Run in debug mode

.github/workflows/rworkflows_dev.yml

@@ -53,4 +53,5 @@ jobs:
         run_docker: ${{ true }}
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         free_diskspace: ${{ true }}
-        miniforge_variant: false
+        miniforge_variant: ${{ false }}
+        run_debug: ${{ true }}

R/dependencies_linux.R

@@ -4,7 +4,8 @@
 #' Linux OS environment.
 #' Includes all dependencies listed by \link[remotes]{system_requirements}, 
 #' in addition to user-specified dependencies via \code{extra}.
-#' @param prefix Prefix to prepend to the command.
+#' Set to \code{NULL} to return a character vector of dependencies instead.
+#' @param prefix Prefix to prepend to the command. 
 #' @param extra Additional dependencies to install.
 #' @param verbose Print messages.
 #' @inheritParams remotes::system_requirements
@@ -41,8 +42,13 @@ dependencies_linux <- function(os = "ubuntu",
                                                  os_release = os_release,
                                                  ...)
                )
-  deps <- unique(c(deps,extra))
-  cmd <- paste(prefix,paste(deps,collapse = " "))
-  messager(cmd,v=verbose)
-  cat(cmd)
+  deps <- sort(unique(c(deps,extra)))
+  #### Return ####
+  if(is.null(prefix)){
+    return(deps)
+  } else {
+    cmd <- paste(prefix,paste(deps,collapse = " ")) 
+    messager(cmd,v=verbose)
+    cat(cmd)
+  }
 }

action.yml

@@ -96,6 +96,7 @@ inputs:
       (e.g. {{ secrets.PAT_GITHUB }}) which allows access to private
       repositories. Read here for more details: 
       https://docs.github.com/en/actions/security-guides/automatic-token-authentication.
+    required: true
   cache_version: 
     description: >
       Which cache version to use. 
@@ -159,6 +160,11 @@ inputs:
     description: >
       Free up additional disk space by deleting non-essential sofwares.
     default: false
+  run_debug:
+    description: >
+      Whether to enable interactive debug mode using the
+      [tmate action](https://github.com/mxschmitt/action-tmate).
+    default: false
 
 runs:
   using: 'composite'
@@ -169,6 +175,10 @@ runs:
       with:
         github_token: ${{ inputs.GITHUB_TOKEN }}
         comment_on_pr: false
+
+    - name: 🪲 Setup interactive debugging
+      if: inputs.run_debug == 'true'
+      uses: mxschmitt/action-tmate@v3
 
     - name: 💾 Free Disk Space
       if: inputs.free_diskspace == 'true' && runner.os == 'Linux'

inst/templates/Dockerfile

@@ -10,7 +10,10 @@ RUN Rscript -e 'if(!require("remotes")) install.packages("remotes"); \
 #### --Step 3--: Install system dependencies ####
 RUN sysreqs=$(Rscript -e 'rworkflows::dependencies_linux(package="rworkflows")') && \ 
     sudo -s eval "$sysreqs"
-#### --Step 2--: Create a buildzone folder ####
+# Cleanup unnecessary apt files
+RUN apt-get clean && \ 
+    rm -rf /var/lib/apt/lists/*
+#### --Step 4--: Create a buildzone folder ####
 # BiocCheck requires the buildzone to have the same name as the R package
 ARG PKG
 RUN echo $PKG

tests/testthat/test-dependencies_linux.R

@@ -4,4 +4,8 @@ test_that("dependencies_linux works", {
     dependencies_linux(package="rworkflows")
   )
   testthat::expect_true(grepl("^apt-get update",cmd))
+
+  #### prefix=NULL ####
+  deps <- dependencies_linux(package="rworkflows", prefix=NULL)
+  testthat::expect_true(length(deps)>10)
 })