(v1.6.0.9050) printing NA in custom_eucast_rules()

.github/workflows/check.yaml

@@ -96,7 +96,7 @@ jobs:
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
         # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
-        # we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
+        # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
         # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
         run: |
           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
@@ -109,29 +109,33 @@ jobs:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
 
-      - name: Install AMR and tinytest and update dependencies
+      - name: Unpack AMR and install R dependencies
+        if: always()
         run: |
+          tar -xf data-raw/AMR_latest.tar.gz
           source("data-raw/_install_deps.R")
         shell: Rscript {0}
         
       - name: Show session info
+        if: always()
         run: |
           options(width = 100)
           utils::sessionInfo()
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
         
-      - name: Unpack shipped version and remove vignettes
-        if: always()
+      - name: Only keep vignettes on release version
+        if: matrix.config.r != 'release'
+        # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
         run: |
-          tar -xf data-raw/AMR_latest.tar.gz
           rm -rf AMR/vignettes
-          Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION')"
-          Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[gsub(' +', '', readLines('AMR/DESCRIPTION')) != ''], 'AMR/DESCRIPTION')"
-          find AMR -name 'DESCRIPTION' -exec cat '{}' \; || true
+          Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
+          rm AMR/DESCRIPTION
+          mv AMR/DESCRIPTION2 AMR/DESCRIPTION
         shell: bash
         
       - name: Run R CMD check
+        if: always()
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_FORCE_SUGGESTS_: false
@@ -142,7 +146,7 @@ jobs:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
           R_RUN_TINYTEST: true
         run: |
-          R CMD check --no-manual --no-vignettes --no-build-vignettes --ignore-vignettes AMR
+          R CMD check --no-manual AMR
         shell: bash
 
       - name: Show unit tests output