fixes

.github/workflows/check-pr.yaml

@@ -33,7 +33,7 @@ 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 }}
 

.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

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9064
+Version: 1.8.1.9066
 Date: 2022-09-23
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.1.9064
+# AMR 1.8.1.9066
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

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(

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),

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")
 
@@ -308,8 +307,6 @@ expect_equal(
   rep("UNKNOWN", 3)
 )
 
-expect_null(mo_failures())
-
 expect_error(translate_allow_uncertain(5))
 
 # debug mode

tests/tinytest.R

@@ -38,11 +38,25 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
     set_AMR_locale("English")
     # get dir.exists(), trimws() and strrep() if on old R
     if (getRversion() < "3.2.0") {
+      anyNA <- AMR:::anyNA
       dir.exists <- AMR:::dir.exists
+      file.size <- AMR:::file.size
+      file.mtime <- AMR:::file.mtime
+      isNamespaceLoaded <- AMR:::isNamespaceLoaded
+      lengths <- AMR:::lengths
     }
     if (getRversion() < "3.3.0") {
-      trimws <- AMR:::trimws
       strrep <- AMR:::strrep
+      trimws <- AMR:::trimws
+    }
+    if (getRversion() < "3.4.2") {
+      isFALSE <- AMR:::isFALSE
+    }
+    if (getRversion() < "3.6.0") {
+      str2lang <- AMR:::str2lang
+    }
+    if (getRversion() < "4.0.0") {
+      deparse1 <- AMR:::deparse1
     }
     # start the unit tests
     out <- test_package("AMR",