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Merged
eliotmcintire merged 2 commits into from
May 22, 2026
Merged

Better caching during installations/pkgDeps #152

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0c8b5be
fix(pak): honor type="source" in the pak path (binary-lag downgrade)
eliotmcintire May 17, 2026
8aeec57
fix(pak): make dep-resolution cache key type-aware (source vs binary)
eliotmcintire May 17, 2026
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10 changes: 6 additions & 4 deletions R/Require2.R
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Original file line number Diff line number Diff line change
Expand Up @@ -362,13 +362,13 @@ Require <- function(packages,
withCallingHandlers(
pkgDT <- pakDepsToPkgDT(packages, which = which, libPaths = libPaths,
standAlone = standAlone, verbose = verbose,
purge = purge, install = install),
purge = purge, install = install, type = type),
message = function(m) invokeRestart("muffleMessage")
)
} else {
pkgDT <- pakDepsToPkgDT(packages, which = which, libPaths = libPaths,
standAlone = standAlone, verbose = verbose,
purge = purge, install = install)
purge = purge, install = install, type = type)
}
} else if (!skipDepResolution) {
if (length(which)) {
Expand Down Expand Up @@ -480,12 +480,14 @@ Require <- function(packages,
} else {
pkgDT <- pakInstallFiltered(pkgDT, libPaths = libPaths, repos = repos,
standAlone = standAlone, verbose = verbose,
forceUpgrade = identical(install, "force"))
forceUpgrade = identical(install, "force"),
type = type)
# Invalidate the dep-tree cache: installed state changed, so the next
# call should re-resolve rather than use a stale cached result.
pakDepsCacheInvalidate(pkgsForPak = trimVersionNumber(HEADtoNone(pkgDT$packageFullName)),
wh = whichToDILES(doDeps),
repos = repos)
repos = repos,
type = type)
## Recovery: if pakInstallFiltered left any rows flagged
## .txtCouldNotBeInstalled, probe internet once. If missing,
## switch to offlineMode and retry those rows via the pak
Expand Down
58 changes: 49 additions & 9 deletions R/pak.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,22 @@ pakCall <- function(expr, verbose = getOption("Require.verbose")) {
}
}

# When the caller explicitly requested type = "source", force pak to resolve
# AND install from source only. pak ignores base R's getOption("pkgType"); its
# source-vs-binary selection is driven by pkgdepends' `platforms` config, which
# is settable from the main process via options(pkg.platforms=) (read when pak
# builds the proposal, before the subprocess is spawned). The default is
# c(<this platform>, "source"); pinning it to "source" stops pak from "keeping"
# or installing a stale CRAN binary when the source tree is newer -- the
# binary-lag downgrade where pak resolves reproducible 3.1.0 (source) but only
# the 3.0.0 binary exists on Windows/Mac, leaving the user silently downgraded.
# Returns the previous options() list for on.exit(options(old)) restoration, or
# NULL when no override was applied (caller skips the on.exit in that case).
forcePakSourceIfRequested <- function(type) {
if (!identical(type, "source")) return(NULL)
options(pkg.platforms = "source")
}

pakErrorHandling <- function(err, pkg, packages, verbose = getOption("Require.verbose")) {
grp <- c(
.txtCntInstllDep, .txtFailedToBuildSrcPkg, .txtConflictsWith,
Expand Down Expand Up @@ -1613,14 +1629,22 @@ pakWhoNeeds <- function(pkg, pak_result = NULL) {
# ---------------------------------------------------------------------------
.pakDepsCacheTTL <- 24 * 3600 # 24 hours default

pakDepsCacheKey <- function(pkgsForPak, wh, repos, userPkgs = NULL) {
pakDepsCacheKey <- function(pkgsForPak, wh, repos, userPkgs = NULL,
type = getOption("pkgType")) {
tmp <- tempfile()
on.exit(unlink(tmp), add = TRUE)
# coerce to character vectors: options(repos = list(...)) is a supported
# pattern, and sort() errors on list input with 'x must be atomic'
payload <- list(pkgs = sort(as.character(unlist(pkgsForPak, use.names = FALSE))),
wh = sort(as.character(unlist(wh))),
repos = sort(as.character(unlist(repos, use.names = FALSE))))
repos = sort(as.character(unlist(repos, use.names = FALSE))),
# Source-only resolution is a different dep-tree problem than
# binary/both: pak picks the source version (e.g. reproducible
# 3.1.0) where the binary path would "keep" the older binary
# (3.0.0). Without this, a type="source" call reuses a
# binary-era cached pak_result and the source intent is
# silently lost -- the exact binary-lag downgrade symptom.
srcOnly = isTRUE(identical(type, "source")))
# `userPkgs` (when supplied) carries the user's original version-bearing
# refs, e.g. c("stringfish (<= 0.15.8)", "qs (== 0.27.3)"). pak::pkg_deps()
# only sees `pkgsForPak` -- the version-stripped form -- so without folding
Expand All @@ -1644,10 +1668,12 @@ pakDepsCacheDir <- function() {
file.path(cacheDir(), "pak", "pkg_deps")
}

pakDepsResolve <- function(pkgsForPak, wh, repos, verbose, purge, userPkgs = NULL) {
pakDepsResolve <- function(pkgsForPak, wh, repos, verbose, purge, userPkgs = NULL,
type = getOption("pkgType")) {

# --- 1. Compute cache key ---
key <- pakDepsCacheKey(pkgsForPak, wh, repos, userPkgs = userPkgs)
key <- pakDepsCacheKey(pkgsForPak, wh, repos, userPkgs = userPkgs,
type = type)
envKey <- paste0("pakDeps_", key)
cacheDir <- pakDepsCacheDir()
cacheFile <- file.path(cacheDir, paste0(key, ".rds"))
Expand Down Expand Up @@ -1886,8 +1912,10 @@ pakDepsResolve <- function(pkgsForPak, wh, repos, verbose, purge, userPkgs = NUL
# (installed state changed; cache key stays the same but should be revalidated
# sooner than the normal TTL would allow).
# ---------------------------------------------------------------------------
pakDepsCacheInvalidate <- function(pkgsForPak, wh, repos, userPkgs = NULL) {
key <- tryCatch(pakDepsCacheKey(pkgsForPak, wh, repos, userPkgs = userPkgs),
pakDepsCacheInvalidate <- function(pkgsForPak, wh, repos, userPkgs = NULL,
type = getOption("pkgType")) {
key <- tryCatch(pakDepsCacheKey(pkgsForPak, wh, repos, userPkgs = userPkgs,
type = type),
error = function(e) NULL)
if (is.null(key)) return(invisible(NULL))
envKey <- paste0("pakDeps_", key)
Expand All @@ -1901,14 +1929,19 @@ pakDepsCacheInvalidate <- function(pkgsForPak, wh, repos, userPkgs = NULL) {
# This replaces the pkgDep() + parsePackageFullname() + ... pipeline when usePak = TRUE.
pakDepsToPkgDT <- function(packages, which, libPaths, standAlone, verbose,
purge = getOption("Require.purge", FALSE),
install = TRUE) {
install = TRUE, type = getOption("pkgType")) {
pakLoad <- tryCatch(loadNamespace("pak"),
error = function(e) e)
if (inherits(pakLoad, "error")) {
stop("Please install pak (loadNamespace('pak') failed: ",
conditionMessage(pakLoad), ")", call. = FALSE)
}

# Honour an explicit type = "source": pin pak to source-only resolution for
# the duration of this call (covers the nested pakDepsResolve/pak::pkg_deps).
oldPlatforms <- forcePakSourceIfRequested(type)
if (!is.null(oldPlatforms)) on.exit(options(oldPlatforms), add = TRUE)

# pak spawns a subprocess that inherits .libPaths(). Set .libPaths() to match
# Require's standAlone semantics before calling pak, then restore on exit.
#
Expand Down Expand Up @@ -2008,7 +2041,8 @@ pakDepsToPkgDT <- function(packages, which, libPaths, standAlone, verbose,
repos = getOption("repos"),
verbose = verbose,
purge = purge,
userPkgs = resolvedPkgs)
userPkgs = resolvedPkgs,
type = type)

if (is.null(pak_result)) {
messageVerbose("pak::pkg_deps: all strategies failed; using direct package list only.",
Expand Down Expand Up @@ -2609,9 +2643,15 @@ pakSerialInstall <- function(pkgs, lib, repos, verbose) {
# Install only the packages Require has determined need installing (needInstall == .txtInstall).
# pak is called with exact version pins or any:: to avoid re-resolving deps.
pakInstallFiltered <- function(pkgDT, libPaths, repos, standAlone, verbose,
forceUpgrade = FALSE) {
forceUpgrade = FALSE, type = getOption("pkgType")) {
if (!requireNamespace("pak", quietly = TRUE)) stop("Please install pak")

# Honour an explicit type = "source": without this, pak's install step can
# "keep" or fetch the older platform binary even after the resolve picked the
# newer source version, producing the silent binary-lag downgrade.
oldPlatforms <- forcePakSourceIfRequested(type)
if (!is.null(oldPlatforms)) on.exit(options(oldPlatforms), add = TRUE)

# Mirror the same .libPaths() logic as pakDepsToPkgDT so the install subprocess
# sees the same library set that was used for dependency resolution.
pakLib <- tryCatch(dirname(find.package("pak")), error = function(e) NULL)
Expand Down
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