From 44ebba01b4eb89b8c36fe59c64874e48b8dbe945 Mon Sep 17 00:00:00 2001 From: b_falquet <64274616+BFalquet@users.noreply.github.com> Date: Wed, 9 Oct 2024 08:47:16 +0200 Subject: [PATCH 1/2] [skip vbump] CRAN release 0.2.7 (#782) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit [skip vbump] https://github.com/insightsengineering/chevron/issues/781 - update NEWS - update DESCRIPTION and bump dependencies versions thank you for the review --------- Co-authored-by: Liming Li （李黎明） --- DESCRIPTION | 10 +- NEWS.md | 6 +- R/utils.R | 8 +- man/format_date.Rd | 8 +- tests/testthat/_snaps/vst01.md | 704 ---------------------- tests/testthat/test-ael01_nollt.R | 5 + tests/testthat/test-ael02.R | 2 + tests/testthat/test-ael03.R | 2 + tests/testthat/test-aet01.R | 5 + tests/testthat/test-aet01_aesi.R | 3 + tests/testthat/test-aet02.R | 2 + tests/testthat/test-aet03.R | 1 + tests/testthat/test-aet04.R | 3 +- tests/testthat/test-aet05.R | 1 + tests/testthat/test-aet05_all.R | 1 + tests/testthat/test-aet10.R | 1 + tests/testthat/test-cfbt01.R | 2 + tests/testthat/test-chevron_tlg-methods.R | 22 + tests/testthat/test-cml02a_gl.R | 2 + tests/testthat/test-cmt01a.R | 3 + tests/testthat/test-cmt02_pt.R | 1 + tests/testthat/test-coxt01.R | 3 +- tests/testthat/test-coxt02.R | 3 +- tests/testthat/test-dmt01.R | 9 + tests/testthat/test-dst01.R | 6 + tests/testthat/test-dtht01.R | 2 + tests/testthat/test-egt01.R | 1 + tests/testthat/test-egt02.R | 1 + tests/testthat/test-egt03.R | 3 + tests/testthat/test-egt05_qtcat.R | 2 + tests/testthat/test-empty_report.R | 2 +- tests/testthat/test-ext01.R | 5 + tests/testthat/test-fstg01.R | 3 + tests/testthat/test-fstg02.R | 4 + tests/testthat/test-kmg01.R | 4 + tests/testthat/test-lbt01.R | 2 + tests/testthat/test-lbt04.R | 4 + tests/testthat/test-lbt05.R | 5 +- tests/testthat/test-lbt06.R | 2 + tests/testthat/test-lbt07.R | 2 + tests/testthat/test-lbt14.R | 11 + tests/testthat/test-lbt15.R | 6 + tests/testthat/test-mht01.R | 3 + tests/testthat/test-mng01.R | 7 + tests/testthat/test-pdt01.R | 2 + tests/testthat/test-pdt02.R | 2 + tests/testthat/test-rmpt01.R | 3 + tests/testthat/test-rmpt03.R | 3 + tests/testthat/test-rmpt04.R | 3 + tests/testthat/test-rmpt05.R | 3 + tests/testthat/test-rmpt06.R | 2 + tests/testthat/test-rspt01.R | 6 + tests/testthat/test-ttet01.R | 3 + tests/testthat/test-vst01.R | 13 +- tests/testthat/test-vst02.R | 1 + 55 files changed, 200 insertions(+), 723 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a7582a533..2f2452089 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: chevron Title: Standard TLGs for Clinical Trials Reporting -Version: 0.2.6.9021 -Date: 2024-09-16 +Version: 0.2.7 +Date: 2024-09-27 Authors@R: c( person("Liming", "Li", , "liming.li@roche.com", role = c("aut", "cre")), person("Benoit", "Falquet", , "benoit.falquet@roche.com", role = "aut"), @@ -31,7 +31,7 @@ Imports: dplyr (>= 1.1.0), dunlin (>= 0.1.7), forcats (>= 1.0.0), - formatters (>= 0.5.8), + formatters (>= 0.5.9), ggplot2 (>= 3.4.0), glue (>= 1.0.0), grid, @@ -43,9 +43,9 @@ Imports: purrr (>= 0.3.0), rlang (>= 1.0.0), rlistings (>= 0.2.9), - rtables (>= 0.6.8), + rtables (>= 0.6.10), stringr (>= 1.4.1), - tern (>= 0.9.5), + tern (>= 0.9.6), tibble (>= 2.0.0), utils Suggests: diff --git a/NEWS.md b/NEWS.md index c92e15812..5db1dcda5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,8 @@ -# chevron 0.2.6.9021 +# chevron 0.2.7 -* Add `AEL02`, `AEL03`, `CML02A_gl` templates. +* Add the `AEL02`, `AEL03` and `CML02A_gl` templates. * Modify the post processing of `MHT01` to allow multiple `row_split_var`. -* Improve the `report_null` method to facilitate the creation of null reports +* Improve the `report_null` method to facilitate the creation of null reports. * Export the `std_postprocessing` function to simplify post processing logic. * `AET01` can now additionally display the number of death and withdrawal using the `show_wd` argument. * `MNG01` line type can now be controlled with the `line_type` argument. diff --git a/R/utils.R b/R/utils.R index 7ea505ba6..4ff7c76bf 100755 --- a/R/utils.R +++ b/R/utils.R @@ -424,8 +424,12 @@ listing_format_chevron <- function() { #' @export #' @examples #' format_date("%d%b%Y")(as.Date("2021-01-01")) -#' format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "NZ")) -#' format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "US/Pacific")) +#' if ("NZ" %in% OlsonNames()) { +#' format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "NZ")) +#' } +#' if ("US/Pacific" %in% OlsonNames()) { +#' format_date("%d%b%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "US/Pacific")) +#' } format_date <- function(date_format = "%d%b%Y") { function(x, ...) { toupper( diff --git a/man/format_date.Rd b/man/format_date.Rd index e4de31517..1abb29a6f 100644 --- a/man/format_date.Rd +++ b/man/format_date.Rd @@ -20,6 +20,10 @@ The date is extracted at the location of the measure, not at the location of the } \examples{ format_date("\%d\%b\%Y")(as.Date("2021-01-01")) -format_date("\%d\%b\%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "NZ")) -format_date("\%d\%b\%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "US/Pacific")) +if ("NZ" \%in\% OlsonNames()) { + format_date("\%d\%b\%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "NZ")) +} +if ("US/Pacific" \%in\% OlsonNames()) { + format_date("\%d\%b\%Y")(as.POSIXct("2021-01-01 00:00:01", tz = "US/Pacific")) +} } diff --git a/tests/testthat/_snaps/vst01.md b/tests/testthat/_snaps/vst01.md index 384a6ffe1..025cd837f 100644 --- a/tests/testthat/_snaps/vst01.md +++ b/tests/testthat/_snaps/vst01.md @@ -92,182 +92,6 @@ Median 93.876 -4.665 Min - Max 71.91 - 138.54 -44.47 - 29.11 \s\n - Parameter: Pulse Rate - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 79.848 (13.356) NE (NE) 82.170 (18.331) NE (NE) - Median 78.706 NE 78.554 NE - Min - Max 48.94 - 102.62 NE - NE 55.11 - 122.56 NE - NE - BASELINE - n 15 15 - Mean (SD) 81.896 (10.297) 85.584 (14.663) - Median 81.733 80.261 - Min - Max 62.38 - 102.46 63.62 - 115.60 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 73.932 (16.268) -7.963 (15.197) 81.615 (15.744) -3.969 (19.689) - Median 77.008 -7.885 82.358 -0.486 - Min - Max 37.37 - 97.36 -35.04 - 21.67 53.97 - 102.01 -61.63 - 26.24 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 77.164 (14.067) -4.731 (19.872) 80.645 (7.774) -4.939 (17.465) - Median 80.424 -7.412 80.107 -9.642 - Min - Max 51.40 - 102.39 -40.41 - 36.25 66.90 - 92.92 -38.18 - 20.90 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 83.812 (12.679) 1.916 (16.213) 83.354 (18.590) -2.230 (19.940) - Median 87.736 2.160 86.412 3.513 - Min - Max 46.95 - 102.74 -28.74 - 25.43 43.66 - 107.29 -29.19 - 43.67 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 74.829 (12.786) -7.067 (16.097) 79.151 (12.081) -6.433 (17.236) - Median 76.227 -5.506 78.650 -8.084 - Min - Max 48.95 - 95.54 -38.03 - 13.57 54.79 - 105.87 -35.78 - 25.73 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 79.792 (11.206) -2.104 (13.269) 87.561 (17.865) 1.977 (19.814) - Median 82.997 -0.210 82.023 3.049 - Min - Max 55.68 - 92.89 -24.05 - 20.22 65.33 - 128.99 -50.27 - 32.78 - \s\n - Parameter: Pulse Rate - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 79.679 (15.350) NE (NE) - Median 76.903 NE - Min - Max 59.79 - 110.03 NE - NE - BASELINE - n 15 - Mean (SD) 77.107 (14.159) - Median 78.950 - Min - Max 52.36 - 96.61 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 76.625 (15.814) -0.482 (20.797) - Median 79.731 8.488 - Min - Max 48.84 - 104.77 -37.33 - 28.64 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 79.044 (13.193) 1.937 (15.609) - Median 74.361 5.695 - Min - Max 65.32 - 111.55 -22.38 - 27.05 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 75.924 (10.045) -1.183 (16.167) - Median 74.720 0.057 - Min - Max 61.17 - 95.54 -27.66 - 27.57 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 77.979 (14.535) 0.872 (20.465) - Median 78.231 2.808 - Min - Max 51.48 - 104.71 -33.19 - 44.14 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 84.617 (17.937) 7.510 (21.612) - Median 84.022 12.943 - Min - Max 34.86 - 110.03 -42.18 - 41.69 - \s\n - Parameter: Respiratory Rate - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 15.043 (3.455) NE (NE) 16.400 (3.741) NE (NE) - Median 15.743 NE 16.303 NE - Min - Max 5.75 - 20.24 NE - NE 9.79 - 25.68 NE - NE - BASELINE - n 15 15 - Mean (SD) 13.353 (5.061) 16.270 (5.086) - Median 13.202 15.898 - Min - Max 4.68 - 23.59 9.51 - 25.27 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 15.832 (5.336) 2.478 (6.550) 14.301 (4.143) -1.969 (6.549) - Median 13.364 3.245 13.556 -0.768 - Min - Max 7.24 - 24.69 -12.99 - 14.74 7.80 - 21.64 -14.50 - 8.50 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 15.195 (5.532) 1.842 (6.646) 16.335 (6.402) 0.065 (8.770) - Median 15.137 3.348 15.710 0.144 - Min - Max 2.50 - 24.34 -15.54 - 9.87 8.02 - 26.40 -17.25 - 14.68 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 12.757 (6.587) -0.597 (5.529) 16.806 (5.518) 0.537 (8.174) - Median 11.334 1.128 17.496 -0.116 - Min - Max 0.62 - 22.74 -12.26 - 5.99 6.06 - 26.22 -17.50 - 11.77 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 14.950 (4.443) 1.597 (4.795) 14.464 (4.510) -1.805 (6.965) - Median 15.727 2.893 13.246 -0.655 - Min - Max 7.98 - 21.41 -8.31 - 7.94 5.60 - 20.66 -14.26 - 11.00 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 13.632 (6.374) 0.279 (8.063) 19.383 (5.590) 3.113 (6.914) - Median 13.068 0.442 18.527 1.760 - Min - Max 2.34 - 24.54 -17.58 - 9.42 11.62 - 28.62 -6.74 - 18.02 - \s\n - Parameter: Respiratory Rate - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 15.781 (4.800) NE (NE) - Median 16.645 NE - Min - Max 7.32 - 21.56 NE - NE - BASELINE - n 15 - Mean (SD) 15.339 (3.052) - Median 15.491 - Min - Max 10.90 - 20.89 