diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index df7ddcd9..07053e51 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -128,18 +128,6 @@ jobs: as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - # - name: Only keep vignettes on release version - - name: Remove vignettes - # if: matrix.config.r != 'release' - if: always() - # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite - run: | - rm -rf AMR/vignettes - Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')" - rm AMR/DESCRIPTION - mv AMR/DESCRIPTION2 AMR/DESCRIPTION - shell: bash - - name: Run R CMD check if: always() env: diff --git a/DESCRIPTION b/DESCRIPTION index 573a6c00..27a19207 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.7.1.9038 -Date: 2021-09-01 +Version: 1.7.1.9039 +Date: 2021-09-03 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 29c592e8..295ae5fe 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9038 -## Last updated: 1 September 2021 +# `AMR` 1.7.1.9039 +## Last updated: 3 September 2021 ### Breaking changes * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 77b33e0a..37a3fa0d 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index f81cd642..6017af9c 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9038 + 1.7.1.9039 @@ -190,7 +190,7 @@ @@ -240,12 +240,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9038

-
+
+

+ Unreleased AMR 1.7.1.9039

+

-Last updated: 1 September 2021 +Last updated: 3 September 2021

diff --git a/inst/tinytest/test-ab_class_selectors.R b/inst/tinytest/test-ab_class_selectors.R index 2f9aadee..e00b07dc 100644 --- a/inst/tinytest/test-ab_class_selectors.R +++ b/inst/tinytest/test-ab_class_selectors.R @@ -56,6 +56,7 @@ expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5) expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5) +expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5) # filter using any() or all() expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5) diff --git a/tests/tinytest.R b/tests/tinytest.R index 074ebc99..f381561f 100644 --- a/tests/tinytest.R +++ b/tests/tinytest.R @@ -34,13 +34,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) { "inst/tinytest", "tinytest"), verbose = 99, - pattern = "first.*\\.[rR]$", color = FALSE) cat("SUMMARY:\n") print(summary(out)) cat("WARNINGS:\n") print(warnings()) cat(attributes(out)$duration, "\n") - } }