diff --git a/.github/workflows/check-old.yaml b/.github/workflows/check-old.yaml index d87d2b9f..1773e16c 100644 --- a/.github/workflows/check-old.yaml +++ b/.github/workflows/check-old.yaml @@ -52,7 +52,7 @@ jobs: - {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - + env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} @@ -105,7 +105,7 @@ jobs: rm DESCRIPTION mv DESCRIPTION2 DESCRIPTION shell: bash - + - name: Run R CMD check if: always() env: @@ -129,7 +129,7 @@ jobs: R CMD check --as-cran --no-manual --run-donttest --run-dontrun AMR_*.tar.gz shell: bash - - name: Show unit tests output + - name: Show tinytest output if: always() run: | cd ../AMR.Rcheck diff --git a/.github/workflows/check-recent.yaml b/.github/workflows/check-recent.yaml index 053ff003..415f5fd6 100644 --- a/.github/workflows/check-recent.yaml +++ b/.github/workflows/check-recent.yaml @@ -56,12 +56,12 @@ jobs: - {os: macOS-latest, r: 'devel', allowfail: false} - {os: windows-latest, r: 'devel', allowfail: false} - {os: ubuntu-latest, r: 'devel', allowfail: false} - + # current 'release' version: - {os: macOS-latest, r: '4.2', allowfail: false} - {os: windows-latest, r: '4.2', allowfail: false} - {os: ubuntu-latest, r: '4.2', allowfail: false} - + # older versions (see also check-old.yaml for even older versions): - {os: ubuntu-latest, r: '4.1', allowfail: false} - {os: ubuntu-latest, r: '4.0', allowfail: false} @@ -96,3 +96,10 @@ jobs: # during 'R CMD check', R_LIBS_USER will be overwritten, so: R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} R_RUN_TINYTEST: true + + - name: Show tinytest output + if: always() + run: | + cd ../AMR.Rcheck + find . -name 'tinytest.Rout*' -exec cat '{}' \; ||> + shell: bash diff --git a/DESCRIPTION b/DESCRIPTION index 785be4a2..3ccd371c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9080 +Version: 1.8.2.9081 Date: 2023-01-05 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 7fe9060a..cf241734 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9080 +# AMR 1.8.2.9081 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* diff --git a/R/sysdata.rda b/R/sysdata.rda index e7d3d6f9..0788095e 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/man/g.test.Rd b/man/g.test.Rd index 940bc86e..5081cc04 100644 --- a/man/g.test.Rd +++ b/man/g.test.Rd @@ -21,7 +21,7 @@ g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE) \item{y}{a numeric vector; ignored if \code{x} is a matrix. If \code{x} is a factor, \code{y} should be a factor of the same length.} -\item{p}{a vector of probabilities of the same length of \code{x}. +\item{p}{a vector of probabilities of the same length as \code{x}. An error is given if any entry of \code{p} is negative.} \item{rescale.p}{a logical scalar; if TRUE then \code{p} is rescaled