Mac test fixes + pak cascade fix

DESCRIPTION

@@ -15,8 +15,8 @@ Description: A single key function, 'Require' that makes rerun-tolerant
 URL: 
     https://Require.predictiveecology.org,
     https://github.com/PredictiveEcology/Require
-Date: 2026-04-01
-Version: 1.1.0.9001
+Date: 2026-04-30
+Version: 1.1.0.9030
 Authors@R: c(
     person(given = "Eliot J B",
            family = "McIntire",
@@ -37,6 +37,7 @@ Depends:
 Imports:
     data.table (>= 1.10.4),
     methods,
+    pak,
     sys,
     tools,
     utils
@@ -47,7 +48,6 @@ Suggests:
     fpCompare,
     gitcreds,
     httr,
-    pak,
     parallel,
     rematch2,
     rmarkdown,

R/Require-helpers.R

@@ -411,8 +411,78 @@ installedVers <- function(pkgDT, libPaths, standAlone = FALSE) {
   }
 
   installed <- !is.na(pkgDT$Version)
-  if (any(installed)) {
-    set(pkgDT, NULL, "installed", installed)
+  set(pkgDT, NULL, "installed", installed)
+  pkgDT
+}
+
+# When a package is already loaded in the current R session with a version
+# that satisfies the user's version constraint, mark it as installed so the
+# downstream gate skips reinstall. Trying to upgrade a loaded package whose
+# namespace is imported by another loaded package (e.g. `reproducible` ->
+# `climateData`) is the most common cause of pak's
+# "Error : ! error in pak subprocess" — pak can't unload the live namespace
+# to swap in the new version, the subprocess aborts, and the user is left
+# with a useless generic error. If the loaded version already meets the
+# requested constraint, there is no reason to reinstall in the first place.
+#
+# Side-effect: also flags `loadedSufficient = TRUE` so doLoads() can attach
+# via `require(x, character.only = TRUE)` without `lib.loc`, avoiding R's
+# "cannot be unloaded because <X> is imported by <Y>" error path.
+useLoadedIfSufficient <- function(pkgDT,
+                                  libPaths = .libPaths(),
+                                  standAlone = FALSE,
+                                  verbose = getOption("Require.verbose")) {
+  if (!NROW(pkgDT)) return(pkgDT)
+  if (!"needInstall" %in% names(pkgDT)) return(pkgDT)
+  candidates <- which(pkgDT[["needInstall"]] %in% .txtInstall)
+  if (!length(candidates)) return(pkgDT)
+  loaded <- loadedNamespaces()
+  loaded <- setdiff(loaded, .basePkgs)
+  if (!length(loaded)) return(pkgDT)
+  if (!"loadedSufficient" %in% names(pkgDT))
+    set(pkgDT, NULL, "loadedSufficient", FALSE)
+  # standAlone = TRUE means the user wants the package physically present in
+  # libPaths[1]; a namespace loaded from another library does NOT satisfy that.
+  effectiveLibPaths <- if (isTRUE(standAlone))
+    normPath(libPaths[1L]) else normPath(libPaths)
+  intercepted <- character(0)
+  reasons <- character(0)
+  for (i in candidates) {
+    pkg <- pkgDT[["Package"]][i]
+    if (!pkg %in% loaded) next
+    loadedVer <- tryCatch(as.character(getNamespaceVersion(pkg)),
+                          error = function(e) NA_character_)
+    if (is.na(loadedVer) || !nzchar(loadedVer)) next
+    vSpec <- pkgDT[["versionSpec"]][i]
+    ineq  <- pkgDT[["inequality"]][i]
+    hasConstraint <- !is.na(vSpec) && nzchar(vSpec) &&
+                     !is.na(ineq) && nzchar(ineq)
+    if (hasConstraint) {
+      ok <- isTRUE(compareVersion2(loadedVer, vSpec, ineq))
+      if (!ok) next
+    }
+    lp <- tryCatch(dirname(system.file(package = pkg)),
+                   error = function(e) NA_character_)
+    if (!nzchar(lp)) lp <- NA_character_
+    if (!is.na(lp) && !normPath(lp) %in% effectiveLibPaths) next
+    set(pkgDT, i, "installed",          TRUE)
+    set(pkgDT, i, "installedVersionOK", TRUE)
+    set(pkgDT, i, "needInstall",        .txtDontInstall)
+    set(pkgDT, i, "Version",            loadedVer)
+    if (!is.na(lp)) set(pkgDT, i, "LibPath", lp)
+    set(pkgDT, i, "loadedSufficient",   TRUE)
+    intercepted <- c(intercepted, pkg)
+    reasons <- c(reasons,
+                 if (hasConstraint)
+                   paste0(pkg, " ", loadedVer, " satisfies ", ineq, " ", vSpec)
+                 else
+                   paste0(pkg, " ", loadedVer, " (no version constraint)"))
+  }
+  if (length(intercepted)) {
+    messageVerbose(
+      "Already loaded with sufficient version, skipping reinstall: ",
+      paste(unique(reasons), collapse = "; "),
+      verbose = verbose, verboseLevel = 1)
   }
   pkgDT
 }

