diff --git a/.github/workflows/check-pr.yaml b/.github/workflows/check-pr.yaml index 2299ac1e..c4a0dfde 100644 --- a/.github/workflows/check-pr.yaml +++ b/.github/workflows/check-pr.yaml @@ -33,8 +33,8 @@ name: R-code-check-PR jobs: R-code-check-PR: # do not run if we are the authors - the other checks will already run - if: ${{ github.event.comment.author_association }} != 'MEMBER' && ${{ github.event.comment.author_association }} != 'OWNER' - + if: ${{ github.event.comment.author_association }} != 'CONTRIBUTOR' && ${{ github.event.comment.author_association }} != 'MEMBER' && ${{ github.event.comment.author_association }} != 'OWNER' && ${{ github.context.payload.comment.author_association }} != 'CONTRIBUTOR' && ${{ github.context.payload.comment.author_association }} != 'MEMBER' && ${{ github.context.payload.comment.author_association }} != 'OWNER' + runs-on: ${{ matrix.config.os }} continue-on-error: ${{ matrix.config.allowfail }} @@ -55,7 +55,7 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes - + steps: - uses: actions/checkout@v3 diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 0d9fcb58..989df794 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -151,19 +151,9 @@ jobs: find . -name 'tinytest.Rout*' -exec cat '{}' \; || true shell: bash - - name: Show dir - continue-on-error: true - if: always() - run: | - echo ${GITHUB_WORKSPACE} - echo "---" - ls ${GITHUB_WORKSPACE} - echo "---" - ls ${GITHUB_WORKSPACE}.Rcheck - - name: Upload artifacts if: always() uses: actions/upload-artifact@v2 with: name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }} - path: /home/runner/work/AMR/AMR.Rcheck + path: ${GITHUB_WORKSPACE}.Rcheck diff --git a/DESCRIPTION b/DESCRIPTION index 9d70bf38..7e60fe1e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.1.9064 +Version: 1.8.1.9065 Date: 2022-09-23 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index fcd4ab27..891bbac2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.1.9064 +# AMR 1.8.1.9065 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/mo.R b/R/mo.R index 8300b245..4c914f13 100755 --- a/R/mo.R +++ b/R/mo.R @@ -852,7 +852,7 @@ trimws2 <- function(x) { } parse_and_convert <- function(x) { - if (tryCatch(is.character(x) && Encoding(x) == "unknown", error = function(e) FALSE)) { + if (tryCatch(is.character(x) && all(Encoding(x) == "unknown", na.rm = TRUE), error = function(e) FALSE)) { return(x) } tryCatch( diff --git a/R/zzz.R b/R/zzz.R index 88e42763..1e03f862 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -25,7 +25,6 @@ # set up package environment, used by numerous AMR functions pkg_env <- new.env(hash = FALSE) -pkg_env$mo_failed <- character(0) pkg_env$mo_uncertainties <- data.frame( uncertainty = integer(0), input = character(0), diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R index 2475aa98..30ae419a 100644 --- a/inst/tinytest/test-mo.R +++ b/inst/tinytest/test-mo.R @@ -225,7 +225,6 @@ expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN") # check old names expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT") -print(mo_renamed()) expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT")) expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")