working

.Rprofile

@@ -1,46 +1,87 @@
-# Use the local user's .Rprofile when interactive.
-# Good for keeping local preferences and shortcuts, but not always reproducible.
-local({
-  user_rprof <- Sys.getenv("R_PROFILE_USER", file.path(Sys.getenv("HOME"), ".Rprofile"))
-  if(interactive() && file.exists(user_rprof)) source(user_rprof)
-})
+# The .Rprofile file is loaded at the start of every R session and can be used
+# to set common options and settings. As {targets} starts a new session for each 
+# target, it should be limited to options and avoid loading packages or other
+# heavy tasks. Messages and diagnostics should be limited to interactive sessions.
+
+# ---- Function definitions ----------------------------------------------------
+local({ # Wrapping in `local()` avoids side effects or cluttering the environment
+
+  load_env <- function(
+    env_files = list.files(all.files = TRUE, pattern = "^\\.env.*"),
+    verbose = TRUE) {
+    for (f in env_files) {
+      tryCatch(
+        readRenviron(f),
+        error = function(e) {
+          if (verbose) {
+            if (isTRUE(suppressWarnings(readBin(f, "character", 2))[2] == "GITCRYPT")) {
+              message("`", f, "` is encrypted, not loading. Run `git-crypt unlock`.")
+            } else {
+              message("Error reading ", f, ": ", e$message, ". Not loading.")
+            }
+          }
+        })
+    }
+  }
+
+  # ---- Interactive-only ------------------------------------------------------
+  if (interactive()) {
+    # Source the user's .Rprofile if it exists, but other options will clobber it
+    user_rprof <- Sys.getenv("R_PROFILE_USER", normalizePath("~/.Rprofile", mustWork = FALSE))
+    if (file.exists(user_rprof) && nzchar("USE_CAPSULE")) {
+      source(user_rprof)
+    }
+    load_env(verbose = TRUE)
+
+    options(
+      renv.config.startup.quiet = FALSE,
+      renv.config.synchronized.check = TRUE,
+      renv.config.dependency.errors = "reported"
+    )
+
+    if (!nzchar("USE_CAPSULE") && requireNamespace("capsule", quietly = TRUE)) {
+      capsule::whinge()
+    }
+
 
-# Load .env environment variables
-if (file.exists(".env")) {
-  if(isTRUE(suppressWarnings(readBin(".env", "character", 2))[2] == "GITCRYPT")) {
-    message(".env file is encrypted, not reading. Use git-crypt unlock to decrypt")
+
   } else {
-    try(readRenviron(".env"))
+    # ---- Non-interactive only ------------------------------------------------
+
+    load_env(verbose = FALSE)
+    options(
+      renv.config.startup.quiet = TRUE,
+      renv.config.synchronized.check = FALSE, # Avoid the check in every sub-process
+      renv.config.dependency.errors = "ignored"
+    )
   }
-}
+
+  # ---- All sessions ----------------------------------------------------------
+  options(
+    renv.config.install.verbose = TRUE  # See what is happening when packages are installed
+  )
+
+  if (requireNamespace("renv", quietly = TRUE)) {
+    renv::settings$ignored.packages(c("ehaproj", "tflow", "fnmate"))
+  }
+
+  if (!nzchar("USE_CAPSULE")) {
+    source("renv/activate.R")
+    load_env(verbose = FALSE) # Load again because renv can clobber env vars
+  }
+
+
+})
 
-options(
-  repos = c(RSPM = "https://packagemanager.rstudio.com/all/latest",
-            CRAN = "https://cran.rstudio.com/"),
-  renv.config.auto.snapshot = TRUE, ## Attempt to keep renv.lock updated automatically
-  tidyverse.quiet = TRUE
-)
 
-# Since RSPM does not provide Mac binaries, always install packages from CRAN
-# on mac or windows, even if renv.lock specifies they came from RSPM
-if (Sys.info()[["sysname"]] %in% c("Darwin", "Windows")) {
-  options(renv.config.repos.override = c(
-    CRAN = "https://cran.rstudio.com/",
-    INLA = "https://inla.r-inla-download.org/R/testing"))
-} else if (Sys.info()[["sysname"]] == "Linux") {
-  options(renv.config.repos.override = c(
-    RSPM = "https://packagemanager.rstudio.com/all/latest",
-    INLA = "https://inla.r-inla-download.org/R/testing"))
+# ---- Startup message ---------------------------------------------------------
+if (interactive() && Sys.getenv("RSTUDIO") == "1") {
+  setHook("rstudio.sessionInit", function(newSession) {
+    if (newSession) {
+      cat("\014")
+      cat("\033[38;5;196m▃▃▃▃▃▃\033[39m\033[38;5;214m▃▃▃▃▃▃\033[39m\033[38;5;226m▃▃▃▃▃▃\033[39m\033[38;5;34m▃▃▃▃▃▃\033[39m\033[38;5;27m▃▃▃▃▃▃\033[39m\033[38;5;91m▃▃▃▃▃▃\033[39m")
+      cat("\n")
+    }
+  }, action = "append")
 }
 
-# Load the local library
-if(file.exists("renv/activate.R")) source("renv/activate.R")
-
-# If project packages have conflicts define them here, we start with common ones
-if(requireNamespace("conflicted", quietly = TRUE)) {
-  conflicted::conflict_prefer("filter", "dplyr", quiet = TRUE)
-  conflicted::conflict_prefer("count", "dplyr", quiet = TRUE)
-  conflicted::conflict_prefer("select", "dplyr", quiet = TRUE)
-  conflicted::conflict_prefer("set_names", "magrittr", quiet = TRUE)
-  conflicted::conflict_prefer("View", "utils", quiet = TRUE)
-}

.env_user

@@ -0,0 +1 @@
+USE_TARGETS=1

.github/workflows/make-targets.yml

@@ -8,30 +8,30 @@ on:
 # Alternately, for jobs such as updating dashboard, you can set a regular schedule
   #schedule:
   #  - cron: "0 8 * * *"
-      
+
 jobs:
   container-workflow-template:
     runs-on: ubuntu-latest                                # Run on GitHub Actions runner
     #runs-on: [self-hosted, linux, x64, onprem-aegypti]   # Run the workflow on EHA aegypti runner (permissions required)
     #runs-on: [self-hosted, linux, x64, onprem-prospero]  # Run the workflow on EHA prospero runner  (permissions required)
     container:
-      image: rocker/verse:4.2.1
-      
+      image: rocker/r-ver:4.2.1
+
     steps:
-    
+
     steps:
       # update to: git config --global --add safe.directory /__w/your-repo/your-repo
       - name: update permissions for container based workflows
       	run: git config --global --add safe.directory /__w/container-template/container-template
-      
+
       - uses: actions/checkout@v2
-      
+
       - name: Install system dependencies
         run: |
           apt-get update && apt-get install -y --no-install-recommends \
           libcurl4-openssl-dev \
           libssl-dev
-          
+
       - name: Install packages from renv.lock (with cache)
         if: ${{ !env.ACT }}  ## Doesn't work locally with ACT
         uses: r-lib/actions/setup-renv@v2
@@ -43,14 +43,14 @@ jobs:
         run: |
           renv::restore()
         shell: Rscript {0}
-        
+
       - name: Run targets workflow
         run: |
           targets::tar_make()
         shell: Rscript {0}
-        
+
       - name: On failure, launch a temporary interactive debugging session
         uses: mxschmitt/action-tmate@v3
         if: ${{ failure() }}
         timeout-minutes: 15
-      
+