidths.Rmd’
--- re-building ‘junco.Rmd’ using rmarkdown
Quitting from junco.Rmd:272-344 [subgroup_tables]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]
---
Backtrace:
▆
1. ├─... %>% build_table(adae, alt_counts_df = adsl)
2. └─rtables::build_table(., adae, alt_counts_df = adsl)
3. └─base::lapply(...)
4. └─rtables (local) FUN(X[[i]], ...)
5. └─rtables:::recursive_applysplit(...)
6. ├─rtables:::.make_split_kids(...)
7. └─rtables:::.make_split_kids(...)
8. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
9. ├─base::unlist(...)
10. └─base::mapply(...)
11. └─rtables (local) `<fn>`(...)
12. └─rtables:::recursive_applysplit(...)
13. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'junco.Rmd' failed with diagnostics:
Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]
--- failed re-building ‘junco.Rmd’
--- re-building ‘standard_column_structures.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘standard_column_structures.Rmd’
--- re-building ‘table_and_listing_customizations.Rmd’ using rmarkdown
Quitting from table_and_listing_customizations.Rmd:76-163 [orientation_rtf]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[Male]
---
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl)
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'table_and_listing_customizations.Rmd' failed with diagnostics:
Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[Male]
--- failed re-building ‘table_and_listing_customizations.Rmd’
SUMMARY: processing the following files failed:
‘junco.Rmd’ ‘table_and_listing_customizations.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [174s/241s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.6
Check: examples
Result: ERROR
Running examples in ‘junco-Ex.R’ failed
The error most likely occurred in:
> ### Name: a_freq_j
> ### Title: Analysis/statistical function for count and percentage in core
> ### columns and (optional) relative risk columns
> ### Aliases: a_freq_j s_freq_j a_freq_j_with_exclude
>
> ### ** 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 <- ex_adsl |> select("USUBJID", "SEX", "ARM")
> adae <- ex_adae |> select("USUBJID", "AEBODSYS", "AEDECOD")
> adae[["TRTEMFL"]] <- "Y"
>
> trtvar <- "ARM"
> ctrl_grp <- "B: Placebo"
> adsl$colspan_trt <- factor(ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"),
+ levels = c("Active Study Agent", " ")
+ )
>
> adsl$rrisk_header <- "Risk Difference (%) (95% CI)"
> adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp))
>
> adae <- adae |> left_join(adsl)
Joining with `by = join_by(USUBJID)`
>
> colspan_trt_map <- create_colspan_map(adsl,
+ non_active_grp = "B: Placebo",
+ non_active_grp_span_lbl = " ",
+ active_grp_span_lbl = "Active Study Agent",
+ colspan_var = "colspan_trt",
+ trt_var = trtvar
+ )
>
> ref_path <- c("colspan_trt", " ", trtvar, ctrl_grp)
>
> lyt <- basic_table(show_colcounts = TRUE) |>
+ split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map)) |>
+ split_cols_by(trtvar) |>
+ split_cols_by("rrisk_header", nested = FALSE) |>
+ split_cols_by(trtvar, labels_var = "rrisk_label", split_fun = remove_split_levels(ctrl_grp))
>
> lyt1 <- lyt |>
+ analyze("TRTEMFL",
+ show_labels = "hidden",
+ afun = a_freq_j,
+ extra_args = list(
+ method = "wald",
+ .stats = c("count_unique_denom_fraction"),
+ ref_path = ref_path
+ )
+ )
>
> result1 <- build_table(lyt1, adae, alt_counts_df = adsl)
>
> result1
Active Study Agent Risk Difference (%) (95% CI)
A: Drug X C: Combination B: Placebo A: Drug X vs B: Placebo C: Combination vs B: Placebo