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 14.673 (6.117) -0.666 (7.274) - Median 16.835 2.369 - Min - Max 1.65 - 20.89 -15.56 - 8.01 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 16.777 (5.546) 1.439 (5.186) - Median 17.770 1.783 - Min - Max 2.57 - 22.56 -10.09 - 9.60 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 14.975 (5.562) -0.364 (6.029) - Median 15.340 -0.615 - Min - Max 4.81 - 22.60 -10.55 - 10.78 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 14.016 (8.365) -1.323 (9.534) - Median 15.704 0.213 - Min - Max 1.00 - 27.54 -14.36 - 13.97 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 15.623 (5.417) 0.284 (7.141) - Median 15.202 -0.157 - Min - Max 4.46 - 29.18 -11.90 - 13.69 - \s\n Parameter: Systolic Blood Pressure ——————————————————————————————————————————————————————————————————————————————————————————————————— @@ -355,182 +179,6 @@ Mean (SD) 143.592 (33.170) -10.581 (44.799) Median 148.501 -2.385 Min - Max 92.18 - 191.05 -78.77 - 64.35 - \s\n - Parameter: Temperature - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 36.273 (1.136) NE (NE) 36.731 (1.142) NE (NE) - Median 36.131 NE 36.506 NE - Min - Max 34.07 - 38.59 NE - NE 34.97 - 39.04 NE - NE - BASELINE - n 15 15 - Mean (SD) 36.763 (1.167) 36.707 (1.528) - Median 36.694 37.144 - Min - Max 35.08 - 38.72 33.65 - 38.92 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 36.280 (0.543) -0.483 (1.022) 36.292 (1.378) -0.415 (1.957) - Median 36.194 -0.609 36.451 -0.344 - Min - Max 35.37 - 37.06 -2.07 - 1.11 33.03 - 38.47 -4.72 - 2.24 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 37.090 (1.136) 0.328 (1.647) 36.577 (1.291) -0.130 (1.799) - Median 37.138 0.153 36.113 0.300 - Min - Max 34.44 - 38.95 -2.34 - 2.85 34.86 - 39.29 -3.52 - 2.55 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 36.725 (1.003) -0.038 (1.441) 36.546 (1.008) -0.161 (1.701) - Median 36.616 0.029 36.378 -0.368 - Min - Max 35.24 - 38.26 -3.25 - 2.34 35.08 - 38.17 -2.59 - 4.13 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 36.545 (1.070) -0.218 (1.859) 36.574 (1.024) -0.133 (1.994) - Median 36.299 -0.701 36.546 -0.436 - Min - Max 34.87 - 39.00 -3.85 - 3.10 34.77 - 38.98 -2.74 - 4.07 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 37.038 (0.918) 0.275 (1.334) 36.823 (1.247) 0.117 (1.387) - Median 36.945 0.346 36.839 -0.476 - Min - Max 35.71 - 38.45 -2.78 - 2.77 34.69 - 38.91 -1.76 - 3.06 - \s\n - Parameter: Temperature - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 36.565 (1.112) NE (NE) - Median 36.681 NE - Min - Max 35.30 - 38.90 NE - NE - BASELINE - n 15 - Mean (SD) 36.383 (0.963) - Median 36.496 - Min - Max 34.71 - 37.92 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 36.848 (0.936) 0.465 (1.458) - Median 36.973 0.399 - Min - Max 35.28 - 38.18 -1.44 - 2.99 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 36.620 (1.077) 0.237 (1.595) - Median 36.519 0.690 - Min - Max 34.89 - 38.33 -3.02 - 2.47 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 36.697 (0.694) 0.314 (1.312) - Median 36.679 0.841 - Min - Max 35.14 - 37.64 -2.77 - 2.63 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 36.738 (0.760) 0.355 (0.872) - Median 36.585 0.352 - Min - Max 35.29 - 38.24 -0.91 - 2.14 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 36.716 (1.056) 0.333 (1.344) - Median 36.404 0.500 - Min - Max 35.26 - 38.64 -1.83 - 3.72 - \s\n - Parameter: Weight - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 81.827 (23.644) NE (NE) 61.563 (19.272) NE (NE) - Median 80.182 NE 62.147 NE - Min - Max 40.48 - 133.35 NE - NE 23.27 - 92.39 NE - NE - BASELINE - n 15 15 - Mean (SD) 76.532 (15.588) 70.870 (12.845) - Median 71.929 66.405 - Min - Max 56.24 - 102.43 54.36 - 96.85 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 71.171 (19.805) -5.360 (23.082) 69.872 (17.781) -0.998 (20.176) - Median 65.106 -6.780 70.971 -2.628 - Min - Max 47.03 - 123.95 -49.07 - 40.63 30.55 - 93.75 -35.86 - 28.87 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 80.484 (18.937) 3.952 (22.123) 72.940 (20.302) 2.070 (17.837) - Median 75.792 3.284 71.374 3.396 - Min - Max 44.83 - 112.37 -36.68 - 35.07 35.00 - 106.69 -32.41 - 26.17 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 68.100 (15.095) -8.431 (18.100) 71.883 (18.376) 1.013 (22.760) - Median 66.175 -7.353 76.267 3.928 - Min - Max 30.53 - 91.08 -46.15 - 29.48 20.87 - 95.04 -43.57 - 29.54 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 73.294 (18.861) -3.238 (18.094) 71.553 (17.090) 0.683 (16.404) - Median 76.829 -0.941 70.705 -1.527 - Min - Max 24.32 - 98.14 -44.46 - 18.39 43.61 - 107.47 -26.14 - 43.89 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 66.719 (15.750) -9.812 (26.403) 68.162 (15.787) -2.708 (20.179) - Median 64.046 -5.370 67.480 -1.537 - Min - Max 33.02 - 95.14 -69.42 - 26.72 45.71 - 102.63 -36.52 - 30.47 - \s\n - Parameter: Weight - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 64.923 (16.678) NE (NE) - Median 62.745 NE - Min - Max 26.70 - 94.66 NE - NE - BASELINE - n 15 - Mean (SD) 71.676 (16.922) - Median 68.883 - Min - Max 27.15 - 107.89 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 74.799 (13.706) 3.123 (21.964) - Median 71.374 4.336 - Min - Max 53.19 - 96.54 -32.10 - 51.00 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 67.267 (19.187) -4.409 (25.986) - Median 60.651 -5.246 - Min - Max 35.56 - 102.05 -67.52 - 33.50 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 70.442 (21.914) -1.234 (25.307) - Median 72.649 5.691 - Min - Max 31.36 - 101.13 -45.69 - 32.28 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 77.447 (21.174) 5.771 (25.479) - Median 86.161 19.614 - Min - Max 41.60 - 112.40 -40.90 - 35.30 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 65.688 (23.847) -5.988 (35.176) - Median 71.788 -7.456 - Min - Max 12.04 - 114.55 -71.68 - 87.41 # run vst01 works as expected @@ -626,182 +274,6 @@ Median 93.876 -4.665 Min - Max 71.91 - 138.54 -44.47 - 29.11 \s\n - Parameter: Pulse Rate - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 79.848 (13.356) NE (NE) 82.170 (18.331) NE (NE) - Median 78.706 NE 78.554 NE - Min - Max 48.94 - 102.62 NE - NE 55.11 - 122.56 NE - NE - BASELINE - n 15 15 - Mean (SD) 81.896 (10.297) 85.584 (14.663) - Median 81.733 80.261 - Min - Max 62.38 - 102.46 63.62 - 115.60 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 73.932 (16.268) -7.963 (15.197) 81.615 (15.744) -3.969 (19.689) - Median 77.008 -7.885 82.358 -0.486 - Min - Max 37.37 - 97.36 -35.04 - 21.67 53.97 - 102.01 -61.63 - 26.24 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 77.164 (14.067) -4.731 (19.872) 80.645 (7.774) -4.939 (17.465) - Median 80.424 -7.412 80.107 -9.642 - Min - Max 51.40 - 102.39 -40.41 - 36.25 66.90 - 92.92 -38.18 - 20.90 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 83.812 (12.679) 1.916 (16.213) 83.354 (18.590) -2.230 (19.940) - Median 87.736 2.160 86.412 3.513 - Min - Max 46.95 - 102.74 -28.74 - 25.43 43.66 - 107.29 -29.19 - 43.67 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 74.829 (12.786) -7.067 (16.097) 79.151 (12.081) -6.433 (17.236) - Median 76.227 -5.506 78.650 -8.084 - Min - Max 48.95 - 95.54 -38.03 - 13.57 54.79 - 105.87 -35.78 - 25.73 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 79.792 (11.206) -2.104 (13.269) 87.561 (17.865) 1.977 (19.814) - Median 82.997 -0.210 82.023 3.049 - Min - Max 55.68 - 92.89 -24.05 - 20.22 65.33 - 128.99 -50.27 - 32.78 - \s\n - Parameter: Pulse Rate - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 79.679 (15.350) NE (NE) - Median 76.903 NE - Min - Max 59.79 - 110.03 NE - NE - BASELINE - n 15 - Mean (SD) 77.107 (14.159) - Median 78.950 - Min - Max 52.36 - 96.61 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 76.625 (15.814) -0.482 (20.797) - Median 79.731 8.488 - Min - Max 48.84 - 104.77 -37.33 - 28.64 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 79.044 (13.193) 1.937 (15.609) - Median 74.361 5.695 - Min - Max 65.32 - 111.55 -22.38 - 27.05 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 75.924 (10.045) -1.183 (16.167) - Median 74.720 0.057 - Min - Max 61.17 - 95.54 -27.66 - 27.57 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 77.979 (14.535) 0.872 (20.465) - Median 78.231 2.808 - Min - Max 51.48 - 104.71 -33.19 - 44.14 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 84.617 (17.937) 7.510 (21.612) - Median 84.022 12.943 - Min - Max 34.86 - 110.03 -42.18 - 41.69 - \s\n - Parameter: Respiratory Rate - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 15.043 (3.455) NE (NE) 16.400 (3.741) NE (NE) - Median 15.743 NE 16.303 NE - Min - Max 5.75 - 20.24 NE - NE 9.79 - 25.68 NE - NE - BASELINE - n 15 15 - Mean (SD) 13.353 (5.061) 16.270 (5.086) - Median 13.202 15.898 - Min - Max 4.68 - 23.59 9.51 - 25.27 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 15.832 (5.336) 2.478 (6.550) 14.301 (4.143) -1.969 (6.549) - Median 13.364 3.245 13.556 -0.768 - Min - Max 7.24 - 24.69 -12.99 - 14.74 7.80 - 21.64 -14.50 - 8.50 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 15.195 (5.532) 1.842 (6.646) 16.335 (6.402) 0.065 (8.770) - Median 15.137 3.348 15.710 0.144 - Min - Max 2.50 - 24.34 -15.54 - 9.87 8.02 - 26.40 -17.25 - 14.68 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 12.757 (6.587) -0.597 (5.529) 16.806 (5.518) 0.537 (8.174) - Median 11.334 1.128 17.496 -0.116 - Min - Max 0.62 - 22.74 -12.26 - 5.99 6.06 - 26.22 -17.50 - 11.77 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 14.950 (4.443) 1.597 (4.795) 14.464 (4.510) -1.805 (6.965) - Median 15.727 2.893 13.246 -0.655 - Min - Max 7.98 - 21.41 -8.31 - 7.94 5.60 - 20.66 -14.26 - 11.00 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 13.632 (6.374) 0.279 (8.063) 19.383 (5.590) 3.113 (6.914) - Median 13.068 0.442 18.527 1.760 - Min - Max 2.34 - 24.54 -17.58 - 9.42 11.62 - 28.62 -6.74 - 18.02 - \s\n - Parameter: