fix: Correct Non-Numeric argument errors and Update gh-actions for compatibility

.github/workflows/R-CMD-check.yaml

@@ -13,7 +13,6 @@ name: R-CMD-check
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
-
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
@@ -30,13 +29,19 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev
 
       - name: Query dependencies
         run: |
@@ -45,28 +50,26 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Cache R packages (Linux and macOS)
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
-
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Install missing packages on Windows
+        if: runner.os == 'Windows'
+        run: |
+          install.packages(c('curl', 'openssl', 'testthat', 'hms', 'dplyr', 'rlang', 'tibble', 'progress', 'remotes', 'rcmdcheck'))
+        shell: Rscript {0}
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false

.github/workflows/test-coverage.yaml

@@ -10,15 +10,20 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev
 
       - name: Query dependencies
         run: |
@@ -28,19 +33,36 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          key: ${{ runner.os }}-R-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-R-${{ hashFiles('.github/R-version') }}-1-
 
       - name: Install dependencies
         run: |
-          install.packages(c("remotes"))
+          install.packages(c("remotes", "covr"))
           remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Check for missing packages
+        run: |
+          missing_pkgs <- setdiff(c("covr", "testthat"), rownames(installed.packages()))
+          if (length(missing_pkgs) > 0) {
+            cat("Missing packages:", paste(missing_pkgs, collapse = ", "), "\n")
+            install.packages(missing_pkgs)
+          } else {
+            cat("All required packages are installed.\n")
+          }
+        shell: Rscript {0}
+
+      - name: Run tests
+        run: |
+          testthat::test_local()
         shell: Rscript {0}
 
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

R/mx_api.R

@@ -39,12 +39,10 @@ mx_api_content <- function(from_date = "2013-01-01",
                            server = "medrxiv",
                            include_info = FALSE) {
 
-
   # Check that the user is connected to the internet
   internet_check()
 
   # Check server
-
   "%notin%" <- Negate("%in%")
 
   if (server %notin% c("medrxiv", "biorxiv")) {
@@ -56,10 +54,10 @@ mx_api_content <- function(from_date = "2013-01-01",
 
   # Get descriptive details and page number
   details_link <- api_link(server, from_date, to_date, "0")
-
   details <- api_to_df(details_link)
 
   count <- as.numeric(details$messages[1, 6])
+
   pages <- floor(count / 100)
 
   message("Estimated total number of records as per API metadata: ", count)
@@ -69,14 +67,13 @@ mx_api_content <- function(from_date = "2013-01-01",
     dplyr::filter(doi == "")
 
   # Get data
-  pb <-
-    progress::progress_bar$new(
-      format = paste0(
-        "Downloading... [:bar] :current/:total ",
-        "(:percent) Est. time remaining: :eta"
-      ),
-      total = count
-    )
+  pb <- progress::progress_bar$new(
+    format = paste0(
+      "Downloading... [:bar] :current/:total ",
+      "(:percent) Est. time remaining: :eta"
+    ),
+    total = count
+  )
 
   pb$tick(0)
 
@@ -99,12 +96,11 @@ mx_api_content <- function(from_date = "2013-01-01",
   }
 
   # Clean data
-
   message("Number of records retrieved from API: ", nrow(df))
 
-  if (nrow(df)!= count) {
+  if (nrow(df) != count) {
     message(paste0("The estimated \"total number\" as per the metadata ", #nocov
-    "can sometimes be artifically inflated."))                            #nocov
+    "can sometimes be artificially inflated."))                           #nocov
   }
 
   if (clean == TRUE) {

R/mx_crosscheck.R

@@ -16,25 +16,31 @@ mx_crosscheck <- function() {
   internet_check()
   mx_info()
 
-  # Get number of unique records in the medRxiv archive ---------------------
-
+  # Get number of unique records in the medRxiv archive
   base_link <- api_link("medrxiv", "2019-01-01", as.character(Sys.Date()), "0")
-
   details <- api_to_df(base_link)
 
-  reference <- details$messages[1, 6]
+  # Ensure 'reference' is numeric
+  reference <- as.numeric(details$messages[1, 6])
+  if (is.na(reference)) {
+    stop("Reference value is not numeric.")
+  }
 
-  # Get number of unique records extracted ----------------------------------
+  # Get number of unique records extracted
   data <- suppressMessages(mx_search(mx_snapshot(),
     query = "*",
     deduplicate = FALSE
   ))
 
-  extracted <- nrow(data)
+  # Ensure 'extracted' is numeric
+  extracted <- as.numeric(nrow(data))
+  if (is.na(extracted)) {
+    stop("Extracted value is not numeric.")
+  }
 
   diff <- reference - extracted
 
-  if (identical(reference, extracted) == TRUE) {
+  if (identical(reference, extracted)) {
     message("No records added/updated since last snapshot.") # nocov
   } else {
     message(paste0(