dieghernan · dependabot · Oct 6, 2025 · Oct 6, 2025 · Oct 6, 2025 · Oct 6, 2025
diff --git a/.github/workflows/manual-debug.yml b/.github/workflows/manual-debug.yml
@@ -1,71 +1,61 @@
-name: manual-debug
-
-on:
-  workflow_dispatch:
-    inputs:
-      path:
-        description: |
-          Path to the R package root, if the package is not at the top level of
-          the repository.
-        default: "."
-        required: false
-        type: string
-      package:
-        description: |
-          Package to check. If provided, it would have priority over the
-          package on the repo.
-        required: false
-        default: ""
-        type: string
-      statuses:
-        description: |
-          Create an issue if one or more of the following statuses are
-          reported on the check report. This is a comma-separated string of
-          statuses. Default value is ''WARN,ERROR'. Allowed statuses are
-          'NOTE', 'WARN', and 'ERROR'.
-        default: "WARN,ERROR"
-        required: false
-        type: string
-      fail-on-error:
-        description: |
-          Logical, should the action error if CRAN checks are not ok?
-        default: "false"
-        required: false
-        type: boolean
-      create-issue:
-        description: |
-          Logical, create an issue on CRAN failed checks
-        default: "true"
-        required: false
-        type: boolean
-      issue-assignees:
-        description: |
-          Whom should the issue be assigned to if errors are
-          encountered in the CRAN status checks?
-          This is a comma-separated string of GitHub usernames.
-          If undefined or empty, no assignments are made.
-        default: ""
-        required: false
-        type: string
-
-jobs:
-  check:
-    runs-on: ubuntu-latest
-    permissions: write-all
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v5
-
-      - name: Check
-        uses: dieghernan/cran-status-check@main
-        with:
-          path: ${{ inputs.path }}
-          package: ${{ inputs.package }}
-          statuses: ${{ inputs.statuses }}
-          fail-on-error: ${{ inputs.fail-on-error }}
-          create-issue: ${{ inputs.create-issue }}
-          issue-assignees: ${{ inputs.issue-assignees }}
-
+name: manual-debug
+
+on:
+  workflow_dispatch:
+    inputs:
+      path:
+        description: |
+          Path to the R package root, if the package is not at the top level of
+          the repository.
+        default: "."
+        required: false
+        type: string
+      package:
+        description: |
+          Package to check. If provided, it would have priority over the
+          package on the repo.
+        required: false
+        default: ""
+        type: string
+      fail-on-error:
+        description: |
+          Logical, should the action error if CRAN checks are not ok?
+        default: "false"
+        required: false
+        type: boolean
+      create-issue:
+        description: |
+          Logical, create an issue on CRAN failed checks
+        default: "true"
+        required: false
+        type: boolean
+      issue-assignees:
+        description: |
+          Whom should the issue be assigned to if errors are
+          encountered in the CRAN status checks?
+          This is a comma-separated string of GitHub usernames.
+          If undefined or empty, no assignments are made.
+        default: ""
+        required: false
+        type: string
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Check
+        uses: dieghernan/cran-status-check@main
+        with:
+          path: ${{ inputs.path }}
+          package: ${{ inputs.package }}
+          fail-on-error: ${{ inputs.fail-on-error }}
+          create-issue: ${{ inputs.create-issue }}
+          issue-assignees: ${{ inputs.issue-assignees }}
+
diff --git a/action.yml b/action.yml
@@ -19,14 +19,6 @@ inputs:
     required: false
     default: ""
     type: string
-  statuses:
-    description: |
-      CRAN status to check. This is a comma-separated string of
-      statuses. Default value is ''WARN,ERROR'. Allowed statuses are
-      'NOTE', 'WARN', and 'ERROR'.
-    default: "WARN,ERROR"
-    required: false
-    type: string
   fail-on-error:
     description: |
       Logical, should the action error if CRAN checks are not ok?
@@ -48,7 +40,12 @@ inputs:
     default: ""
     required: false
     type: string
-
+  statuses:
+    description: |
+      DEPRECATED
+    default: ""
+    required: false
+    type: string
 # Workflow derived from pharmaverse/admiralci
 # See for the original work from which this workflow is derived
 # https://github.com/pharmaverse/admiralci/blob/61347fe11955297818b3ca7814fc7328f2ad7840/.github/workflows/cran-status.yml
@@ -85,7 +82,6 @@ runs:
     - name: Compute Cran Status codes
       uses: dieghernan/cran-status-check/docker@main
       with:
-        statuses: "${{ inputs.statuses }}"
         package: "${{ steps.pkg.outputs.package_name }}"
 
