diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index d4ef49d8..62c35ab4 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -117,9 +117,8 @@ jobs: brew install mariadb-connector-c - name: Install dependencies - if: always() run: | - utils::install.packages(strsplit(utils::packageDescription("AMR")$Suggests, ",\n")[[1]]) + utils::update.packages(ask = FALSE) shell: Rscript {0} - name: Session info @@ -151,10 +150,14 @@ jobs: if: always() run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash + + - name: Install packages to check for new deps + run: | + R CMD INSTALL data-raw/AMR_*.tar.gz - name: Upload check results if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results + name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results path: check diff --git a/DESCRIPTION b/DESCRIPTION index 57719f67..516052e5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.4.0.9056 -Date: 2021-01-03 +Version: 1.4.0.9057 +Date: 2021-01-04 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index cea1f980..7e8509a3 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.4.0.9056 -## Last updated: 3 January 2021 +# AMR 1.4.0.9057 +## 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()`): ```r diff --git a/data-raw/AMR_1.4.0.9056.tar.gz b/data-raw/AMR_1.4.0.9057.tar.gz similarity index 81% rename from data-raw/AMR_1.4.0.9056.tar.gz rename to data-raw/AMR_1.4.0.9057.tar.gz index c1c3c8fe..a9f84586 100644 Binary files a/data-raw/AMR_1.4.0.9056.tar.gz and b/data-raw/AMR_1.4.0.9057.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 923581a4..4c364517 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 01c3cc91..93db29cb 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057 diff --git a/docs/articles/index.html b/docs/articles/index.html index bc285408..ce30f144 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057 diff --git a/docs/authors.html b/docs/authors.html index f41dcaed..11961739 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057 diff --git a/docs/index.html b/docs/index.html index 4b5badce..6a843cd7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057 diff --git a/docs/news/index.html b/docs/news/index.html index a383bc88..e47eb46f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057 @@ -236,13 +236,13 @@ Source: NEWS.md -
-

-AMR 1.4.0.9056 Unreleased +
+

+AMR 1.4.0.9057 Unreleased

-
+

-Last updated: 3 January 2021 +Last updated: 4 January 2021

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 20be7fcd..1f77b335 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: 2021-01-03T22:35Z +last_built: 2021-01-04T08:49Z 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 40cb648c..5bb80701 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057

diff --git a/docs/survey.html b/docs/survey.html index b64c607b..6ee3611d 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9056 + 1.4.0.9057