diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index ca8c18a6..bc030010 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -102,12 +102,13 @@ jobs: shell: Rscript {0} - name: Query dependencies + if: matrix.config.r != '3.0' run: | saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - name: Cache R packages - if: runner.os != 'Windows' + if: runner.os != 'Windows' && matrix.config.r != '3.0' # && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' uses: actions/cache@v1 with: @@ -145,7 +146,8 @@ jobs: _R_CHECK_LENGTH_1_LOGIC2_: verbose run: | tar -xf data-raw/AMR_latest.tar.gz - R CMD check AMR -no-manual -as-cran + rm -rf AMR/vignettes + R CMD check AMR shell: bash - name: Run R CMD check on Linux and macOS @@ -158,12 +160,15 @@ jobs: _R_CHECK_LENGTH_1_LOGIC2_: verbose run: | tar -xf data-raw/AMR_latest.tar.gz + rm -rf AMR/vignettes R CMD check AMR --no-manual --as-cran shell: bash - name: Show testthat output if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true + run: | + ls -lh + find check -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload check results diff --git a/DESCRIPTION b/DESCRIPTION index 40c53a02..4178f1d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.6.0.9025 +Version: 1.6.0.9026 Date: 2021-05-13 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index f6fd1754..82cff2bd 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.6.0.9025 +# `AMR` 1.6.0.9026 ## Last updated: 13 May 2021 ### New diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 7ae67f82..95d81af6 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 72f99453..f0391d12 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b75c1157..20d64666 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 diff --git a/docs/articles/index.html b/docs/articles/index.html index b9a4299e..eaecbb28 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 diff --git a/docs/authors.html b/docs/authors.html index ec71a7ed..8d416e49 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 diff --git a/docs/index.html b/docs/index.html index b9f99bb3..a29c7eb3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 diff --git a/docs/news/index.html b/docs/news/index.html index 964bb198..82ca8a18 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9023

+
+

+ Unreleased AMR 1.6.0.9026

Last updated: 13 May 2021 @@ -262,7 +262,7 @@
  • The documentation of the first_isolate() and key_antimicrobials() functions has been completely rewritten.
    • -
  • Added ggplot() method for resistance_predict() +
  • Added ggplot() method for resistance_predict()

    • @@ -348,7 +348,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info

    • -

  • ggplot() generics for classes <mic> and <disk>

    • +

  • ggplot() generics for classes <mic> and <disk>

  • Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:

    @@ -405,7 +405,7 @@
 
  • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
    • 
 
  • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
    • 
 
  • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
    • 
-
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    • 
+
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    •
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5e8dc398..b1e08e3f 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: 2021-05-13T17:31Z +last_built: 2021-05-13T19:15Z 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 d2aeef5d..1d602ba6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026
    diff --git a/docs/survey.html b/docs/survey.html index 5e9b786b..23412017 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9023 + 1.6.0.9026 diff --git a/tests/testthat/test-atc_online.R b/tests/testthat/test-atc_online.R index 72c67912..f014c0bf 100644 --- a/tests/testthat/test-atc_online.R +++ b/tests/testthat/test-atc_online.R @@ -27,6 +27,7 @@ context("atc_online.R") test_that("atc_online works", { skip_on_cran() + skip_if_not_installed("curl") skip_if_not(curl::has_internet()) expect_gte(length(atc_online_groups(ab_atc("AMX"))), 1)