       # Report check
@@ -116,9 +112,9 @@ runs:
 
     - name: Report Status
       if: steps.err.outputs.error == 'true' && inputs.create-issue == 'true'
-      uses: peter-evans/create-issue-from-file@v5
+      uses: peter-evans/create-issue-from-file@v6
       with:
-        title: "URGENT! Failed CRAN Checks for ${{ steps.pkg.outputs.package_name }}: ${{ steps.today.outputs.date }}"
+        title: "URGENT! ${{ steps.pkg.outputs.package_name }} at risk on CRAN: ${{ steps.today.outputs.date }}"
         content-filepath: ././cran-status.md
         assignees: ${{ inputs.issue-assignees }}
 
@@ -127,6 +123,6 @@ runs:
       shell: bash
       run: |
         # Stop action
-        echo "::error::CRAN checks are not OK, see Job Summary of this GH action for details"
+        echo "::error::Package at risk, see Job Summary of this GH action for details"
         exit 1
 
diff --git a/docker/action.yml b/docker/action.yml
@@ -1,28 +1,16 @@
-# Workflow derived from https://github.com/pharmaverse/admiralci
-
-name: CRAN Status Check
-description: Creates a summary of issues reported on the CRAN status check page for a given R package
-
-inputs:
-  package:
-    description: |
-      Package name of the current R package deployed to CRAN
-    required: true
-    type: string
-  statuses:
-    description: |
-      Create an issue if one or more of the following
-      statuses are reported on the check report.
-      This is a comma-separated string of statuses.
-      Allowed statuses are 'NOTE', 'WARN', and 'ERROR'
-    default: 'ERROR'
-    required: false
-    type: string
-
-runs:
-  using: 'docker'
-  image: './Dockerfile'
-  args:
-    - ${{ inputs.package }}
-    - ${{ inputs.statuses }}
-
+# Workflow derived from https://github.com/pharmaverse/admiralci
+
+name: CRAN Status Check
+description: Creates a summary of issues reported on the CRAN status check page for a given R package
+
+inputs:
+  package:
+    description: |
+      Package name of the current R package deployed to CRAN
+    required: true
+    type: string
+runs:
+  using: 'docker'
+  image: './Dockerfile'
+  args:
+    - ${{ inputs.package }}
diff --git a/docker/check-status.R b/docker/check-status.R
@@ -26,11 +26,6 @@ option_list <- list(
     type = "character",
     help = "package name (REQUIRED)",
     metavar = "character"
-  ),
-  make_option(c("-s", "--statuses"),
-    type = "character", default = "ERROR,WARN,NOTE",
-    help = "status types (comma separated list, e.g. ERROR,WARN,NOTE",
-    metavar = "character"
   )
 )
 opt_parser <- OptionParser(option_list = option_list)
@@ -43,17 +38,21 @@ cran_status <- function(x) {
 
 # 2. Get Inputs ----
 pkg <- opt$package # paste(desc::desc_get(keys = "Package"))
-# Get input status
-status_types <- opt$statuses
-statuses <- unlist(strsplit(status_types, split = ","))
-
 url <- sprintf("https://cran.r-project.org/web/checks/check_results_%s.html", pkg)
 
