diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index f68e56c53..29053e107 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -144,6 +144,7 @@ jobs: _R_CHECK_DEPENDS_ONLY_: true _R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose + R_LIBS_USER: ${{ env.R_LIBS_USER }} run: | tar -xf data-raw/AMR_latest.tar.gz rm -rf AMR/vignettes @@ -158,10 +159,11 @@ jobs: _R_CHECK_DEPENDS_ONLY_: true _R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose + R_LIBS_USER: ${{ env.R_LIBS_USER }} run: | tar -xf data-raw/AMR_latest.tar.gz rm -rf AMR/vignettes - R CMD check AMR --no-manual --as-cran --no-vignettes --library='/Users/runner/work/_temp/Library' + R CMD check AMR --no-manual --no-vignettes shell: bash - name: Show testthat output diff --git a/DESCRIPTION b/DESCRIPTION index f0d58ecb7..85711e997 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.6.0.9028 +Version: 1.6.0.9030 Date: 2021-05-13 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index cc8b053de..465c8846e 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.6.0.9028 +# `AMR` 1.6.0.9030 ## Last updated: 13 May 2021 ### New diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index bbb90353b..c6468c07b 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 2965cacd3..33f02b6ce 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b6137c4d3..425aa90d5 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030 diff --git a/docs/articles/index.html b/docs/articles/index.html index 0fffc9dcf..1ae9f88ab 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030 diff --git a/docs/authors.html b/docs/authors.html index 6ed6a3c1d..a726d9f28 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030 diff --git a/docs/index.html b/docs/index.html index 06280279e..8ea1630fe 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030 diff --git a/docs/news/index.html b/docs/news/index.html index 8a6912f1f..5f95edd08 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9028

+
+

+ Unreleased AMR 1.6.0.9030

Last updated: 13 May 2021 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 75389aea5..f0c65a8b8 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: 2021-05-13T20:43Z +last_built: 2021-05-13T21:04Z 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 03e9e9c34..0996b8d73 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030

diff --git a/docs/survey.html b/docs/survey.html index 2c068b0da..f52d7b9b6 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9028 + 1.6.0.9030
diff --git a/tests/testthat.R b/tests/testthat.R index bd43bc4c1..42c8134b7 100755 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -27,7 +27,10 @@ # able to install it. Yet, we want basic R CMD CHECK's in those R versions # as well, so only run unit tests in later R versions: if (require("testthat", warn.conflicts = FALSE)) { - library(testthat) library(AMR) + # print non-base packages + print(as.data.frame(utils::installed.packages())[which(is.na(as.data.frame(utils::installed.packages())$Priority)), + "Version", + drop = FALSE]) test_check("AMR") } diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R index e17141b53..51698e293 100755 --- a/tests/testthat/test-mdro.R +++ b/tests/testthat/test-mdro.R @@ -119,7 +119,7 @@ test_that("mdro works", { pza = sample_rsi(), MFX = sample_rsi(), KAN = sample_rsi()) - expect_gt(n_distinct(mdr_tb(x)), 2) + expect_gt(length(unique(mdr_tb(x))), 2) # check the guideline by Magiorakos et al. (2012), the default guideline stau <- data.frame(mo = c("S. aureus", "S. aureus", "S. aureus", "S. aureus"), diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R index 87041d806..9b7f751e2 100644 --- a/tests/testthat/test-resistance_predict.R +++ b/tests/testthat/test-resistance_predict.R @@ -48,10 +48,12 @@ test_that("prediction of rsi works", { info = TRUE))) pdf(NULL) # prevent Rplots.pdf being created expect_silent(plot(x)) - expect_silent(ggplot_rsi_predict(x)) - expect_silent(ggplot(x)) - expect_error(ggplot_rsi_predict(example_isolates)) - + if (suppressWarnings(require("ggplot2"))) { + expect_silent(ggplot_rsi_predict(x)) + expect_silent(ggplot(x)) + expect_error(ggplot_rsi_predict(example_isolates)) + } + expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), model = "binomial", col_ab = "AMX",