diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index f32a98e4..1b735ad5 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -57,25 +57,33 @@ jobs: - {os: windows-latest, r: 'devel', allowfail: true} - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - # these are the current release of R - - {os: macOS-latest, r: 'release', allowfail: false} - - {os: windows-latest, r: 'release', allowfail: false} - - {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - # these are the previous release of R - - {os: macOS-latest, r: 'oldrel', allowfail: false} - - {os: windows-latest, r: 'oldrel', allowfail: false} - - {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - # test against all released versions of R >= 3.0, we support them all! + # test all systems against all released versions of R >= 3.0, we support them all! + - {os: macOS-latest, r: '4.1', allowfail: false} + - {os: windows-latest, r: '4.1', allowfail: false} - {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '4.0', allowfail: false} + - {os: windows-latest, r: '4.0', allowfail: false} - {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.6', allowfail: false} + - {os: windows-latest, r: '3.6', allowfail: false} - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.5', allowfail: false} + - {os: windows-latest, r: '3.5', allowfail: false} - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.4', allowfail: false} + - {os: windows-latest, r: '3.4', allowfail: false} - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.3', allowfail: false} + - {os: windows-latest, r: '3.3', allowfail: false} - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.2', allowfail: false} + - {os: windows-latest, r: '3.2', allowfail: false} - {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.1', allowfail: false} + - {os: windows-latest, r: '3.1', allowfail: false} - {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '3.0', allowfail: false} + - {os: windows-latest, r: '3.0', allowfail: false} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: @@ -163,5 +171,5 @@ jobs: if: always() uses: actions/upload-artifact@v2 with: - name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }} + name: artifacts-r-${{ matrix.config.r }}-${{ matrix.config.os }} path: AMR.Rcheck diff --git a/DESCRIPTION b/DESCRIPTION index 6d0273a5..2f273501 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.7.1.9003 -Date: 2021-06-14 +Version: 1.7.1.9004 +Date: 2021-06-15 Title: Antimicrobial Resistance Data Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index dbf01028..68e8bca0 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9003 -## Last updated: 14 June 2021 +# `AMR` 1.7.1.9004 +## Last updated: 15 June 2021 ### Changed * Added more antibiotic class selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()` diff --git a/R/mo.R b/R/mo.R index 804263dc..9bcdee85 100755 --- a/R/mo.R +++ b/R/mo.R @@ -2048,15 +2048,11 @@ parse_and_convert <- function(x) { x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]] } } - x_class <- class(x) - x <- as.character(x) - x[is.null(x)] <- NA - parsed <- iconv(x, to = "UTF-8") + parsed <- iconv(as.character(x), to = "UTF-8") parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT") parsed <- gsub('"', "", parsed, fixed = TRUE) parsed <- gsub(" +", " ", parsed, perl = TRUE) parsed <- trimws(parsed) - class(parsed) <- x_class parsed }, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)` parsed diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 09022039..328e744a 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 1c20f110..a8039e26 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index ee2efb42..36fbf52a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 766be8e5..3a85c03f 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004 @@ -192,7 +192,7 @@

Data sets for download / own use

-

14 June 2021

+

15 June 2021

Source: vignettes/datasets.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 0cde0e7d..b1c2cc15 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004
diff --git a/docs/authors.html b/docs/authors.html index 3046f59d..865cc4a8 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004 diff --git a/docs/index.html b/docs/index.html index cd49a985..e45f10f1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004 diff --git a/docs/news/index.html b/docs/news/index.html index da14c8df..a7fb950b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004 @@ -236,12 +236,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9003

-
+
+

+ Unreleased AMR 1.7.1.9004

+

-Last updated: 14 June 2021 +Last updated: 15 June 2021

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c0dcb1fb..e4790d59 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: 2021-06-14T20:36Z +last_built: 2021-06-15T08:50Z 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 431c240c..ffbd55b0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004

diff --git a/docs/survey.html b/docs/survey.html index 9616b05c..10de0e0c 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9003 + 1.7.1.9004