 # 3. Tests -----
 cat("Testing package:", pkg, "\n-----\n")
-## a. Url not reachable ----
 
-if (httr::http_error(url)) {
+# Getting database
+options(repos = c(CRAN = "https://cloud.r-project.org"))
+pkg_db <- tools::CRAN_package_db() %>%
+  as_tibble() %>%
+  filter(Package == pkg)
+
+
+## a. Not in database ----
+
+if (nrow(pkg_db) == 0) {
   cat(
     paste0("::warning::Package ", pkg, " not found on CRAN.")
   )
@@ -62,41 +61,57 @@ if (httr::http_error(url)) {
     paste0(":x: **Package ", pkg, " not found on CRAN**:\n\n")
   )
 
-  cran_status(paste0("Error accessing url:\n", url))
+  cran_status(paste0("Check url:\n", url))
 
   # Copy to issue
   file.copy("cran-status.md", "issue.md")
 }
 
-## b. Found on CRAN, check issues ----
+## b. Found on CRAN, check deadline ----
 
 if (!file.exists("cran-status.md")) {
+  deadline <- pkg_db %>% pull(Deadline)
+
   scrap <- url %>%
     read_html()
 
   cranchecks <- scrap %>%
     html_element("table") %>%
     html_table()
 
-  any_error <- any(cranchecks$Status %in% statuses)
   additional <- grepl("Additional", html_text(scrap), ignore.case = TRUE)
 
-  ### i. Has issues ----
-  if (any_error) {
+  # Is on deadline?
+  is_deadline <- !is.na(deadline)
+
+  if (is_deadline) {
+    # Notify
     cran_status(sprintf(
-      ":x: **CRAN checks for %s resulted in one or more (`%s`)s**:\n\n",
+      ":x: **Package %s at risk for removal by `%s`**:\n\n",
       pkg,
-      status_types
+      deadline
     ))
-    cran_status("\nSee the table below for a summary of the checks run by CRAN:\n\n")
-    cran_status(knitr::kable(cranchecks))
+
+    cat("::warning::Package at risk for removal")
+  } else {
     cran_status(sprintf(
-      "\n\nAll details and logs are available here: %s\n\n", url
+      ":white_check_mark: **Package %s is not at risk for removal",
+      pkg
     ))
-    cat("::warning::One or more CRAN checks resulted in an invalid status\n")
+
+    cat("Package is not at risk for removal")
   }
 
-  ### ii. Has additional issues ----
+  # Additional info
+
+  # Add checks
+  cran_status("\nSee the table below for a summary of the checks run by CRAN:\n\n")
+  cran_status(knitr::kable(cranchecks))
+  cran_status(sprintf(
+    "\n\nAll details and logs are available here: %s", url
+  ))
+
+  # Additional issues
 
   if (additional) {
     cran_status(sprintf(
@@ -109,27 +124,7 @@ if (!file.exists("cran-status.md")) {
     cat(paste0("::warning::", pkg, " has Additional issues\n"))
   }
 
-  ## So far if cran-status.md exists, generate issue
-  if (file.exists("cran-status.md")) file.copy("cran-status.md", "issue.md")
-
-  ### iii. All OK ----
-  # If no issue has been generated
 
-  if (!file.exists("cran-status.md")) {
-    cat(
-      sprintf("None of this status found in the CRAN table. (status=%s)", status_types)
-    )
-
-    cran_status(sprintf(
-      ":white_check_mark: **CRAN error for %s not found with (`%s`)s**:\n\n",
-      pkg,
-      status_types
-    ))
-
-    cran_status("\nSee the table below for a summary of the checks run by CRAN:\n\n")
-    cran_status(knitr::kable(cranchecks))
-    cran_status(sprintf(
-      "\n\nAll details and logs are available here: %s", url
-    ))
-  }
+  # Prepare the issue
+  if (is_deadline) file.copy("cran-status.md", "issue.md")
 }
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
@@ -1,2 +1,2 @@
 #!/usr/bin/env bash
-Rscript /app/check-status.R -p "${INPUT_PACKAGE}" -s "${INPUT_STATUSES}"
+Rscript /app/check-status.R -p "${INPUT_PACKAGE}"