(v1.6.0.9035) unit tests

.github/workflows/check.yaml

@@ -108,20 +108,20 @@ jobs:
         run: |
           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
 
-      - name: Update package dependencies
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-20
+          restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-20
+
+      - name: Update AMR package dependencies
         run: |
           install.packages("data-raw/AMR_latest.tar.gz")
           source("data-raw/_install_deps.R")
         shell: Rscript {0}
         
-      - name: Cache R packages
-        # if: runner.os != 'Windows'
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }} # -${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}
-
       - name: Session info
         run: |
           options(width = 100)
@@ -161,10 +161,10 @@ jobs:
           R CMD check AMR --no-manual --no-vignettes
         shell: bash
 
-      - name: Show testthat output
+      - name: Show unit tests output
         if: always()
         run: |
-          find . -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload check results

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9032
+Version: 1.6.0.9035
 Date: 2021-05-15
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9032
+# `AMR` 1.6.0.9035
 ## <small>Last updated: 15 May 2021</small>
 
 ### New

data-raw/_install_deps.R

@@ -31,7 +31,7 @@ to_update <- as.data.frame(old.packages(), stringsAsFactors = FALSE)
 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),
-           message = function(m) invisible(),
+           # message = function(m) invisible(),
            warning = function(w) message(w$message),
            error = function(e) message(e$message))
 }
@@ -39,7 +39,7 @@ for (i in seq_len(length(to_install))) {
 for (i in seq_len(length(to_update))) {
   cat("Updating package", to_install[i], "\n")
   tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
-           message = function(m) invisible(),
+           # message = function(m) invisible(),
            warning = function(w) message(w$message),
            error = function(e) message(e$message))
 }

tests/tinytest.R

@@ -25,6 +25,8 @@
 
 # test only on GitHub Actions and at home - not on CRAN as tests are lengthy
 if (identical(Sys.getenv("R_TINYTEST"), "true")) {
+  print(.libPaths())
+  print(as.data.frame(utils::installed.packages())[, "Version", drop = FALSE])
   library(tinytest)
   library(AMR)
   test_package("AMR")