Merge branch 'develop' into master

.Rprofile

@@ -1,3 +1 @@
-# renv::settings$ignored.packages(c("devtools", "Covid19Mirai"), persist = FALSE)
 source("renv/activate.R")
-

.github/workflows/ci-cd.yml

@@ -55,6 +55,10 @@ jobs:
       - name: Activate renv and restore packages with cache
         uses: r-lib/actions/setup-renv@v2
 
+      # - name: Install renv Development tools
+      #   run: renv::install()
+      #   shell: Rscript {0}
+
       - name: Fetch and rebuild latest data
         if: github.event_name == 'schedule'
         run: |

DESCRIPTION

@@ -38,7 +38,6 @@ Imports:
     scales,
     COVID19,
     grDevices,
-    pkgload,
     rlang,
     zoo
 Encoding: UTF-8
@@ -47,6 +46,7 @@ RoxygenNote: 7.2.3
 Suggests: 
     rsconnect,
     spelling,
+    pkgload,
     testthat (>= 3.0.0),
     sf,
     packrat

deploy/deploy-shinyapps.R

@@ -7,13 +7,12 @@ rsconnect::setAccountInfo(
 )
 
 # to be added since rsconnect >1
-options(rsconnect.packrat = FALSE)
+options(rsconnect.packrat = TRUE)
 
 rsconnect::deployApp(
   account = "miraisolutions",
   appName = "covid19",
-  forceUpdate = TRUE, # to be added since rsconnect >1
-  quarto = FALSE # to be added since rsconnect >1
+  forceUpdate = TRUE # to be added since rsconnect >1
   # exclude hidden files and renv directory (if present)
   # appFiles = setdiff(list.files(), "renv")
 )

renv/activate.R

@@ -2,12 +2,27 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.0"
+  version <- "1.0.2"
   attr(version, "sha") <- NULL
 
   # the project directory
   project <- getwd()
 
+  # use start-up diagnostics if enabled
+  diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+  if (diagnostics) {
+    start <- Sys.time()
+    profile <- tempfile("renv-startup-", fileext = ".Rprof")
+    utils::Rprof(profile)
+    on.exit({
+      utils::Rprof(NULL)
+      elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+      writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+      writeLines(sprintf("- Profile: %s", profile))
+      print(utils::summaryRprof(profile))
+    }, add = TRUE)
+  }
+
   # figure out whether the autoloader is enabled
   enabled <- local({
 
@@ -504,7 +519,7 @@ local({
 
     # open the bundle for reading
     # We use gzcon for everything because (from ?gzcon)
-    # > Reading from a connection which does not supply a ‘gzip’ magic
+    # > Reading from a connection which does not supply a 'gzip' magic
     # > header is equivalent to reading from the original connection
     conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
     on.exit(close(conn))
@@ -767,10 +782,12 @@ local({
   renv_bootstrap_validate_version <- function(version, description = NULL) {
 
     # resolve description file
-    description <- description %||% {
-      path <- getNamespaceInfo("renv", "path")
-      packageDescription("renv", lib.loc = dirname(path))
-    }
+    #
+    # avoid passing lib.loc to `packageDescription()` below, since R will
+    # use the loaded version of the package by default anyhow. note that
+    # this function should only be called after 'renv' is loaded
+    # https://github.com/rstudio/renv/issues/1625
+    description <- description %||% packageDescription("renv")
 
     # check whether requested version 'version' matches loaded version of renv
     sha <- attr(version, "sha", exact = TRUE)
@@ -841,7 +858,7 @@ local({
     hooks <- getHook("renv::autoload")
     for (hook in hooks)
       if (is.function(hook))
-        tryCatch(hook(), error = warning)
+        tryCatch(hook(), error = warnify)
 
     # load the project
     renv::load(project)
@@ -982,10 +999,15 @@ local({
 
   }
 
-  renv_bootstrap_version_friendly <- function(version, sha = NULL) {
+  renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
     sha <- sha %||% attr(version, "sha", exact = TRUE)
-    parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L)))
-    paste(parts, collapse = " ")
+    parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+    paste(parts, collapse = "")
+  }
+
+  renv_bootstrap_exec <- function(project, libpath, version) {
+    if (!renv_bootstrap_load(project, libpath, version))
+      renv_bootstrap_run(version, libpath)
   }
 
   renv_bootstrap_run <- function(version, libpath) {
@@ -1017,6 +1039,14 @@ local({
     commandArgs()[[1]] == "RStudio"
   }
 
+  # Used to work around buglet in RStudio if hook uses readline
+  renv_bootstrap_flush_console <- function() {
+    tryCatch({
+      tools <- as.environment("tools:rstudio")
+      tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
+    }, error = function(cnd) {})
+  }
+
   renv_json_read <- function(file = NULL, text = NULL) {
 
     jlerr <- NULL
@@ -1155,25 +1185,15 @@ local({
   # construct full libpath
   libpath <- file.path(root, prefix)
 
-  # attempt to load
-  if (renv_bootstrap_load(project, libpath, version))
-    return(TRUE)
-
   if (renv_bootstrap_in_rstudio()) {
+    # RStudio only updates console once .Rprofile is finished, so
+    # instead run code on sessionInit
     setHook("rstudio.sessionInit", function(...) {
-      renv_bootstrap_run(version, libpath)
-
-      # Work around buglet in RStudio if hook uses readline
-      tryCatch(
-        {
-          tools <- as.environment("tools:rstudio")
-          tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
-        },
-        error = function(cnd) {}
-      )
+      renv_bootstrap_exec(project, libpath, version)
+      renv_bootstrap_flush_console()
     })
   } else {
-    renv_bootstrap_run(version, libpath)
+    renv_bootstrap_exec(project, libpath, version)
   }
 
   invisible()