R/RequireOptions.R

@@ -84,9 +84,11 @@ RequireOptions <- function() {
       "terra",
       "units"
     ), # c("raster", "s2", "sf", "sp", "units")
+    Require.snapshotInstaller = "pak",
+    Require.snapshotInstallerUsePPM = TRUE,
     Require.standAlone = TRUE,
     Require.useCranCache = FALSE,
-    Require.usePak = FALSE,
+    Require.usePak = TRUE,
     Require.updateRprofile = FALSE,
     Require.verbose = 1
   )

R/extract.R

@@ -50,9 +50,20 @@ extractPkgName <- function(pkgs, filenames) {
 #' ))
 extractVersionNumber <- function(pkgs, filenames) {
   if (!missing(pkgs)) {
-    hasVersionNum <- grepl(grepExtractPkgs, pkgs, perl = FALSE)
-    out <- rep(NA, length(pkgs))
-    out[hasVersionNum] <- gsub(grepExtractPkgs, "\\2", pkgs[hasVersionNum], perl = FALSE)
+    ## Strip pak's source prefixes (any::, cran::, github::, url::) before
+    ## attempting version extraction; without this an "any::pkg@ver" ref
+    ## doesn't match either form.
+    pkgsBare <- sub("^[A-Za-z][A-Za-z0-9+.-]*::", "", pkgs)
+    hasVersionNum <- grepl(grepExtractPkgs, pkgsBare, perl = FALSE)
+    out <- rep(NA, length(pkgsBare))
+    out[hasVersionNum] <- gsub(grepExtractPkgs, "\\2", pkgsBare[hasVersionNum], perl = FALSE)
+    ## Also handle pak's "pkg@ver" form -- skip GitHub refs (owner/repo@sha)
+    ## by requiring no "/" in the part before "@".
+    if (isTRUE(getOption("Require.usePak", FALSE))) {
+      atForm <- is.na(out) & grepl("@", pkgsBare, fixed = TRUE) &
+        !grepl("/", sub("@.*$", "", pkgsBare), fixed = TRUE)
+      out[atForm] <- sub("^[^@]+@", "", pkgsBare[atForm])
+    }
   } else {
     if (!missing(filenames)) {
       fnsSplit <- strsplit(basename(filenames), "_")
@@ -115,12 +126,27 @@ trimVersionNumber <- function(pkgs) {
   if (!is.null(pkgs)) {
     nas <- is.na(pkgs)
     if (any(!nas)) {
+      ## Strip pak source prefixes first (any::, cran::, etc.) so the bare
+      ## name matches downstream string ops (installed.packages() rownames,
+      ## pkg_history lookups). Leave url:: alone -- those callers usually
+      ## want the URL preserved.
+      hasPrefix <- grepl("^[A-Za-z][A-Za-z0-9+.-]*::", pkgs[!nas]) &
+        !startsWith(pkgs[!nas], "url::")
+      pkgs[!nas][hasPrefix] <- sub("^[A-Za-z][A-Za-z0-9+.-]*::", "", pkgs[!nas][hasPrefix])
       ew <- endsWith(pkgs[!nas], ")")
-      if (getOption("Require.usePak", FALSE))
-        ew <- ew | grepl("@", pkgs[!nas])
       if (any(ew)) {
         pkgs[!nas][ew] <- gsub(paste0("\n|\t|", .grepVersionNumber), "", pkgs[!nas][ew])
       }
+      ## pak "pkg@ver" form. Skip GitHub refs (owner/repo@sha) by requiring
+      ## no "/" before the "@". Only active when usePak so non-pak callers
+      ## keep their existing behavior.
+      if (isTRUE(getOption("Require.usePak", FALSE))) {
+        atForm <- grepl("@", pkgs[!nas], fixed = TRUE) &
+          !grepl("/", sub("@.*$", "", pkgs[!nas]), fixed = TRUE)
+        if (any(atForm)) {
+          pkgs[!nas][atForm] <- sub("@.+$", "", pkgs[!nas][atForm])
+        }
+      }
     }
     pkgs
   }

R/helpers.R

@@ -640,8 +640,13 @@ SysInfo <-
 }
 
 .runLongExamples <- function() {
-  .isDevelVersion() ||
-    Sys.getenv("R_REQUIRE_RUN_ALL_EXAMPLES") == "true"
+  # Auto-enable based on .isDevelVersion() is unsafe: with
+  # `--run-dontrun --run-donttest` (default in r-lib/actions/check-r-package),
+  # every dev-version R CMD check runs the full Require::Install() cascade
+  # for every example in Require.Rd — hours on a cold CI runner.
+  # Require explicit opt-in (R_REQUIRE_RUN_ALL_EXAMPLES=true) regardless of
+  # version. Devs can set it in .Renviron locally.
+  Sys.getenv("R_REQUIRE_RUN_ALL_EXAMPLES") == "true"
 }
 
 doCranCacheCheck <- function(localFiles, verbose = getOption("Require.verbose")) {