diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b1721fda..09b504cf 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -116,7 +116,7 @@ coverage: script: - apt-get install --yes git # install missing and outdated packages - - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' + - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE)' # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd - Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov', exclusions = c('R/atc_online.R', 'R/mo_source.R', 'R/resistance_predict.R')); cat('Code coverage:', covr::percent_coverage(cc))" coverage: '/Code coverage: \d+\.\d+/' diff --git a/DESCRIPTION b/DESCRIPTION index 7278687f..9c3addf1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.7.1.9019 -Date: 2019-07-30 +Version: 0.7.1.9020 +Date: 2019-08-03 Title: Antimicrobial Resistance Analysis Authors@R: c( person( diff --git a/NEWS.md b/NEWS.md index e29e9c86..a66cba0f 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9019 +# AMR 0.7.1.9020 ### Breaking * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. diff --git a/appveyor.yml b/appveyor.yml index 920694a4..f82022c8 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -39,7 +39,7 @@ environment: GCC_PATH: mingw_64 WARNINGS_ARE_ERRORS: 1 PKGTYPE: win.binary - USE_RTOOLS: true + # USE_RTOOLS: true matrix: - R_VERSION: release diff --git a/codecov.yml b/codecov.yml index 50a3f625..40a77d53 100644 --- a/codecov.yml +++ b/codecov.yml @@ -18,3 +18,4 @@ coverage: ignore: - "R/atc_online.R" - "R/mo_source.R" + - "R/resistance_predict.R" diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d1e9c8df..afc950b3 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9019 + 0.7.1.9020 diff --git a/docs/articles/index.html b/docs/articles/index.html index e2bc89d3..3d0cdfde 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9019 + 0.7.1.9020 diff --git a/docs/authors.html b/docs/authors.html index e6be7ac4..afd686da 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9019 + 0.7.1.9020 diff --git a/docs/index.html b/docs/index.html index e1e50d79..4424837a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.7.1.9019 + 0.7.1.9020 diff --git a/docs/news/index.html b/docs/news/index.html index dd3e3c42..3f979420 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9019 + 0.7.1.9020 @@ -225,9 +225,9 @@ -
+

-AMR 0.7.1.9019 Unreleased +AMR 0.7.1.9020 Unreleased

@@ -1198,7 +1198,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.7.1.9019
    • +
  • 0.7.1.9020
  • 0.7.1
  • 0.7.0
  • 0.6.1
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index 7675812b..cf06cb79 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9019 + 0.7.1.9020