(v1.6.0.9044) betalactams() selector

.github/workflows/check.yaml

@@ -97,8 +97,9 @@ jobs:
         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
+        # 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
+          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
 
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
@@ -109,10 +110,7 @@ jobs:
           key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
 
       - name: Install AMR and tinytest and update dependencies
-        # some old R instances have trouble installing tinytest, so we ship it too
         run: |
-          install.packages("data-raw/AMR_latest.tar.gz")
-          trimws <- AMR:::trimws; install.packages("data-raw/tinytest_1.2.4.tar.gz")
           source("data-raw/_install_deps.R")
         shell: Rscript {0}
         
@@ -122,26 +120,16 @@ jobs:
           utils::sessionInfo()
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
-
-      - name: Run R CMD check on Windows
-        if: runner.os == 'Windows'
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-          _R_CHECK_DEPENDS_ONLY_: true
-          _R_CHECK_LENGTH_1_CONDITION_: verbose
-          _R_CHECK_LENGTH_1_LOGIC2_: verbose
-          # 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: Unpack shipped version and remove vignettes
+        if: always()
         run: |
           tar -xf data-raw/AMR_latest.tar.gz
           rm -rf AMR/vignettes
-          R CMD check AMR
+          Rscript -e "writeLines(readLines('DESCRIPTION')[!grepl('VignetteBuilder', readLines('DESCRIPTION'))], 'DESCRIPTION')"
         shell: bash
-
-      - name: Run R CMD check on Linux and macOS
-        if: runner.os != 'Windows'
+        
+      - name: Run R CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_FORCE_SUGGESTS_: false
@@ -152,9 +140,7 @@ jobs:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
           R_RUN_TINYTEST: true
         run: |
-          tar -xf data-raw/AMR_latest.tar.gz
-          rm -rf AMR/vignettes
-          R CMD check AMR --no-manual --no-vignettes
+          R CMD check --no-manual --no-vignettes AMR
         shell: bash
 
       - name: Show unit tests output