diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index e4d9c3b7..bfb1713e 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -59,6 +59,8 @@ jobs: - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'release', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'oldrel', allowfail: true, 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: '3.0', allowfail: true, 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: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} diff --git a/DESCRIPTION b/DESCRIPTION index eb6cf705..c830c822 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.4.0.9060 +Version: 1.4.0.9061 Date: 2021-01-04 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 45f1c904..ed9fe9a9 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.4.0.9060 +# AMR 1.4.0.9061 ## Last updated: 4 January 2021 ### New * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`): diff --git a/data-raw/AMR_1.4.0.9060.tar.gz b/data-raw/AMR_1.4.0.9061.tar.gz similarity index 83% rename from data-raw/AMR_1.4.0.9060.tar.gz rename to data-raw/AMR_1.4.0.9061.tar.gz index d19c9781..80d69692 100644 Binary files a/data-raw/AMR_1.4.0.9060.tar.gz and b/data-raw/AMR_1.4.0.9061.tar.gz differ diff --git a/docs/404.html b/docs/404.html index d2be3138..80acc5ce 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b2f23b85..f27fe245 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061 diff --git a/docs/articles/index.html b/docs/articles/index.html index e62c032e..52e593b0 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061 diff --git a/docs/authors.html b/docs/authors.html index 14f2739a..0673f3fb 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061 diff --git a/docs/index.html b/docs/index.html index 5fc50fd8..883c4418 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061 diff --git a/docs/news/index.html b/docs/news/index.html index f3e04c0c..340ff200 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.4.0.9060 Unreleased +
+

+AMR 1.4.0.9061 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 21cd2f6e..872b5c60 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: 2021-01-04T12:36Z +last_built: 2021-01-04T13:15Z 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 3ca53671..2ee69cb8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061

diff --git a/docs/survey.html b/docs/survey.html index e3d205cc..bc08705d 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9060 + 1.4.0.9061
diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R index 01eaa5a3..17854ce0 100644 --- a/tests/testthat/test-zzz.R +++ b/tests/testthat/test-zzz.R @@ -108,8 +108,8 @@ test_that("imports work", { for (i in seq_len(length(import_functions))) { fn <- names(import_functions)[i] pkg <- unname(import_functions[i]) - # package should be in Suggests field of DESCRIPTION - expect(pkg %in% strsplit(packageDescription("AMR")$Suggests, ",\n")[[1]], + # package should be in DESCRIPTION + expect(pkg %in% gsub("[^A-Za-z]", "", readLines(file("DESCRIPTION"))), failure_message = paste0("Package ", pkg, " is not in Suggests field")) # function should exist in foreign pkg namespace expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),