diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 9166e90c..069bccde 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -52,13 +52,13 @@ jobs: config: - {os: macOS-latest, r: 'devel', allowfail: true} - {os: macOS-latest, r: 'release', allowfail: false} - - {os: macOS-latest, r: 'oldrel', allowfail: true} + - {os: macOS-latest, r: 'oldrel', allowfail: false} - - {os: windows-latest, r: 'devel', allowfail: false} + - {os: windows-latest, r: 'devel', allowfail: true} - {os: windows-latest, r: 'release', allowfail: false} - {os: windows-latest, r: 'oldrel', allowfail: false} - - {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} @@ -66,11 +66,11 @@ jobs: - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} @@ -78,8 +78,8 @@ jobs: - {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} env: @@ -124,8 +124,9 @@ jobs: as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - - name: Only keep vignettes on release version - if: matrix.config.r != 'release' + # - name: Only keep vignettes on release version + - name: Remove vignettes + # if: matrix.config.r != 'release' # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite run: | rm -rf AMR/vignettes diff --git a/DESCRIPTION b/DESCRIPTION index e456921d..a667e869 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.6.0.9050 +Version: 1.6.0.9052 Date: 2021-05-20 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index b2f40e96..f1e9256a 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.6.0.9050 +# `AMR` 1.6.0.9052 ## Last updated: 20 May 2021 ### Breaking change diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index a3543351..d1f42355 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -1150,6 +1150,9 @@ percentage <- function(x, digits = NULL, ...) { if (is.null(digits)) { digits <- getdecimalplaces(x) } + if (is.null(digits) || is.na(digits) || !is.numeric(digits)) { + digits <- 2 + } # round right: percentage(0.4455) and format(as.percentage(0.4455), 1) should return "44.6%", not "44.5%" x_formatted <- format(round2(as.double(x), digits = digits + 2) * 100, diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index a31dcbcc..a87013e2 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/tinytest_1.2.4.patched.tar.gz b/data-raw/tinytest_1.2.4.patched.tar.gz index 6fac8488..5aadffe9 100644 Binary files a/data-raw/tinytest_1.2.4.patched.tar.gz and b/data-raw/tinytest_1.2.4.patched.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 7ebba78c..10bf3c16 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 607ff1b5..429063cc 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 39339b9e..9983fd7b 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 diff --git a/docs/articles/index.html b/docs/articles/index.html index 5482848d..ffc76852 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 diff --git a/docs/authors.html b/docs/authors.html index 7f7da5c5..ae231822 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 diff --git a/docs/index.html b/docs/index.html index 45d37b8c..e5aa98ea 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 diff --git a/docs/news/index.html b/docs/news/index.html index cd254c5b..d92bd809 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9050

+
+

+ Unreleased AMR 1.6.0.9052

Last updated: 20 May 2021 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9f57ff13..3bd93d60 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-05-20T08:10Z +last_built: 2021-05-20T09:42Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 63a3578e..dae8f1a7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052

diff --git a/docs/survey.html b/docs/survey.html index 4fbf51a0..f9dd9a35 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9050 + 1.6.0.9052