Respiratory Rate - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 15.781 (4.800) NE (NE) - Median 16.645 NE - Min - Max 7.32 - 21.56 NE - NE - BASELINE - n 15 - Mean (SD) 15.339 (3.052) - Median 15.491 - Min - Max 10.90 - 20.89 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 14.673 (6.117) -0.666 (7.274) - Median 16.835 2.369 - Min - Max 1.65 - 20.89 -15.56 - 8.01 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 16.777 (5.546) 1.439 (5.186) - Median 17.770 1.783 - Min - Max 2.57 - 22.56 -10.09 - 9.60 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 14.975 (5.562) -0.364 (6.029) - Median 15.340 -0.615 - Min - Max 4.81 - 22.60 -10.55 - 10.78 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 14.016 (8.365) -1.323 (9.534) - Median 15.704 0.213 - Min - Max 1.00 - 27.54 -14.36 - 13.97 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 15.623 (5.417) 0.284 (7.141) - Median 15.202 -0.157 - Min - Max 4.46 - 29.18 -11.90 - 13.69 - \s\n Parameter: Systolic Blood Pressure ——————————————————————————————————————————————————————————————————————————————————————————————————— @@ -889,180 +361,4 @@ Mean (SD) 143.592 (33.170) -10.581 (44.799) Median 148.501 -2.385 Min - Max 92.18 - 191.05 -78.77 - 64.35 - \s\n - Parameter: Temperature - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 36.273 (1.136) NE (NE) 36.731 (1.142) NE (NE) - Median 36.131 NE 36.506 NE - Min - Max 34.07 - 38.59 NE - NE 34.97 - 39.04 NE - NE - BASELINE - n 15 15 - Mean (SD) 36.763 (1.167) 36.707 (1.528) - Median 36.694 37.144 - Min - Max 35.08 - 38.72 33.65 - 38.92 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 36.280 (0.543) -0.483 (1.022) 36.292 (1.378) -0.415 (1.957) - Median 36.194 -0.609 36.451 -0.344 - Min - Max 35.37 - 37.06 -2.07 - 1.11 33.03 - 38.47 -4.72 - 2.24 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 37.090 (1.136) 0.328 (1.647) 36.577 (1.291) -0.130 (1.799) - Median 37.138 0.153 36.113 0.300 - Min - Max 34.44 - 38.95 -2.34 - 2.85 34.86 - 39.29 -3.52 - 2.55 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 36.725 (1.003) -0.038 (1.441) 36.546 (1.008) -0.161 (1.701) - Median 36.616 0.029 36.378 -0.368 - Min - Max 35.24 - 38.26 -3.25 - 2.34 35.08 - 38.17 -2.59 - 4.13 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 36.545 (1.070) -0.218 (1.859) 36.574 (1.024) -0.133 (1.994) - Median 36.299 -0.701 36.546 -0.436 - Min - Max 34.87 - 39.00 -3.85 - 3.10 34.77 - 38.98 -2.74 - 4.07 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 37.038 (0.918) 0.275 (1.334) 36.823 (1.247) 0.117 (1.387) - Median 36.945 0.346 36.839 -0.476 - Min - Max 35.71 - 38.45 -2.78 - 2.77 34.69 - 38.91 -1.76 - 3.06 - \s\n - Parameter: Temperature - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 36.565 (1.112) NE (NE) - Median 36.681 NE - Min - Max 35.30 - 38.90 NE - NE - BASELINE - n 15 - Mean (SD) 36.383 (0.963) - Median 36.496 - Min - Max 34.71 - 37.92 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 36.848 (0.936) 0.465 (1.458) - Median 36.973 0.399 - Min - Max 35.28 - 38.18 -1.44 - 2.99 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 36.620 (1.077) 0.237 (1.595) - Median 36.519 0.690 - Min - Max 34.89 - 38.33 -3.02 - 2.47 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 36.697 (0.694) 0.314 (1.312) - Median 36.679 0.841 - Min - Max 35.14 - 37.64 -2.77 - 2.63 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 36.738 (0.760) 0.355 (0.872) - Median 36.585 0.352 - Min - Max 35.29 - 38.24 -0.91 - 2.14 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 36.716 (1.056) 0.333 (1.344) - Median 36.404 0.500 - Min - Max 35.26 - 38.64 -1.83 - 3.72 - \s\n - Parameter: Weight - - ——————————————————————————————————————————————————————————————————————————————————————————————————— - A: Drug X B: Placebo - Change from Change from - Value at Visit Baseline Value at Visit Baseline - Analysis Visit (N=15) (N=15) (N=15) (N=15) - ——————————————————————————————————————————————————————————————————————————————————————————————————— - SCREENING - n 15 0 15 0 - Mean (SD) 81.827 (23.644) NE (NE) 61.563 (19.272) NE (NE) - Median 80.182 NE 62.147 NE - Min - Max 40.48 - 133.35 NE - NE 23.27 - 92.39 NE - NE - BASELINE - n 15 15 - Mean (SD) 76.532 (15.588) 70.870 (12.845) - Median 71.929 66.405 - Min - Max 56.24 - 102.43 54.36 - 96.85 - WEEK 1 DAY 8 - n 15 15 15 15 - Mean (SD) 71.171 (19.805) -5.360 (23.082) 69.872 (17.781) -0.998 (20.176) - Median 65.106 -6.780 70.971 -2.628 - Min - Max 47.03 - 123.95 -49.07 - 40.63 30.55 - 93.75 -35.86 - 28.87 - WEEK 2 DAY 15 - n 15 15 15 15 - Mean (SD) 80.484 (18.937) 3.952 (22.123) 72.940 (20.302) 2.070 (17.837) - Median 75.792 3.284 71.374 3.396 - Min - Max 44.83 - 112.37 -36.68 - 35.07 35.00 - 106.69 -32.41 - 26.17 - WEEK 3 DAY 22 - n 15 15 15 15 - Mean (SD) 68.100 (15.095) -8.431 (18.100) 71.883 (18.376) 1.013 (22.760) - Median 66.175 -7.353 76.267 3.928 - Min - Max 30.53 - 91.08 -46.15 - 29.48 20.87 - 95.04 -43.57 - 29.54 - WEEK 4 DAY 29 - n 15 15 15 15 - Mean (SD) 73.294 (18.861) -3.238 (18.094) 71.553 (17.090) 0.683 (16.404) - Median 76.829 -0.941 70.705 -1.527 - Min - Max 24.32 - 98.14 -44.46 - 18.39 43.61 - 107.47 -26.14 - 43.89 - WEEK 5 DAY 36 - n 15 15 15 15 - Mean (SD) 66.719 (15.750) -9.812 (26.403) 68.162 (15.787) -2.708 (20.179) - Median 64.046 -5.370 67.480 -1.537 - Min - Max 33.02 - 95.14 -69.42 - 26.72 45.71 - 102.63 -36.52 - 30.47 - \s\n - Parameter: Weight - - —————————————————————————————————————————————————————————————— - C: Combination - Change from - Value at Visit Baseline - Analysis Visit (N=15) (N=15) - —————————————————————————————————————————————————————————————— - SCREENING - n 15 0 - Mean (SD) 64.923 (16.678) NE (NE) - Median 62.745 NE - Min - Max 26.70 - 94.66 NE - NE - BASELINE - n 15 - Mean (SD) 71.676 (16.922) - Median 68.883 - Min - Max 27.15 - 107.89 - WEEK 1 DAY 8 - n 15 15 - Mean (SD) 74.799 (13.706) 3.123 (21.964) - Median 71.374 4.336 - Min - Max 53.19 - 96.54 -32.10 - 51.00 - WEEK 2 DAY 15 - n 15 15 - Mean (SD) 67.267 (19.187) -4.409 (25.986) - Median 60.651 -5.246 - Min - Max 35.56 - 102.05 -67.52 - 33.50 - WEEK 3 DAY 22 - n 15 15 - Mean (SD) 70.442 (21.914) -1.234 (25.307) - Median 72.649 5.691 - Min - Max 31.36 - 101.13 -45.69 - 32.28 - WEEK 4 DAY 29 - n 15 15 - Mean (SD) 77.447 (21.174) 5.771 (25.479) - Median 86.161 19.614 - Min - Max 41.60 - 112.40 -40.90 - 35.30 - WEEK 5 DAY 36 - n 15 15 - Mean (SD) 65.688 (23.847) -5.988 (35.176) - Median 71.788 -7.456 - Min - Max 12.04 - 114.55 -71.68 - 87.41 diff --git a/tests/testthat/test-ael01_nollt.R b/tests/testthat/test-ael01_nollt.R index 54bbb34a1..b398bb65a 100644 --- a/tests/testthat/test-ael01_nollt.R +++ b/tests/testthat/test-ael01_nollt.R @@ -9,6 +9,7 @@ test_that("ael01_nollt works with admh dataset", { test_that("ael01_nollt works with non-default label", { + skip_on_os("windows") proc_data <- syn_data attr(proc_data$adae$AETERM, "label") <- "Investigator-Specified\n Adverse Event Term" res <- expect_silent( @@ -21,6 +22,7 @@ test_that("ael01_nollt works with non-default label", { }) test_that("ael01_nollt can handle all missing values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate( @@ -34,6 +36,7 @@ test_that("ael01_nollt can handle all missing values", { }) test_that("ael01_nollt can handle some missing values", { + skip_on_os("windows") new_aebodsys <- c(NA, "", as.character(syn_data$adae$AEBODSYS[-c(1, 2)])) new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)])) @@ -49,6 +52,7 @@ test_that("ael01_nollt can handle some missing values", { }) test_that("ael01_nollt listing can be split by an additional variable", { + skip_on_os("windows") res <- expect_silent( run( ael01_nollt, @@ -64,6 +68,7 @@ test_that("ael01_nollt listing can be split by an additional variable", { }) test_that("split ael01_nollt listing do not display missing values", { + skip_on_os("windows") proc_data <- syn_data proc_data$admh <- proc_data$admh[proc_data$admh$SEX == "F", ] diff --git a/tests/testthat/test-ael02.R b/tests/testthat/test-ael02.R index 630770070..5b2504db8 100644 --- a/tests/testthat/test-ael02.R +++ b/tests/testthat/test-ael02.R @@ -10,6 +10,7 @@ test_that("ael02 works with adae dataset", { }) test_that("ael02 can handle all missing values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate( @@ -27,6 +28,7 @@ test_that("ael02 can handle all missing values", { test_that("ael02 functions work as expected", { + skip_on_os("windows") res <- expect_silent( ael02_pre(syn_data) %>% ael02_main() diff --git a/tests/testthat/test-ael03.R b/tests/testthat/test-ael03.R index 37cf25d8b..ca034af38 100644 --- a/tests/testthat/test-ael03.R +++ b/tests/testthat/test-ael03.R @@ -10,6 +10,7 @@ test_that("ael03 works with adae dataset", { }) test_that("ael03 can handle all missing values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate( @@ -27,6 +28,7 @@ test_that("ael03 can handle all missing values", { # ael03 functions ---- test_that("ael03 functions work as expected", { + skip_on_os("windows") res <- expect_silent( ael03_pre(syn_data) %>% ael03_main() diff --git a/tests/testthat/test-aet01.R b/tests/testthat/test-aet01.R index d42fc0d25..6b89019cb 100644 --- a/tests/testthat/test-aet01.R +++ b/tests/testthat/test-aet01.R @@ -15,6 +15,7 @@ test_that("aet01 can handle all NA values", { }) test_that("aet01 can handle some NA values", { + skip_on_os("windows") new_aesdth <- c(NA, "", as.character(syn_data$adae$AESDTH[-c(1, 2)])) new_aeser <- c(NA, "", as.character(syn_data$adae$AESER[-c(1, 2)])) @@ -30,12 +31,14 @@ test_that("aet01 can handle some NA values", { }) test_that("aet01 can use custom anl_vars", { + skip_on_os("windows") proc_data <- syn_data res <- expect_silent(run(aet01, proc_data, anl_vars = list(safety_var = "FATAL"))) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("aet01 fails on incomplete data input", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate(AESER = NULL) @@ -48,6 +51,7 @@ test_that("aet01 fails on incomplete data input", { }) test_that("aet01 can use custom medconcept_var", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae$SMQ01 <- with_label(proc_data$adae$SMQ01NAM != "", "SMQ 01") res <- expect_silent( @@ -66,6 +70,7 @@ test_that("aet01 can use custom medconcept_var", { }) test_that("aet01 can conditionally show the number of withdrawal", { + skip_on_os("windows") expect_silent(res <- run(aet01, syn_data, arm_var = "ARM", show_wd = FALSE)) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) diff --git a/tests/testthat/test-aet01_aesi.R b/tests/testthat/test-aet01_aesi.R index b0ed8a3cd..c5263b4c7 100644 --- a/tests/testthat/test-aet01_aesi.R +++ b/tests/testthat/test-aet01_aesi.R @@ -20,6 +20,7 @@ test_that("aet01_aesi can handle all NA values", { }) test_that("aet01_aesi can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate( @@ -31,12 +32,14 @@ test_that("aet01_aesi can handle some NA values", { }) test_that("aet01_aesi works with `ALL` argument", { + skip_on_os("windows") proc_data <- syn_data res <- expect_silent(run(aet01_aesi, proc_data, aesi_vars = c("ALL"))) expect_snapshot(cat(export_as_txt(res, lpp = 100, cpp = 200))) }) test_that("aet01_aesi_check fails on incomplete data input", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate(AEOUT = NULL) diff --git a/tests/testthat/test-aet02.R b/tests/testthat/test-aet02.R index 216749fc1..4dbb5e8c4 100644 --- a/tests/testthat/test-aet02.R +++ b/tests/testthat/test-aet02.R @@ -15,6 +15,7 @@ test_that("aet02 fails on incomplete data input", { }) test_that("aet02 handle empty data input", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% filter( @@ -25,6 +26,7 @@ test_that("aet02 handle empty data input", { }) test_that("aet02 can have different levels of row_split", { + skip_on_os("windows") res1 <- run(aet02, syn_data, row_split_var = NULL) res2 <- run(aet02, syn_data, row_split_var = c("AEBODSYS", "AEDECOD")) expect_snapshot(cat(export_as_txt(res1, lpp = 100))) diff --git a/tests/testthat/test-aet03.R b/tests/testthat/test-aet03.R index b52b35aab..b27dc5c97 100644 --- a/tests/testthat/test-aet03.R +++ b/tests/testthat/test-aet03.R @@ -11,6 +11,7 @@ test_that("aet03 can handle NA values", { }) test_that("aet03 can handle some NA values", { + skip_on_os("windows") new_aebodsys <- c(NA, "", as.character(syn_data$adae$AEBODSYS[-c(1, 2)])) new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)])) new_asev <- c(NA, "", as.character(syn_data$adae$ASEV[-c(1, 2)])) diff --git a/tests/testthat/test-aet04.R b/tests/testthat/test-aet04.R index 6cdc5349b..bbcdb936f 100644 --- a/tests/testthat/test-aet04.R +++ b/tests/testthat/test-aet04.R @@ -8,7 +8,7 @@ test_that("aet04 can handle NA values", { res1 <- expect_silent(run(aet04, proc_data)) expect_snapshot(cat(export_as_txt(res1, lpp = 100))) - + skip_on_os("windows") grade_groups <- list( "Grade 1-2" = c("1", "2"), "Grade 3-4" = c("3", "4"), @@ -26,6 +26,7 @@ test_that("aet04 can handle NA values", { }) test_that("aet04 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae[1:2, c("AEBODSYS", "AEDECOD")] <- NA res1 <- expect_silent(run(aet04, proc_data)) diff --git a/tests/testthat/test-aet05.R b/tests/testthat/test-aet05.R index dee7bed38..503260236 100644 --- a/tests/testthat/test-aet05.R +++ b/tests/testthat/test-aet05.R @@ -8,6 +8,7 @@ test_that("aet05 can handle NA values", { }) test_that("aet05 can handle some NA values", { + skip_on_os("windows") new_paramcd <- c( as.character(syn_data$adsaftte$PARAMCD[1:4]), NA, "", as.character(syn_data$adsaftte$PARAMCD[-rep(1:6)]) diff --git a/tests/testthat/test-aet05_all.R b/tests/testthat/test-aet05_all.R index 1f8eb7e26..64307affc 100644 --- a/tests/testthat/test-aet05_all.R +++ b/tests/testthat/test-aet05_all.R @@ -8,6 +8,7 @@ test_that("aet05_all can handle NA values", { }) test_that("aet05_all can handle some NA values", { + skip_on_os("windows") new_paramcd <- c(NA, "", as.character(syn_data$adsaftte$PARAMCD[-c(1, 2)])) proc_data <- syn_data diff --git a/tests/testthat/test-aet10.R b/tests/testthat/test-aet10.R index 459159886..398c6379f 100644 --- a/tests/testthat/test-aet10.R +++ b/tests/testthat/test-aet10.R @@ -11,6 +11,7 @@ test_that("aet10 can handle NA values", { }) test_that("aet10 can handle some NA values", { + skip_on_os("windows") new_aedecod <- c(NA, "", as.character(syn_data$adae$AEDECOD[-c(1, 2)])) proc_data <- syn_data diff --git a/tests/testthat/test-cfbt01.R b/tests/testthat/test-cfbt01.R index 700fd73f0..0e3201cbc 100644 --- a/tests/testthat/test-cfbt01.R +++ b/tests/testthat/test-cfbt01.R @@ -1,6 +1,7 @@ # cfbt01 functions ---- test_that("cfbt01 functions with default argument value return expected result with test data", { + skip_on_os("windows") pre_data <- cfbt01_pre(syn_data, dataset = "advs") raw_res <- cfbt01_main(pre_data, dataset = "advs") res <- cfbt01_post(raw_res) @@ -10,6 +11,7 @@ test_that("cfbt01 functions with default argument value return expected result w # cfbt01 ---- test_that("cfbt01 can handle n = 0 and outputs NE instead of infs and NAs", { + skip_on_os("windows") proc_data <- dunlin::log_filter( syn_data, PARAMCD %in% c("DIABP", "SYSBP"), "advs" diff --git a/tests/testthat/test-chevron_tlg-methods.R b/tests/testthat/test-chevron_tlg-methods.R index 11b425c5d..23313af21 100644 --- a/tests/testthat/test-chevron_tlg-methods.R +++ b/tests/testthat/test-chevron_tlg-methods.R @@ -9,6 +9,7 @@ test_that("run works as expected for chevron_t object", { }) test_that("run works as expected for chevron_t object when auto_pre = FALSE", { + skip_on_os("windows") proc_data <- syn_adv proc_data$adsl <- proc_data$adsl %>% mutate(DOMAIN = "ADSL") @@ -17,12 +18,14 @@ test_that("run works as expected for chevron_t object when auto_pre = FALSE", { }) test_that("run works as expected with argument printed", { + skip_on_os("windows") res <- capture_output(tbl <- run(aet02, syn_adv, prune_0 = TRUE, verbose = TRUE)) expect_snapshot(cat(res)) expect_snapshot(cat(export_as_txt(tbl, lpp = 100))) }) test_that("run works as expected with argument printed if the user argument is complicated", { + skip_on_os("windows") user_args <- list(prune_0 = TRUE, not_used = iris, lbl_overall = "All Patients", row_split_var = "AEHLT") res <- capture_output(tbl <- run(aet02, syn_adv, user_args = user_args, verbose = TRUE)) expect_snapshot(cat(res)) @@ -30,6 +33,7 @@ test_that("run works as expected with argument printed if the user argument is c }) test_that("run uses the argument passed through the ellipsis in priority", { + skip_on_os("windows") user_args <- list(prune_0 = TRUE, not_used = iris, lbl_overall = "All Patients", row_split_var = "AEHLT") res <- capture_output( tbl <- run( @@ -47,12 +51,14 @@ test_that("run uses the argument passed through the ellipsis in priority", { }) test_that("run works as expected with partial match argument", { + skip_on_os("windows") res <- capture_output(tbl <- run(aet02, syn_adv, prune_0 = TRUE, verbose = TRUE, arm_var = "ARM")) expect_snapshot(cat(res)) expect_snapshot(cat(export_as_txt(tbl, lpp = 100))) }) test_that("run displays the symbols when available", { + skip_on_os("windows") user_args <- list(prune_0 = TRUE, not_used = iris, lbl_overall = "All Patients", row_split_var = "AEHLT") arm_param <- "ARM" res <- capture_output( @@ -74,12 +80,14 @@ test_that("run displays the symbols when available", { # args_ls ---- test_that("args_ls works as expected", { + skip_on_os("windows") res <- expect_silent(args_ls(aet04)) expect_list(res, len = 3, names = "named") expect_names(names(res), identical.to = c("main", "preprocess", "postprocess")) }) test_that("args_ls works as expected when simplify is TRUE", { + skip_on_os("windows") res <- expect_silent(args_ls(aet04, simplify = TRUE)) expect_list(res, len = 7, names = "named") expect_names( @@ -91,6 +99,7 @@ test_that("args_ls works as expected when simplify is TRUE", { }) test_that("args_ls works as expected with custom chevron_tlg object", { + skip_on_os("windows") obj <- aet04 preprocess(obj) <- function(adam_db, arm_var = "overwritten", new_arg = "NEW", ...) { adam_db @@ -110,12 +119,14 @@ test_that("args_ls works as expected with custom chevron_tlg object", { # main ---- test_that("main works as expected", { + skip_on_os("windows") skip_on_covr() res <- main(aet04) expect_identical(res, aet04_main) }) test_that("main setter works as expected", { + skip_on_os("windows") func <- function(adam_db, ...) { build_table(basic_table(), adam_db) } @@ -125,6 +136,7 @@ test_that("main setter works as expected", { }) test_that("main setter throw an error as expected", { + skip_on_os("windows") func <- function(adam_db) { build_table(basic_table(), adam_db) } @@ -137,12 +149,14 @@ test_that("main setter throw an error as expected", { # preprocess ---- test_that("preprocess works as expected", { + skip_on_os("windows") skip_on_covr() res <- preprocess(aet04) expect_identical(res, aet04_pre) }) test_that("preprocess setter works as expected", { + skip_on_os("windows") func <- function(adam_db, ...) adam_db obj <- aet04 preprocess(obj) <- func @@ -150,6 +164,7 @@ test_that("preprocess setter works as expected", { }) test_that("preprocess sends an error as expected", { + skip_on_os("windows") func <- function(adam_db) adam_db obj <- aet04 expect_error(preprocess(obj) <- func, "Variable 'object@preprocess': Must have formal arguments: ....", @@ -160,11 +175,13 @@ test_that("preprocess sends an error as expected", { # postprocess ---- test_that("postprocess works as expected", { + skip_on_os("windows") res <- postprocess(aet04) expect_identical(res, aet04@postprocess) }) test_that("postprocess setter works as expected", { + skip_on_os("windows") func <- function(tlg, ...) tlg obj <- aet04 postprocess(obj) <- func @@ -172,6 +189,7 @@ test_that("postprocess