(N=134) (N=132) (N=134) (N=134) (N=132)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Y 122/134 (91.0%) 120/132 (90.9%) 123/134 (91.8%) -0.7 (-7.5, 6.0) -0.9 (-7.6, 5.9)
>
> x_drug_x <- list(length(unique(subset(adae, adae[[trtvar]] == "A: Drug X")[["USUBJID"]])))
> N_x_drug_x <- length(unique(subset(adsl, adsl[[trtvar]] == "A: Drug X")[["USUBJID"]]))
> y_placebo <- list(length(unique(subset(adae, adae[[trtvar]] == ctrl_grp)[["USUBJID"]])))
> N_y_placebo <- length(unique(subset(adsl, adsl[[trtvar]] == ctrl_grp)[["USUBJID"]]))
>
> tern::stat_propdiff_ci(
+ x = x_drug_x,
+ N_x = N_x_drug_x,
+ y = y_placebo,
+ N_y = N_y_placebo
+ )
[[1]]
[1] -0.7462687 -7.4525893 5.9600520
>
> x_combo <- list(length(unique(subset(adae, adae[[trtvar]] == "C: Combination")[["USUBJID"]])))
> N_x_combo <- length(unique(subset(adsl, adsl[[trtvar]] == "C: Combination")[["USUBJID"]]))
>
> tern::stat_propdiff_ci(
+ x = x_combo,
+ N_x = N_x_combo,
+ y = y_placebo,
+ N_y = N_y_placebo
+ )
[[1]]
[1] -0.8819539 -7.6386167 5.8747089
>
>
> extra_args_rr <- list(
+ denom = "n_altdf",
+ denom_by = "SEX",
+ riskdiff = FALSE,
+ .stats = c("count_unique")
+ )
>
> extra_args_rr2 <- list(
+ denom = "n_altdf",
+ denom_by = "SEX",
+ riskdiff = TRUE,
+ ref_path = ref_path,
+ method = "wald",
+ .stats = c("count_unique_denom_fraction"),
+ na_str = rep("NA", 3)
+ )
>
> lyt2 <- basic_table(
+ top_level_section_div = " ",
+ colcount_format = "N=xx"
+ ) |>
+ split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map)) |>
+ split_cols_by(trtvar, show_colcounts = TRUE) |>
+ split_cols_by("rrisk_header", nested = FALSE) |>
+ split_cols_by(trtvar,
+ labels_var = "rrisk_label", split_fun = remove_split_levels("B: Placebo"),
+ show_colcounts = FALSE
+ ) |>
+ split_rows_by("SEX", split_fun = drop_split_levels) |>
+ summarize_row_groups("SEX",
+ cfun = a_freq_j,
+ extra_args = append(extra_args_rr, list(label_fstr = "Gender: %s"))
+ ) |>
+ split_rows_by("TRTEMFL",
+ split_fun = keep_split_levels("Y"),
+ indent_mod = -1L,
+ section_div = c(" ")
+ ) |>
+ summarize_row_groups("TRTEMFL",
+ cfun = a_freq_j,
+ extra_args = append(extra_args_rr2, list(
+ label =
+ "Subjects with >=1 AE", extrablankline = TRUE
+ ))
+ ) |>
+ split_rows_by("AEBODSYS",
+ split_label = "System Organ Class",
+ split_fun = trim_levels_in_group("AEDECOD"),
+ label_pos = "topleft",
+ section_div = c(" "),
+ nested = TRUE
+ ) |>
+ summarize_row_groups("AEBODSYS",
+ cfun = a_freq_j,
+ extra_args = extra_args_rr2
+ ) |>
+ analyze("AEDECOD",
+ afun = a_freq_j,
+ extra_args = extra_args_rr2
+ )
>
> result2 <- build_table(lyt2, adae, alt_counts_df = adsl)
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]->TRTEMFL[Y]
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [160s/168s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ancova_combined.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘ancova_combined.Rmd’
--- re-building ‘auto_colwidths.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘auto_colwidths.Rmd’
--- re-building ‘junco.Rmd’ using rmarkdown
Quitting from junco.Rmd:272-344 [subgroup_tables]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]
---
Backtrace:
▆
1. ├─... %>% build_table(adae, alt_counts_df = adsl)
2. └─rtables::build_table(., adae, alt_counts_df = adsl)
3. └─base::lapply(...)
4. └─rtables (local) FUN(X[[i]], ...)
5. └─rtables:::recursive_applysplit(...)
6. ├─rtables:::.make_split_kids(...)
7. └─rtables:::.make_split_kids(...)
8. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
9. ├─base::unlist(...)
10. └─base::mapply(...)
11. └─rtables (local) `<fn>`(...)
12. └─rtables:::recursive_applysplit(...)
13. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'junco.Rmd' failed with diagnostics:
Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]
--- failed re-building ‘junco.Rmd’
--- re-building ‘standard_column_structures.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘standard_column_structures.Rmd’
--- re-building ‘table_and_listing_customizations.Rmd’ using rmarkdown
Quitting from table_and_listing_customizations.Rmd:76-163 [orientation_rtf]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[Male]
---
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl)
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'table_and_listing_customizations.Rmd' failed with diagnostics:
Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[Male]
--- failed re-building ‘table_and_listing_customizations.Rmd’
SUMMARY: processing the following files failed:
‘junco.Rmd’ ‘table_and_listing_customizations.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [167s/197s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [264s/320s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [264s/361s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running 'testthat.R' [230s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
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
>
> test_check("junco")
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
Joining with `by = join_by(USUBJID)`
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
[ FAIL 1 | WARN 0 | SKIP 25 | PASS 840 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 1 | WARN 0 | SKIP 25 | PASS 840 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.1.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'ancova_combined.Rmd' using rmarkdown
--- finished re-building 'ancova_combined.Rmd'
--- re-building 'auto_colwidths.Rmd' using rmarkdown
--- finished re-building 'auto_colwidths.Rmd'
--- re-building 'junco.Rmd' using rmarkdown
--- finished re-building 'junco.Rmd'
--- re-building 'standard_column_structures.Rmd' using rmarkdown
--- finished re-building 'standard_column_structures.Rmd'
--- re-building 'table_and_listing_customizations.Rmd' using rmarkdown
Quitting from table_and_listing_customizations.Rmd:1672-1682 [multiple_docs_table2_display]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `x[[3]]`:
! subscript out of bounds
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'table_and_listing_customizations.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'table_and_listing_customizations.Rmd'
SUMMARY: processing the following file failed:
'table_and_listing_customizations.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running 'testthat.R' [340s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> options(rgl.useNULL = TRUE)
> library(testthat)
> library(junco)
Loading required package: formatters
Attaching package: 'formatters'
The following object is masked from 'package:base':
%||%
Loading required package: rtables
Attaching package: 'rtables'
The following object is masked from 'package:utils':
str
>
> test_check("junco")
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
Saving _problems/test-a_freq_j-122.R
Joining with `by = join_by(USUBJID)`
Saving _problems/test-a_freq_resp_var_j-308.R
Joining with `by = join_by(USUBJID, ARM)`
mmrm() registered as emmeans extension
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
none of the combination levels appeared in the colspan treatment map; adding them automatically.
Saving _problems/test-count_pct_relrisk-107.R
Saving _problems/test-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
Saving _problems/test-varia-519.R
Saving _problems/test-varia-638.R
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-a_summarize_aval_chg_diff.R:472:1', 'test-ancova.R:4:1',
'test-docx_exporter_functions.R:9:1', 'test-estimate_proportion_diff.R:1:1',
'test-lsmeans.R:318:1', 'test-lsmeans.R:339:1', 'test-lsmeans.R:348:1',
'test-lsmeans.R:359:1', 'test-lsmeans.R:631:1', 'test-lsmeans.R:658:1',
'test-mmrm.R:81:1', 'test-mmrm.R:151:1', 'test-mmrm_rbmi.R:5:1',
'test-rbmi.R:73:3', 'test-rbmi.R:79:3', 'test-rbmi.R:120:3',
'test-rbmi.R:139:3', 'test-rbmi.R:152:3', 'test-rbmi.R:171:3',
'test-summarize_ancova.R:152:1', 'test-summarize_mmrm.R:15:1',
'test-summarize_mmrm.R:33:1', 'test-summarize_mmrm.R:70:1',
'test-tabulate_lsmeans.R:40:1', 'test-tt_to_tblfile.R:193:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-a_freq_j.R:119:3'): a_freq_j in specific situation error for not passing alt_counts_df ──
Expected `build_table(lyt, adsl)` to throw a error.
── Error ('test-a_freq_resp_var_j.R:308:3'): a_freq_resp_var_j in layout with relative risk column for combined facet ──
Error: Error applying analysis function (var - SEX): Assertion on 'variables' failed: Must be of type 'list' (or 'NULL'), not 'language'.
