(v1.7.1.9046) unit tests

.github/workflows/check.yaml

@@ -77,36 +77,40 @@ jobs:
           - {os: windows-latest, r: '3.4',     allowfail: false}
           - {os: windows-latest, r: '3.3',     allowfail: false}
           - {os: windows-latest, r: '3.2',     allowfail: false}
-
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       R_REPOSITORIES: "https://cran.rstudio.com"
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    
-      R_KEEP_PKG_SOURCE: yes
-      
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
+
-          use-public-rspm: true
+      - name: Install Linux dependencies
-          
+        if: runner.os == 'Linux'
-      - name: show file list
+        # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
-        run: ls -lh
+        # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
-        shell: bash
+        # 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: |
-      - name: Install dependencies
+          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
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
+
+      - name: Unpack AMR and install R dependencies
         if: always()
         run: |
-          install.packages("remotes", repos = c("https://cloud.r-project.org", "https://cran.rstudio.com"))
+          tar -xf data-raw/AMR_latest.tar.gz
-          remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
+          Rscript -e "source('data-raw/_install_deps.R')"
-        shell: Rscript {0}
+        shell: bash
-       
+        
       - name: Show session info
         if: always()
         run: |
@@ -114,26 +118,43 @@ jobs:
           utils::sessionInfo()
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
-
+        
-      - uses: r-lib/actions/check-r-package@v1
+      # # - name: Only keep vignettes on release version
+      # - name: Remove vignettes
+      #   # if: matrix.config.r != 'release'
+      #   if: always()
+      #   # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
+      #   run: |
+      #     rm -rf AMR/vignettes
+      #     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
           _R_CHECK_DEPENDS_ONLY_: true
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
-          R_RUN_TINYTEST: true
           # 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 unit tests output
+        run: |
-        if: always()
+          R CMD check --no-manual --run-donttest --run-dontrun AMR
-        run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
-      - name: Upload check results
+      - name: Show unit tests output
         if: always()
-        uses: actions/upload-artifact@main
+        run: |
+          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload artifacts
+        if: always()
+        uses: actions/upload-artifact@v2
         with:
-          name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
+          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
-          path: check
+          path: AMR.Rcheck

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9045
+Version: 1.7.1.9046
-Date: 2021-09-29
+Date: 2021-10-03
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9045
+# `AMR` 1.7.1.9046
-## <small>Last updated: 29 September 2021</small>
+## <small>Last updated:  3 October 2021</small>
 
 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9046</span>
       </span>
     </div>
 
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">29 September 2021</h4>
+            <h4 data-toc-skip class="date">03 October 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>

docs/news/index.html

@@ -92,7 +92,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9045</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9046</span>
       </span>
     </div>
 
@@ -240,12 +240,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719045" class="section level1">
+    <div id="amr-1719046" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9045">
+<h1 class="page-header" data-toc-text="1.7.1.9046">
-<a href="#amr-1719045" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9045</h1>
+<a href="#amr-1719046" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9046</h1>
-<div id="last-updated-29-september-2021" class="section level2">
+<div id="last-updated-3-october-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>
+<a href="#last-updated-3-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 October 2021</small>
 </h2>
 <div id="breaking-changes" class="section level3">
 <h3 class="hasAnchor">

git_development.sh

@@ -127,7 +127,7 @@ echo "••••••••••••••••••••"
 echo "• Building package •"
 echo "••••••••••••••••••••"
 echo "• Building 'data-raw/AMR_latest.tar.gz'..."
-Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)"
+Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = FALSE, binary = FALSE, quiet = TRUE)"
 rm data-raw/AMR_latest.tar.gz
 mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz