Last updated on 2026-10-01 13:52:05 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.6 | 25.43 | 709.60 | 735.03 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.6 | 16.19 | 465.92 | 482.11 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.6 | 19.00 | 403.49 | 422.49 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.6 | 19.00 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.6 | 34.00 | 709.00 | 743.00 | OK | |
| r-patched-linux-x86_64 | 0.1.6 | 27.44 | 691.03 | 718.47 | ERROR | |
| r-release-linux-x86_64 | 0.1.6 | 23.60 | 688.59 | 712.19 | 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 | 43.00 | 948.00 | 991.00 | ERROR |
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [275s/342s]
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) -2.64 (-4.53, -0.74) -0.11 (-1.89, 1.67) -1.90 (-3.78, -0.02) -1.89 (-3.92, 0.15) -0.95 (-2.25, 0.34) -1.89 (-3.27, -0.51) -1.22 (-2.31, -0.13)
- 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) 2.53 (-0.07, 5.12) 0.74 (-1.93, 3.41) 0.75 (-2.04, 3.53) 1.68 (-0.61, 3.97) 0.74 (-1.60, 3.09) 1.41 (-0.77, 3.60)
── 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-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
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished 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: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
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’ [177s/245s]
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)`
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-estimate_proportion_diff-64.R
[1] 84 84 67 84
Saving _problems/test-summarize_ancova-719.R
[ FAIL 3 | WARN 0 | SKIP 25 | PASS 838 ]
══ 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 ════════════════════════════════════════════════════════════════
── 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(...)
── 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)
── 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 3 | WARN 0 | SKIP 25 | PASS 838 ]
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
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [183s/323s]
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’ [187s/431s]
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’ [274s/389s]
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-patched-linux-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [269s/356s]
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) -2.64 (-4.53, -0.74) -0.11 (-1.89, 1.67) -1.90 (-3.78, -0.02) -1.89 (-3.92, 0.15) -0.95 (-2.25, 0.34) -1.89 (-3.27, -0.51) -1.22 (-2.31, -0.13)
- 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) 2.53 (-0.07, 5.12) 0.74 (-1.93, 3.41) 0.75 (-2.04, 3.53) 1.68 (-0.61, 3.97) 0.74 (-1.60, 3.09) 1.41 (-0.77, 3.60)
── 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-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
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.1.6
Check: tests
Result: ERROR
Running 'testthat.R' [364s]
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) -2.64 (-4.53, -0.74) -0.11 (-1.89, 1.67) -1.90 (-3.78, -0.02) -1.89 (-3.92, 0.15) -0.95 (-2.25, 0.34) -1.89 (-3.27, -0.51) -1.22 (-2.31, -0.13)
- 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) 2.53 (-0.07, 5.12) 0.74 (-1.93, 3.41) 0.75 (-2.04, 3.53) 1.68 (-0.61, 3.97) 0.74 (-1.60, 3.09) 1.41 (-0.77, 3.60)
── 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-oldrel-windows-x86_64