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl, alt_counts_df = adsl) at test-a_freq_resp_var_j.R:308:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Error ('test-count_pct_relrisk.R:107:3'): a_freq_j with val = NA and denom option ──
Error: Error applying analysis function (var - COUNTRY): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt1, adsl) at test-count_pct_relrisk.R:107:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Failure ('test-estimate_proportion_diff.R:64:3'): a_proportion_diff_j works as expected in a table layout ──
Snapshot of code has changed:
old vs new
Code
result
Output
- A B
+ A B
- —————————————————————————————————————————————
+ ———————————————————————————————————————————————————————————————————————————————————
- % Difference (90% CI) 2.0 (-15.6, 19.6)
+ Difference in Response rate (%) and 90% CI (Anderson-Hauck) 2.0 (-15.6, 19.6)
── Failure ('test-summarize_ancova.R:719:3'): a_summarize_ancova_j with multiple combined columns ──
Snapshot of code has changed:
old[5:10] vs new[5:10]
(N=86) (N=96) (N=86) (N=72) (N=182) (N=158) (N=254)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Adjusted comparison (covariates SEX)
- n 83 94 83 72 177 155 249
+ n 83 94 84 72 178 156 250
- Adjusted Mean (95% CI) -2.62 (-4.43, -0.81) -0.11 (-1.81, 1.59) -0.75 (-2.56, 1.06) -1.91 (-3.86, 0.04) -0.41 (-1.65, 0.83) -1.29 (-2.61, 0.04) -0.84 (-1.89, 0.20)
+ Adjusted Mean (95% CI) -2.63 (-4.43, -0.83) -0.11 (-1.80, 1.58) -1.67 (-3.46, 0.12) -1.90 (-3.84, 0.03) -0.84 (-2.07, 0.38) -1.78 (-3.09, -0.46) -1.15 (-2.19, -0.11)
- Difference in Adjusted Means (95% CI) 2.52 (0.03, 5.00) 1.87 (-0.69, 4.43) 0.71 (-1.95, 3.37) 2.21 (0.02, 4.41) 1.33 (-0.91, 3.58) 1.78 (-0.31, 3.87)
+ Difference in Adjusted Means (95% CI) 2.52 (0.05, 4.99) 0.96 (-1.58, 3.49) 0.73 (-1.92, 3.37) 1.78 (-0.40, 3.96) 0.85 (-1.38, 3.08) 1.48 (-0.60, 3.56)
── Error ('test-varia.R:519:3'): a_freq_j works (old count_subject case) ───────
Error: Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: ARM[C: Combination]
Backtrace:
▆
1. └─rtables::build_table(lyt, advs, adsl) at test-varia.R:519:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
── Error ('test-varia.R:638:3'): a_freq_j works (old a_countpat_newlevels case) ──
Error: Error applying analysis function (var - BMRKR2): formal argument ".alt_df_full" matched by multiple actual arguments
occured at (row) path: root
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl) at test-varia.R:638:3
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. └─rtables:::.make_analyzed_tab(...)
── Snapshots ───────────────────────────────────────────────────────────────────
To review and process snapshots locally:
* Locate check directory.
* Copy 'tests/testthat/_snaps' to local package.
* Run `testthat::snapshot_accept()` to accept all changes.
* Run `testthat::snapshot_review()` to review all changes.
[ FAIL 7 | WARN 0 | SKIP 25 | PASS 825 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.1.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'ancova_combined.Rmd' using rmarkdown
--- finished re-building 'ancova_combined.Rmd'
--- re-building 'auto_colwidths.Rmd' using rmarkdown
--- finished re-building 'auto_colwidths.Rmd'
--- re-building 'junco.Rmd' using rmarkdown
Quitting from junco.Rmd:272-344 [subgroup_tables]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]
---
Backtrace:
▆
1. ├─... %>% build_table(adae, alt_counts_df = adsl)
2. └─rtables::build_table(., adae, alt_counts_df = adsl)
3. └─base::lapply(...)
4. └─rtables (local) FUN(X[[i]], ...)
5. └─rtables:::recursive_applysplit(...)
6. ├─rtables:::.make_split_kids(...)
7. └─rtables:::.make_split_kids(...)
8. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
9. ├─base::unlist(...)
10. └─base::mapply(...)
11. └─rtables (local) `<fn>`(...)
12. └─rtables:::recursive_applysplit(...)
13. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'junco.Rmd' failed with diagnostics:
Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[F]
--- failed re-building 'junco.Rmd'
--- re-building 'standard_column_structures.Rmd' using rmarkdown
--- finished re-building 'standard_column_structures.Rmd'
--- re-building 'table_and_listing_customizations.Rmd' using rmarkdown
Quitting from table_and_listing_customizations.Rmd:76-163 [orientation_rtf]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[Male]
---
Backtrace:
▆
1. └─rtables::build_table(lyt, adsl)
2. └─base::lapply(...)
3. └─rtables (local) FUN(X[[i]], ...)
4. └─rtables:::recursive_applysplit(...)
5. ├─rtables:::.make_split_kids(...)
6. └─rtables:::.make_split_kids(...)
7. └─rtables (local) .local(spl, have_controws, make_lrow, ...)
8. ├─base::unlist(...)
9. └─base::mapply(...)
10. └─rtables (local) `<fn>`(...)
11. └─rtables:::recursive_applysplit(...)
12. └─rtables:::.make_ctab(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'table_and_listing_customizations.Rmd' failed with diagnostics:
Error in content (summary) function: Cannot use c() to combine RowsVerticalSection objects with objects of other classes
occured at path: SEX[Male]
--- failed re-building 'table_and_listing_customizations.Rmd'
SUMMARY: processing the following files failed:
'junco.Rmd' 'table_and_listing_customizations.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.