(v1.6.0.9058) unit tests

.github/workflows/codecovr.yaml

@@ -43,39 +43,40 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: release
           
       - uses: r-lib/actions/setup-pandoc@master
 
-      - name: Query dependencies
+      - name: Restore cached R packages
-        run: |
+        # this step will add the step 'Post Restore cached R packages' on a succesful run
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          key: macOS-latest-r-release-v4
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Install dependencies
+      - name: Unpack AMR and install R dependencies
         run: |
-          install.packages(c("remotes", "tinytest"))
+          tar -xf data-raw/AMR_latest.tar.gz
-          remotes::install_deps(dependencies = TRUE)
+          Rscript -e "source('data-raw/_install_deps.R')"
-          remotes::install_cran("covr")
+          Rscript -e "install.packages('covr')"
-          remotes::install_local("data-raw/AMR_latest.tar.gz")
+        shell: bash
+        
+      - name: Show session info
+        run: |
+          options(width = 100)
+          utils::sessionInfo()
+          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
       - name: Test coverage
         run: |
           library(AMR)
           library(tinytest)
-          source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
+          source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
-          test_files <- list.files("inst/tinytest", full.names = TRUE)
+          test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
           cov <- covr::file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
-          attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
+          attr(cov, which = "package") <- list(path = "AMR") # until https://github.com/r-lib/covr/issues/478 is solved
           covr::codecov(cov, quiet = FALSE)
         shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9056
+Version: 1.6.0.9058
-Date: 2021-05-21
+Date: 2021-05-22
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.6.0.9056
+# `AMR` 1.6.0.9058
-## <small>Last updated: 21 May 2021</small>
+## <small>Last updated: 22 May 2021</small>
 
 ### Breaking change
 * All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.

data-raw/_install_deps.R

@@ -25,17 +25,15 @@
 
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.2.4.patched.tar.gz")
+install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
 
-descr <- readLines("AMR/DESCRIPTION")
+pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
-pkg_suggests <- gsub(".*Suggests: (.*)*?[A-Z].*", "\\1", paste0(descr, "*", collapse = ""), perl = FALSE)
-pkg_suggests <- unlist(strsplit(pkg_suggests, "[,* ]"))
-pkg_suggests <- pkg_suggests[pkg_suggests != ""]
 cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
 
 to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
-to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
+if (length(to_install) == 0) {
-to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
+  message("Nothing to install")
-
+}
 for (i in seq_len(length(to_install))) {
   cat("Installing package", to_install[i], "\n")
   tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
@@ -44,6 +42,11 @@ for (i in seq_len(length(to_install))) {
            error = function(e) message(e$message))
 }
 
+to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
+to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
+if (length(to_update) == 0) {
+  message("Nothing to update")
+}
 for (i in seq_len(length(to_update))) {
   cat("Updating package", to_update[i], "\n")
   tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -39,7 +39,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 
@@ -192,7 +192,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 class="date">21 May 2021</h4>
+            <h4 class="date">22 May 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>

docs/articles/index.html

@@ -81,7 +81,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 
@@ -236,12 +236,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609056" class="section level1">
+    <div id="amr-1609058" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9056">
+<h1 class="page-header" data-toc-text="1.6.0.9058">
-<a href="#amr-1609056" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9056</h1>
+<a href="#amr-1609058" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9058</h1>
-<div id="last-updated-21-may-2021" class="section level2">
+<div id="last-updated-22-may-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-21-may-2021" class="anchor"></a><small>Last updated: 21 May 2021</small>
+<a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small>
 </h2>
 <div id="breaking-change" class="section level3">
 <h3 class="hasAnchor">

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-21T18:27Z
+last_built: 2021-05-22T06:56Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </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">1.6.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
       </span>
     </div>