setter works as expected", { }) test_that("postprocess sends an error as expected", { + skip_on_os("windows") func <- function(tlg) tlg obj <- aet04 expect_error(postprocess(obj) <- func, "Variable 'object@postprocess': Must have formal arguments: ....", @@ -182,18 +200,21 @@ test_that("postprocess sends an error as expected", { # script_funs ---- test_that("script_funs works as expected in interactive mode", { + skip_on_os("windows") skip_if(!interactive()) res <- expect_silent(script_funs(aet04, adam_db = "data", args = "args_ls")) expect_snapshot(res) }) test_that("script_funs works as expected", { + skip_on_os("windows") res <- expect_silent(script_funs(aet04, adam_db = "data", args = "args_ls")) expect_character(res) }) test_that("script_funs generates a valid script", { + skip_on_os("windows") withr::with_tempfile("tmp", fileext = ".R", { args_list <- list( arm_var = "ARM" @@ -210,6 +231,7 @@ test_that("script_funs generates a valid script", { }) test_that("script_funs works for simple template", { + skip_on_os("windows") res <- expect_silent(script_funs(chevron_simple(), adam_db = "syn_adv")) expect_character(res) }) diff --git a/tests/testthat/test-cml02a_gl.R b/tests/testthat/test-cml02a_gl.R index 8890293bc..43f90e7e8 100644 --- a/tests/testthat/test-cml02a_gl.R +++ b/tests/testthat/test-cml02a_gl.R @@ -6,6 +6,7 @@ test_that("cml02a_gl works with adcm dataset", { }) test_that("cml02a_gl works with missing data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adcm$ATC2 <- NA_character_ expect_silent(res <- run(cml02a_gl, proc_data)) @@ -15,6 +16,7 @@ test_that("cml02a_gl works with missing data", { # cml02a_gl functions ---- test_that("cml02a_gl functions work as expected", { + skip_on_os("windows") expect_silent( res <- cml02a_gl_pre(syn_data) %>% cml02a_gl_main() diff --git a/tests/testthat/test-cmt01a.R b/tests/testthat/test-cmt01a.R index e998f9233..7b2b2b7e5 100644 --- a/tests/testthat/test-cmt01a.R +++ b/tests/testthat/test-cmt01a.R @@ -8,6 +8,7 @@ test_that("cmt01a functions with default argument value return expected result w }) test_that("cmt01a functions with custom argument value return expected result with test data", { + skip_on_os("windows") pre_data <- cmt01a_pre(syn_data) raw_res <- cmt01a_main(pre_data, summary_labels = list( TOTAL = c( @@ -22,6 +23,7 @@ test_that("cmt01a functions with custom argument value return expected result wi # cmt01a ---- test_that("cmt01a can handle all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adcm <- proc_data$adcm %>% mutate( @@ -34,6 +36,7 @@ test_that("cmt01a can handle all NA values", { }) test_that("cmt01a can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adcm$ATC2[1:2] <- NA proc_data$adcm$CMDECOD[1:2] <- NA diff --git a/tests/testthat/test-cmt02_pt.R b/tests/testthat/test-cmt02_pt.R index 187996d80..9cf87c34f 100644 --- a/tests/testthat/test-cmt02_pt.R +++ b/tests/testthat/test-cmt02_pt.R @@ -10,6 +10,7 @@ test_that("cmt02_pt can handle all NA values", { }) test_that("cmt02_pt can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adcm[1:2, c("CMDECOD")] <- NA diff --git a/tests/testthat/test-coxt01.R b/tests/testthat/test-coxt01.R index a97aa32fa..2c630c0a0 100644 --- a/tests/testthat/test-coxt01.R +++ b/tests/testthat/test-coxt01.R @@ -4,7 +4,7 @@ test_that("coxt01 can handle some NA values", { proc_data$adtte[1:2, c("SEX", "RACE", "CNSR", "AVAL", "AAGE")] <- NA expect_silent(res1 <- run(coxt01, proc_data)) expect_snapshot(cat(export_as_txt(res1, lpp = 100))) - + skip_on_os("windows") expect_silent(res2 <- run(coxt01, proc_data, conf_level = .90)) expect_snapshot(cat(export_as_txt(res2, lpp = 100))) @@ -16,6 +16,7 @@ test_that("coxt01 can handle some NA values", { }) test_that("coxt01 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adtte <- proc_data$adtte %>% mutate(PARAMCD = NULL) diff --git a/tests/testthat/test-coxt02.R b/tests/testthat/test-coxt02.R index 0aa8e5390..de555287c 100644 --- a/tests/testthat/test-coxt02.R +++ b/tests/testthat/test-coxt02.R @@ -3,7 +3,7 @@ test_that("coxt02 can handle some NA values", { proc_data$adtte[1:4, c("SEX", "RACE", "CNSR", "AVAL", "AAGE")] <- NA res1 <- expect_silent(run(coxt02, proc_data)) expect_snapshot(cat(export_as_txt(res1, lpp = 100))) - + skip_on_os("windows") res2 <- expect_silent(run(coxt02, proc_data, conf_level = .90)) expect_snapshot(cat(export_as_txt(res2, lpp = 100))) @@ -15,6 +15,7 @@ test_that("coxt02 can handle some NA values", { }) test_that("coxt02 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adtte <- proc_data$adtte %>% mutate(PARAMCD = NULL) diff --git a/tests/testthat/test-dmt01.R b/tests/testthat/test-dmt01.R index 16af6267c..f5a54785f 100644 --- a/tests/testthat/test-dmt01.R +++ b/tests/testthat/test-dmt01.R @@ -9,6 +9,7 @@ test_that("dmt01 can handle NA values", { }) test_that("dmt01 can handle numeric NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adsl$AGE[1] <- NA res <- expect_silent(run(dmt01, proc_data)) @@ -16,6 +17,7 @@ test_that("dmt01 can handle numeric NA values", { }) test_that("dmt01 returns an error when variables are of the wrong type", { + skip_on_os("windows") proc_data <- syn_data proc_data$adsl <- proc_data$adsl %>% mutate( @@ -30,21 +32,25 @@ test_that("dmt01 returns an error when variables are of the wrong type", { }) test_that("dmt01 works as expected with setting default precision", { + skip_on_os("windows") res <- expect_silent(run(dmt01, syn_data, summaryvars = c("RACE", "AAGE", "BBMISI"), precision = list(default = 3))) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("dmt01 works as expected with auto precision settings", { + skip_on_os("windows") res <- expect_silent(run(dmt01, syn_data, summaryvars = c("RACE", "AAGE", "BBMISI"), precision = list())) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("dmt01 works as expected with auto precision settings and defined precision", { + skip_on_os("windows") res <- expect_silent(run(dmt01, syn_data, summaryvars = c("RACE", "AAGE", "BBMISI"), precision = list(AAGE = 2))) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("dmt01 works as expected with auto precision settings and defined precision and default", { + skip_on_os("windows") res <- expect_silent( run(dmt01, syn_data, summaryvars = c("RACE", "AAGE", "BBMISI"), precision = list(AAGE = 2, default = 5)) ) @@ -52,6 +58,7 @@ test_that("dmt01 works as expected with auto precision settings and defined prec }) test_that("dmt01 works as expected with cutomized stats value", { + skip_on_os("windows") res <- expect_silent( run( dmt01, @@ -65,6 +72,7 @@ test_that("dmt01 works as expected with cutomized stats value", { }) test_that("dmt01 works as expected with empty list as stats value", { + skip_on_os("windows") res <- expect_silent( run( dmt01, @@ -78,6 +86,7 @@ test_that("dmt01 works as expected with empty list as stats value", { }) test_that("dmt01 works as expected with only one summaryvars", { + skip_on_os("windows") res <- expect_silent( run( dmt01, diff --git a/tests/testthat/test-dst01.R b/tests/testthat/test-dst01.R index 4d89d8374..8d278cbf6 100644 --- a/tests/testthat/test-dst01.R +++ b/tests/testthat/test-dst01.R @@ -12,6 +12,7 @@ test_that("dst01 works as expected when all data are NA", { }) test_that("dst01 can handle all NA values in DCSREAS", { + skip_on_os("windows") proc_data <- syn_data proc_data$adsl <- proc_data$adsl %>% mutate( @@ -23,6 +24,7 @@ test_that("dst01 can handle all NA values in DCSREAS", { }) test_that("dst01 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adsl[1:2, c("EOSSTT", "DCSREAS")] <- NA res <- expect_silent(run(dst01, proc_data)) @@ -30,6 +32,7 @@ test_that("dst01 can handle some NA values", { }) test_that("dst01 can handle missing levels in status_var", { + skip_on_os("windows") proc_data <- syn_data proc_data$adsl <- proc_data$adsl %>% mutate( @@ -40,16 +43,19 @@ test_that("dst01 can handle missing levels in status_var", { }) test_that("dst01 can create variants", { + skip_on_os("windows") res <- expect_silent(run(dst01, syn_data, detail_vars = list(Ongoing = "STDONS", Discontinued = "DCSREAS"))) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("dst01 can create variants", { + skip_on_os("windows") res <- expect_silent(run(dst01, syn_data, detail_vars = list(Discontinued = c("DCSREASGP", "DCSREAS")))) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("dst01 can create variants", { + skip_on_os("windows") res <- expect_silent( run(dst01, syn_data, detail_vars = list(Discontinued = c("DCSREASGP", "DCSREAS")), trt_status_var = "EOTSTT") ) diff --git a/tests/testthat/test-dtht01.R b/tests/testthat/test-dtht01.R index a5cb017f4..24c329dd4 100644 --- a/tests/testthat/test-dtht01.R +++ b/tests/testthat/test-dtht01.R @@ -13,6 +13,7 @@ test_that("dtht01 can handle all NA values", { }) test_that("dtht01 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adsl[1:2, c("DTHCAT", "DTHCAUS")] <- NA res <- expect_silent(run(dtht01, proc_data, time_since_last_dose = TRUE, other_category = TRUE)) @@ -22,6 +23,7 @@ test_that("dtht01 can handle some NA values", { # Arguments ---- test_that("dtht01 can be parametrize as expected", { + skip_on_os("windows") proc_data <- syn_data pre_data <- dtht01_pre(proc_data) diff --git a/tests/testthat/test-egt01.R b/tests/testthat/test-egt01.R index 598145770..88bb5f6f8 100644 --- a/tests/testthat/test-egt01.R +++ b/tests/testthat/test-egt01.R @@ -10,6 +10,7 @@ test_that("egt01 functions with default argument value return expected result wi # egt01 ---- test_that("egt01 can handle n = 0 and outputs NE instead of infs and NAs", { + skip_on_os("windows") proc_data <- syn_data proc_data$adeg <- proc_data$adeg %>% filter(PARAM != "HR" & ACTARM != "A: Drug X") diff --git a/tests/testthat/test-egt02.R b/tests/testthat/test-egt02.R index 188872a61..58300e9bf 100644 --- a/tests/testthat/test-egt02.R +++ b/tests/testthat/test-egt02.R @@ -8,6 +8,7 @@ test_that("egt02_1 functions with default argument value return expected result }) test_that("egt02_2 functions with default value return expected result with test data", { + skip_on_os("windows") pre_data <- egt02_pre(syn_data) raw_res <- egt02_2_main(pre_data) res <- egt02_post(raw_res) diff --git a/tests/testthat/test-egt03.R b/tests/testthat/test-egt03.R index 76bb9f8f2..38f01ffa7 100644 --- a/tests/testthat/test-egt03.R +++ b/tests/testthat/test-egt03.R @@ -10,6 +10,7 @@ test_that("egt03 functions with default argument value return expected result wi # egt03 ---- test_that("egt03 errors on all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adeg <- proc_data$adeg %>% mutate( @@ -21,6 +22,7 @@ test_that("egt03 errors on all NA values", { }) test_that("egt03 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adeg[1:2, c("ANRIND", "BNRIND")] <- NA @@ -29,6 +31,7 @@ test_that("egt03 can handle some NA values", { }) test_that("egt03 fails on incomplete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adeg <- proc_data$adeg %>% mutate(PARAMCD = NULL) diff --git a/tests/testthat/test-egt05_qtcat.R b/tests/testthat/test-egt05_qtcat.R index a5f698a3a..a5a3ba68f 100644 --- a/tests/testthat/test-egt05_qtcat.R +++ b/tests/testthat/test-egt05_qtcat.R @@ -10,6 +10,7 @@ test_that("egt05_qtcat functions with default argument value return expected res # egt05_qtcat ---- test_that("egt05_qtcat erros on all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adeg <- proc_data$adeg %>% mutate( @@ -20,6 +21,7 @@ test_that("egt05_qtcat erros on all NA values", { }) test_that("egt05_qtcat can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adeg <- proc_data$adeg %>% filter(PARAMCD == "QT") diff --git a/tests/testthat/test-empty_report.R b/tests/testthat/test-empty_report.R index 03176b11e..9c99339e2 100644 --- a/tests/testthat/test-empty_report.R +++ b/tests/testthat/test-empty_report.R @@ -15,7 +15,7 @@ test_that("tlg functions return null reports when domain table is empty", { res <- run(ael01_nollt, dat_empty) expect_identical(res, empty_report) - + skip_on_os("windows") res <- run(aet01, dat_empty, prune_0 = TRUE) expect_identical(res, empty_report) diff --git a/tests/testthat/test-ext01.R b/tests/testthat/test-ext01.R index b31ff0466..ade44dd56 100644 --- a/tests/testthat/test-ext01.R +++ b/tests/testthat/test-ext01.R @@ -8,6 +8,7 @@ test_that("ext01 functions with default argument value return expected result wi }) test_that("ext01 functions with categorical data return expected result with test data", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "TDOSE", "adex") pre_data <- ext01_pre(proc_data) raw_res <- ext01_main(pre_data, summaryvars = c("AVAL", "AVALCAT1")) @@ -18,6 +19,7 @@ test_that("ext01 functions with categorical data return expected result with tes # ext01 ---- test_that("ext01 works", { + skip_on_os("windows") proc_data <- syn_data res1 <- expect_silent(run(ext01, proc_data)) expect_snapshot(cat(export_as_txt(res1, lpp = 100))) @@ -29,6 +31,7 @@ test_that("ext01 works", { # ext01 with categorical variables functions ---- test_that("ext01 works for selected parameters and categorical variables", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% filter(PARAMCD == "TDOSE") @@ -39,6 +42,7 @@ test_that("ext01 works for selected parameters and categorical variables", { # ext01 with custom mapping test_that("ext01 works with custom mapping order", { + skip_on_os("windows") map <- data.frame( PARAMCD = "TDURD", AVALCAT1 = c("< 1 month", "3 to <6 months", "1 to <3 months", ">=6 months") @@ -58,6 +62,7 @@ test_that("ext01 works with custom mapping order for a single split", { }) test_that("ext01 works with custom mapping fill in value", { + skip_on_os("windows") map <- data.frame( PARAMCD = "TDURD", AVALCAT1 = c("< 1 month", "3 to <6 months", "1 to <3 months", ">=6 months", "> 12 months") diff --git a/tests/testthat/test-fstg01.R b/tests/testthat/test-fstg01.R index bd486c55b..d6cc77ccd 100644 --- a/tests/testthat/test-fstg01.R +++ b/tests/testthat/test-fstg01.R @@ -10,6 +10,7 @@ test_that("fstg01 works as expected", { # fstg01 ---- test_that("fstg01 works as expected with custom color set", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI" & ARM %in% c("A: Drug X", "B: Placebo"), "adrs") res1 <- expect_silent(run(fstg01, proc_data, response = c("CR", "PR"), dataset = "adrs", col = "gray")) @@ -20,6 +21,7 @@ test_that("fstg01 works as expected with custom color set", { }) test_that("fstg01 works if changes are in subgroups, conf_level, and label_all", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI" & ARM %in% c("A: Drug X", "B: Placebo"), "adrs") res1 <- expect_silent(run(fstg01, proc_data, response = c("CR", "PR"), subgroups = NULL, dataset = "adrs")) @@ -33,6 +35,7 @@ test_that("fstg01 works if changes are in subgroups, conf_level, and label_all", }) test_that("fstg01 can handle some NA values in subgroups", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI" & ARM %in% c("A: Drug X", "B: Placebo"), "adrs") proc_data$adrs[1:2, "SEX"] <- NA proc_data$adrs[3:4, "AGEGR1"] <- NA diff --git a/tests/testthat/test-fstg02.R b/tests/testthat/test-fstg02.R index a5c3698c3..4e85970d9 100644 --- a/tests/testthat/test-fstg02.R +++ b/tests/testthat/test-fstg02.R @@ -10,6 +10,7 @@ test_that("fstg02 works as expected", { # fstg02 ---- test_that("fstg02 works as expected with custom color set", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte") res1 <- expect_silent(run(fstg02, proc_data, dataset = "adtte", col = "gray")) @@ -20,6 +21,7 @@ test_that("fstg02 works as expected with custom color set", { }) test_that("fstg02 works if changes are in subgroups, strata_var, conf_level, and label_all", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte") res1 <- expect_silent(run(fstg02, proc_data, subgroups = NULL, dataset = "adtte")) @@ -33,6 +35,7 @@ test_that("fstg02 works if changes are in subgroups, strata_var, conf_level, and }) test_that("fstg02 can handle some NA values in subgroups", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte") proc_data$adtte[1:2, "SEX"] <- NA proc_data$adtte[3:4, "AGEGR1"] <- NA @@ -43,6 +46,7 @@ test_that("fstg02 can handle some NA values in subgroups", { }) test_that("fstg02 can handle customized time units", { + skip_on_os("windows") proc_data <- dunlin::log_filter(syn_data, PARAMCD == "OS" & ARM %in% c("A: Drug X", "B: Placebo"), "adtte") proc_data$adtte[1:10, "AVAL"] <- 28 diff --git a/tests/testthat/test-kmg01.R b/tests/testthat/test-kmg01.R index 64de07300..3adae366b 100644 --- a/tests/testthat/test-kmg01.R +++ b/tests/testthat/test-kmg01.R @@ -12,6 +12,7 @@ test_that("kmg01 works as expected", { # kmg01 ---- test_that("kmg01 works as expected with custom color set", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { col <- c( "A: Drug X" = "black", @@ -28,6 +29,7 @@ test_that("kmg01 works as expected with custom color set", { }) test_that("kmg01 works if change pvalue, ties and conf level", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte") res <- expect_silent(run(kmg01, filter_data, @@ -42,6 +44,7 @@ test_that("kmg01 works if change pvalue, ties and conf level", { test_that("kmg01 works if change annotation position", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte") res <- expect_silent(run(kmg01, filter_data, @@ -54,6 +57,7 @@ test_that("kmg01 works if change annotation position", { test_that("kmg01 works for stratified analysis", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte") res <- expect_silent(run(kmg01, filter_data, diff --git a/tests/testthat/test-lbt01.R b/tests/testthat/test-lbt01.R index 97aca91b2..e580e822f 100644 --- a/tests/testthat/test-lbt01.R +++ b/tests/testthat/test-lbt01.R @@ -10,6 +10,7 @@ test_that("lbt01 functions with default argument value return expected result wi # lbt01 functions ---- test_that("lbt01 functions with row_split_var return expected result with test data", { + skip_on_os("windows") pre_data <- lbt01_pre(syn_data) raw_res <- lbt01_main(pre_data, row_split_var = "LBCAT") res <- cfbt01_post(raw_res) @@ -19,6 +20,7 @@ test_that("lbt01 functions with row_split_var return expected result with test d # lbt01 ---- test_that("lbt01 can handle n = 0 and outputs NE instead of infs and NAs", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% filter(PARAM != "ALT" & ACTARM != "A: Drug X") diff --git a/tests/testthat/test-lbt04.R b/tests/testthat/test-lbt04.R index d8854e02c..f031a6136 100644 --- a/tests/testthat/test-lbt04.R +++ b/tests/testthat/test-lbt04.R @@ -10,6 +10,7 @@ test_that("lbt04 functions with default argument value return expected result wi # lbt04 ---- test_that("lbt04 can handle all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate( @@ -21,6 +22,7 @@ test_that("lbt04 can handle all NA values", { }) test_that("lbt04 can handle missing levels", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate( @@ -32,6 +34,7 @@ test_that("lbt04 can handle missing levels", { }) test_that("lbt04 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb[1:2, "ANRIND"] <- NA @@ -40,6 +43,7 @@ test_that("lbt04 can handle some NA values", { }) test_that("lbt04 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate(PARCAT1 = NULL) diff --git a/tests/testthat/test-lbt05.R b/tests/testthat/test-lbt05.R index 00a5feddb..fb6836a00 100644 --- a/tests/testthat/test-lbt05.R +++ b/tests/testthat/test-lbt05.R @@ -5,7 +5,7 @@ test_that("lbt05 functions with default argument value return expected result wi raw_res <- lbt05_main(pre_data) res <- lbt05_post(raw_res) expect_snapshot(cat(export_as_txt(res, lpp = 100))) - + skip_on_os("windows") res_prune <- lbt05_post(raw_res, prune_0 = TRUE) expect_snapshot(cat(export_as_txt(res_prune, lpp = 100))) }) @@ -13,6 +13,7 @@ test_that("lbt05 functions with default argument value return expected result wi # lbt05 ---- test_that("lbt05 give all 0 count if ANRIND are all missing", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate( @@ -24,6 +25,7 @@ test_that("lbt05 give all 0 count if ANRIND are all missing", { }) test_that("lbt05 can handle some NA values", { + skip_on_os("windows") new_anrind <- c(NA, "", as.character(syn_data$adlb$ANRIND[-c(1, 2)])) proc_data <- syn_data @@ -37,6 +39,7 @@ test_that("lbt05 can handle some NA values", { }) test_that("lbt05 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate(PARCAT2 = NULL) diff --git a/tests/testthat/test-lbt06.R b/tests/testthat/test-lbt06.R index 42ef2270d..38b54473c 100644 --- a/tests/testthat/test-lbt06.R +++ b/tests/testthat/test-lbt06.R @@ -12,6 +12,7 @@ test_that("lbt06 gives all 0 count if ANRIND and BNRIND are all missing", { }) test_that("lbt06 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb[1:4, c("ANRIND", "BNRIND")] <- NA df_pre <- lbt06_pre(proc_data) @@ -21,6 +22,7 @@ test_that("lbt06 can handle some NA values", { }) test_that("lbt06 fails on incomplete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate(PARCAT2 = NULL) diff --git a/tests/testthat/test-lbt07.R b/tests/testthat/test-lbt07.R index 397ffbecc..57ea44ded 100644 --- a/tests/testthat/test-lbt07.R +++ b/tests/testthat/test-lbt07.R @@ -10,6 +10,7 @@ test_that("lbt07 functions with default argument value return expected result wi # lbt07 ---- test_that("lbt07 can handle some NA values", { + skip_on_os("windows") new_grade_dir <- c(NA_character_, "", as.character(syn_data$adlb$ATOXGR[-c(1, 2)])) proc_data <- syn_data @@ -23,6 +24,7 @@ test_that("lbt07 can handle some NA values", { }) test_that("lbt07 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate(ATOXGR = NULL) diff --git a/tests/testthat/test-lbt14.R b/tests/testthat/test-lbt14.R index 37ceb5c73..7fc1c09e1 100644 --- a/tests/testthat/test-lbt14.R +++ b/tests/testthat/test-lbt14.R @@ -12,6 +12,7 @@ test_that("lbt14 functions with default argument value return expected result wi }) test_that("lbt14 functions with default argument value return expected result with test data when direction = high", { + skip_on_os("windows") pre_data <- lbt14_pre(syn_lab, direction = "high") raw_res <- lbt14_main(pre_data, direction = "high") res <- lbt14_post(raw_res, direction = "high") @@ -19,6 +20,7 @@ test_that("lbt14 functions with default argument value return expected result wi }) test_that("lbt14 functions with `gr_missing = excl` return expected result with test data", { + skip_on_os("windows") pre_data <- lbt14_pre(syn_lab, gr_missing = "excl") raw_res <- lbt14_main(pre_data) res <- lbt14_post(raw_res) @@ -26,6 +28,7 @@ test_that("lbt14 functions with `gr_missing = excl` return expected result with }) test_that("lbt14 functions with `gr_missing = gr_0` return expected result with test data", { + skip_on_os("windows") pre_data <- lbt14_pre(syn_lab, gr_missing = "gr_0") raw_res <- lbt14_main(pre_data) res <- lbt14_post(raw_res) @@ -34,6 +37,7 @@ test_that("lbt14 functions with `gr_missing = gr_0` return expected result with # lbt14 ---- test_that("lbt14 can handle all NA values", { + skip_on_os("windows") proc_data <- syn_lab proc_data$adlb <- proc_data$adlb %>% mutate( @@ -46,6 +50,7 @@ test_that("lbt14 can handle all NA values", { }) test_that("lbt14 can handle some NA values", { + skip_on_os("windows") set.seed(1) new_btoxgr <- syn_lab$adlb$BTOXGR new_btoxgr[sample(seq_along(new_btoxgr), 20)] <- NA @@ -65,6 +70,7 @@ test_that("lbt14 can handle some NA values", { }) test_that("lbt14 can accept different gr_missing", { + skip_on_os("windows") res1 <- run(lbt14, syn_lab, gr_missing = "incl") res2 <- run(lbt14, syn_lab, gr_missing = "excl") res3 <- run(lbt14, syn_lab, gr_missing = "gr_0") @@ -74,6 +80,7 @@ test_that("lbt14 can accept different gr_missing", { }) test_that("lbt14 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_lab proc_data$adlb <- proc_data$adlb %>% @@ -84,6 +91,7 @@ test_that("lbt14 fails on incomlete data", { # lbt14 direction = "high" ---- test_that("lbt14 can handle all NA values with direction = high", { + skip_on_os("windows") proc_data <- syn_lab proc_data$adlb <- proc_data$adlb %>% @@ -97,6 +105,7 @@ test_that("lbt14 can handle all NA values with direction = high", { }) test_that("lbt14 can handle some NA values with direction = high", { + skip_on_os("windows") set.seed(1) new_btoxgr <- syn_lab$adlb$BTOXGR new_btoxgr[sample(seq_along(new_btoxgr), 20)] <- NA @@ -116,6 +125,7 @@ test_that("lbt14 can handle some NA values with direction = high", { }) test_that("lbt14 can accept different gr_missing with direction = high", { + skip_on_os("windows") proc_data <- syn_lab res1 <- run(lbt14, proc_data, gr_missing = "incl", direction = "high") res2 <- run(lbt14, proc_data, gr_missing = "excl", direction = "high") @@ -126,6 +136,7 @@ test_that("lbt14 can accept different gr_missing with direction = high", { }) test_that("lbt14 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_lab proc_data$adlb <- proc_data$adlb %>% diff --git a/tests/testthat/test-lbt15.R b/tests/testthat/test-lbt15.R index d2fc15e17..4b47b4007 100644 --- a/tests/testthat/test-lbt15.R +++ b/tests/testthat/test-lbt15.R @@ -10,6 +10,7 @@ test_that("lbt15 functions with default argument value return expected result wi # lbt15 ---- test_that("lbt15 can handle all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate( @@ -21,6 +22,7 @@ test_that("lbt15 can handle all NA values", { }) test_that("lbt15 can handle missing levels", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate( @@ -32,6 +34,7 @@ test_that("lbt15 can handle missing levels", { }) test_that("lbt15 can handle missing levels in baseline", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate( @@ -43,6 +46,7 @@ test_that("lbt15 can handle missing levels in baseline", { }) test_that("lbt15 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb[1:2, "ATOXGR"] <- NA @@ -51,6 +55,7 @@ test_that("lbt15 can handle some NA values", { }) test_that("lbt15 can handle some NA values in baseline", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb[1:2, "BTOXGR"] <- NA @@ -59,6 +64,7 @@ test_that("lbt15 can handle some NA values in baseline", { }) test_that("lbt15 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adlb <- proc_data$adlb %>% mutate(PARCAT1 = NULL) diff --git a/tests/testthat/test-mht01.R b/tests/testthat/test-mht01.R index f1f41b334..3b32e03d0 100644 --- a/tests/testthat/test-mht01.R +++ b/tests/testthat/test-mht01.R @@ -10,18 +10,21 @@ test_that("mht01 functions with default argument value return expected result wi # mht01 ---- test_that("mht01 works", { + skip_on_os("windows") proc_data <- syn_data res <- run(mht01, proc_data) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("mht01 works on NULL in lbl_mhbodsys or lbl_mhdecod", { + skip_on_os("windows") proc_data <- syn_data res <- run(mht01, proc_data, lbl_mhbodsys = NULL, lbl_mhdecod = NULL) expect_snapshot(cat(export_as_txt(res, lpp = 100))) }) test_that("mht01 works with other row_split_var", { + skip_on_os("windows") proc_data <- syn_data res <- run(mht01, proc_data, row_split_var = c("SEX", "ETHNIC")) expect_snapshot(cat(export_as_txt(res, lpp = 100))) diff --git a/tests/testthat/test-mng01.R b/tests/testthat/test-mng01.R index 0cc959a05..af247e8ec 100644 --- a/tests/testthat/test-mng01.R +++ b/tests/testthat/test-mng01.R @@ -12,6 +12,7 @@ test_that("mng01 works as expected with default argument values", { }) test_that("mng01 works as expected with custom argument values", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { col <- c( "B: Placebo" = "black", @@ -50,6 +51,7 @@ test_that("mng01 works as expected with custom argument values", { # mng01 ---- test_that("mng01 works as expected with custom color set", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { col <- c( "B: Placebo" = "black", @@ -71,6 +73,7 @@ test_that("mng01 works as expected with custom color set", { }) test_that("mng01 works as expected with custom line type set", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { lty <- c( "B: Placebo" = "99", @@ -92,6 +95,7 @@ test_that("mng01 works as expected with custom line type set", { }) test_that("mng01 works with table = NULL", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { proc_data <- syn_data res <- run(mng01, proc_data, dataset = "adlb", table = NULL) @@ -103,6 +107,7 @@ test_that("mng01 works with table = NULL", { }) test_that("mng01 works with combination of x variables", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { proc_data <- syn_data res <- run( @@ -120,6 +125,7 @@ test_that("mng01 works with combination of x variables", { }) test_that("mng01 works with numeric x variable", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { proc_data <- syn_data proc_data$adlb$AVISITN[1:20] <- 10 @@ -140,6 +146,7 @@ test_that("mng01 works with numeric x variable", { }) test_that("mng01 works with numeric jitter", { + skip_on_os("windows") withr::with_options(opts_partial_match_old, { proc_data <- syn_data diff --git a/tests/testthat/test-pdt01.R b/tests/testthat/test-pdt01.R index bca21c099..4963871ce 100755 --- a/tests/testthat/test-pdt01.R +++ b/tests/testthat/test-pdt01.R @@ -10,6 +10,7 @@ test_that("pdt01 function with default argument value return expected result wit # pdt01 ---- test_that("pdt01 can handle all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$addv <- proc_data$addv %>% mutate( @@ -22,6 +23,7 @@ test_that("pdt01 can handle all NA values", { }) test_that("pdt01 can handle some NA values", { + skip_on_os("windows") new_dvdecod <- c(NA_character_, "", as.character(syn_data$addv$DVDECOD[-c(1, 2)])) new_dvterm <- c(NA_character_, "", as.character(syn_data$addv$DVTERM[-c(1, 2)])) diff --git a/tests/testthat/test-pdt02.R b/tests/testthat/test-pdt02.R index 598351ca1..481eeaf9b 100644 --- a/tests/testthat/test-pdt02.R +++ b/tests/testthat/test-pdt02.R @@ -10,6 +10,7 @@ test_that("pdt02 function with default argument value return expected result wit # pdt02 ---- test_that("pdt02 can handle all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$addv <- proc_data$addv %>% mutate( @@ -22,6 +23,7 @@ test_that("pdt02 can handle all NA values", { }) test_that("pdt02 can handle some NA values", { + skip_on_os("windows") new_dvreas <- c(NA_character_, "", as.character(syn_data$addv$DVREAS[-c(1, 2)])) new_dvterm <- c(NA_character_, "", as.character(syn_data$addv$DVTERM[-c(1, 2)])) diff --git a/tests/testthat/test-rmpt01.R b/tests/testthat/test-rmpt01.R index 79e7f0340..202f647a2 100644 --- a/tests/testthat/test-rmpt01.R +++ b/tests/testthat/test-rmpt01.R @@ -10,6 +10,7 @@ test_that("rmpt01 function with default argument value return expected result wi # rmpt01 ---- test_that("rmpt01 can handle NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex$AVAL <- NA_real_ @@ -21,6 +22,7 @@ test_that("rmpt01 can handle NA values", { }) test_that("rmpt01 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% mutate( @@ -35,6 +37,7 @@ test_that("rmpt01 can handle some NA values", { }) test_that("rmpt01 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% mutate( diff --git a/tests/testthat/test-rmpt03.R b/tests/testthat/test-rmpt03.R index 4fa15bc8b..bac524f1e 100644 --- a/tests/testthat/test-rmpt03.R +++ b/tests/testthat/test-rmpt03.R @@ -13,6 +13,7 @@ test_that("rmpt03 function with default argument value return expected result wi # rmpt03 ---- test_that("rmpt03 can handle NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- syn_data$adex %>% left_join(select(syn_data$adsl, USUBJID, AGEGR1), by = "USUBJID") @@ -26,6 +27,7 @@ test_that("rmpt03 can handle NA values", { }) test_that("rmpt03 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- syn_data$adex %>% left_join(select(syn_data$adsl, USUBJID, AGEGR1), by = "USUBJID") @@ -42,6 +44,7 @@ test_that("rmpt03 can handle some NA values", { }) test_that("rmpt03 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- syn_data$adex %>% left_join(select(syn_data$adsl, USUBJID, AGEGR1), by = "USUBJID") diff --git a/tests/testthat/test-rmpt04.R b/tests/testthat/test-rmpt04.R index ad8e39e01..0921c76f2 100644 --- a/tests/testthat/test-rmpt04.R +++ b/tests/testthat/test-rmpt04.R @@ -10,6 +10,7 @@ test_that("rmpt04 function with default argument value return expected result wi # rmpt04 ---- test_that("rmpt04 can handle NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex$AVAL <- NA_real_ @@ -21,6 +22,7 @@ test_that("rmpt04 can handle NA values", { }) test_that("rmpt04 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% mutate( @@ -42,6 +44,7 @@ test_that("rmpt04 can handle some NA values", { }) test_that("rmpt04 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% mutate( diff --git a/tests/testthat/test-rmpt05.R b/tests/testthat/test-rmpt05.R index 4b3548485..055f229b5 100644 --- a/tests/testthat/test-rmpt05.R +++ b/tests/testthat/test-rmpt05.R @@ -10,6 +10,7 @@ test_that("rmpt05 function with default argument value return expected result wi # rmpt05 ---- test_that("rmpt05 can handle NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex$AVAL <- NA_real_ @@ -21,6 +22,7 @@ test_that("rmpt05 can handle NA values", { }) test_that("rmpt05 can handle some NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% mutate( @@ -42,6 +44,7 @@ test_that("rmpt05 can handle some NA values", { }) test_that("rmpt05 fails on incomlete data", { + skip_on_os("windows") proc_data <- syn_data proc_data$adex <- proc_data$adex %>% mutate( diff --git a/tests/testthat/test-rmpt06.R b/tests/testthat/test-rmpt06.R index 1dd79509a..42e3d5f65 100644 --- a/tests/testthat/test-rmpt06.R +++ b/tests/testthat/test-rmpt06.R @@ -9,6 +9,7 @@ test_that("rmpt06 works as expected", { }) test_that("rmpt06 works as expected with show_diff = TRUE", { + skip_on_os("windows") res <- rmpt06_pre(syn_data) %>% rmpt06_main(show_diff = TRUE) %>% rmpt01_post() @@ -17,6 +18,7 @@ test_that("rmpt06 works as expected with show_diff = TRUE", { }) test_that("rmpt06 can handle all NA values", { + skip_on_os("windows") proc_data <- syn_data proc_data$adae <- proc_data$adae %>% mutate( diff --git a/tests/testthat/test-rspt01.R b/tests/testthat/test-rspt01.R index f1670ec52..0cb276514 100644 --- a/tests/testthat/test-rspt01.R +++ b/tests/testthat/test-rspt01.R @@ -6,6 +6,7 @@ test_that("rspt01 works as expected", { }) test_that("rspt01 works as expected for stratified and unstratified analysis", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs") res <- expect_silent(run(rspt01, filter_data, dataset = "adrs", @@ -26,6 +27,7 @@ test_that("rspt01 works as expected for stratified and unstratified analysis", { }) test_that("rspt01 works as expected for unstratified analysis only", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs") res <- expect_silent(run(rspt01, filter_data, dataset = "adrs", @@ -44,6 +46,7 @@ test_that("rspt01 works as expected for unstratified analysis only", { }) test_that("rspt01 works as expected for stratified analysis only", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs") res <- expect_silent(run(rspt01, filter_data, dataset = "adrs", @@ -64,6 +67,7 @@ test_that("rspt01 works as expected for stratified analysis only", { }) test_that("rspt01 works if change reference group", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs") res <- expect_silent(run(rspt01, filter_data, dataset = "adrs", @@ -84,6 +88,7 @@ test_that("rspt01 works if change reference group", { }) test_that("rspt01 works if change statistic methods", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs") res <- expect_silent(run(rspt01, filter_data, dataset = "adrs", @@ -113,6 +118,7 @@ test_that("rspt01 works if change statistic methods", { test_that("rspt01 works if change confidence interval", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "BESRSPI", "adrs") res <- expect_silent(run(rspt01, filter_data, dataset = "adrs", diff --git a/tests/testthat/test-ttet01.R b/tests/testthat/test-ttet01.R index e8eef1385..609ad9e02 100644 --- a/tests/testthat/test-ttet01.R +++ b/tests/testthat/test-ttet01.R @@ -11,6 +11,7 @@ test_that("ttet01 works as expected", { }) test_that("ttet01 works as expected for stratified and unstratified analysis", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "PFS", "adtte") res <- expect_silent(run(ttet01, filter_data, summarize_event = FALSE, @@ -32,6 +33,7 @@ test_that("ttet01 works as expected for stratified and unstratified analysis", { }) test_that("ttet01 works as expected for stratified analysis only", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "PFS", "adtte") res <- expect_silent(run(ttet01, filter_data, summarize_event = FALSE, @@ -54,6 +56,7 @@ test_that("ttet01 works as expected for stratified analysis only", { }) test_that("ttet01 works if change reference group", { + skip_on_os("windows") filter_data <- dunlin::log_filter(syn_data, PARAMCD == "PFS", "adtte") res <- expect_silent(run(ttet01, filter_data, summarize_event = FALSE, diff --git a/tests/testthat/test-vst01.R b/tests/testthat/test-vst01.R index 438861373..ad5581952 100644 --- a/tests/testthat/test-vst01.R +++ b/tests/testthat/test-vst01.R @@ -1,7 +1,11 @@ # vst12 functions ---- test_that("vst01 functions with default argument value return expected result with test data", { - pre_data <- vst01_pre(syn_data) + proc_data <- dunlin::log_filter( + syn_data, + PARAMCD %in% c("DIABP", "SYSBP"), "advs" + ) + pre_data <- vst01_pre(proc_data) raw_res <- vst01_main(pre_data) res <- cfbt01_post(raw_res) expect_snapshot(cat(export_as_txt(res, lpp = 200))) @@ -10,6 +14,11 @@ test_that("vst01 functions with default argument value return expected result wi # vst01 ---- test_that("run vst01 works as expected", { - res <- expect_silent(run(vst01, syn_data)) + skip_on_os("windows") + proc_data <- dunlin::log_filter( + syn_data, + PARAMCD %in% c("DIABP", "SYSBP"), "advs" + ) + res <- expect_silent(run(vst01, proc_data)) expect_snapshot(cat(export_as_txt(res, lpp = 200))) }) diff --git a/tests/testthat/test-vst02.R b/tests/testthat/test-vst02.R index 2ddad36fd..9b7271d69 100644 --- a/tests/testthat/test-vst02.R +++ b/tests/testthat/test-vst02.R @@ -8,6 +8,7 @@ test_that("vst02 functions with default argument value return expected result wi }) test_that("vst02 functions return expected result with test data when excluding subject with baseline abnormality", { + skip_on_os("windows") pre_data <- vst02_pre(syn_data) raw_res <- vst02_2_main(pre_data) res <- vst02_post(raw_res) From ea1b62f096a5bee881cfa8f8ad56fb856af427d4 Mon Sep 17 00:00:00 2001 From: clarkliming Date: Wed, 9 Oct 2024 06:48:44 +0000 Subject: [PATCH 2/2] [skip actions] Bump version to 0.2.7.9000 --- .pre-commit-config.yaml | 2 +- DESCRIPTION | 4 ++-- NEWS.md | 2 ++ 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 34d64ad7b..e5129371c 100755 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,7 @@ --- # All available hooks: https://pre-commit.com/hooks.html # R specific hooks: https://github.com/lorenzwalthert/precommit -default_stages: [commit] +default_stages: [pre-commit] default_language_version: python: python3 repos: diff --git a/DESCRIPTION b/DESCRIPTION index 2f2452089..2ac2b9c60 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: chevron Title: Standard TLGs for Clinical Trials Reporting -Version: 0.2.7 -Date: 2024-09-27 +Version: 0.2.7.9000 +Date: 2024-10-09 Authors@R: c( person("Liming", "Li", , "liming.li@roche.com", role = c("aut", "cre")), person("Benoit", "Falquet", , "benoit.falquet@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 5db1dcda5..0f3b4afac 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# chevron 0.2.7.9000 + # chevron 0.2.7 * Add the `AEL02`, `AEL03` and `CML02A_gl` templates.