fix(patches): add rstan entry to skip removed tbb_stddef.h

StanHeaders' init_threadpool_tbb.hpp unconditionally includes the legacy
<tbb/tbb_stddef.h> for TBB version detection, but that header was removed
in oneTBB 2021+ (the version StanHeaders now bundles), so rstan's Module.cpp
fails to compile when rstan is pulled in as a transitive dependency (e.g. of
ctsem).

Pre-define TBB_INTERFACE_NEW via CPPFLAGS so the header's own guard skips the
removed include and selects the modern tbb/global_control.h + tbb/task_arena.h
path that the bundled TBB provides. Preserve -I/usr/local/include since the
CPPFLAGS override replaces the R default.

.crow/build-all-versions-install-deps.yaml

@@ -4,7 +4,7 @@
 # they are merged with build-all-versions' identical declarations.
 variables:
   target_arch:
-    description: "Architecture to build."
+    description: 'Architecture to build.'
     options:
       - amd64
       - arm64
@@ -27,7 +27,7 @@ variables:
       - "noble"
     default: "3.24"
   R_VERSION:
-    description: "Primary R version under /opt/R."
+    description: 'Primary R version under /opt/R.'
     options:
       - 4.5.3
       - 4.4.3
@@ -74,6 +74,10 @@ steps:
     commands:
       # one-time full wipe to fix corrupted .so files from previous failed builds
       # - rm -rf /mnt/cache/R-pkgs
+      # Clear churny pkgcache metadata left by a prior crashed run (the "patched"
+      # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
+      # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs.
+      - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
       # Pin the same bincraft version the build steps use, so the precomputed

.crow/build-all-versions.yaml

@@ -5,7 +5,7 @@
 # Skip list lives in local/excluded-packages.json (read by local/build-all.R).
 variables:
   target_arch:
-    description: "Architecture to build."
+    description: 'Architecture to build.'
     options:
       - amd64
       - arm64
@@ -31,7 +31,7 @@ variables:
       - "resolute"
     default: "3.24"
   R_VERSION:
-    description: "Primary R version under /opt/R."
+    description: 'Primary R version under /opt/R.'
     options:
       - 4.5.3
       - 4.4.3
@@ -116,6 +116,11 @@ steps:
       - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
     commands:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
+      # Clear churny pkgcache metadata left by a prior crashed run (the "patched"
+      # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
+      # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs. Within-run
+      # growth is bounded separately by trim_pkgcache_metadata() in build-all.R.
+      - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
       - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # The primary pass must not rely on build-all-versions-install-deps having
       # run on *this* agent: depends_on only orders the steps, but the cache

docker/buildkitd.toml

@@ -0,0 +1,41 @@
+# BuildKit GC config for the remote buildx builders (artemis/amd64, gaia/arm64).
+#
+# Apply when creating the docker-container builders:
+#   docker buildx create --name artemis --driver docker-container \
+#     --config docker/buildkitd.toml ssh://<user@host-amd64>
+#   docker buildx create --name gaia    --driver docker-container \
+#     --config docker/buildkitd.toml ssh://<user@host-arm64>
+#
+# Why: BuildKit's default GC caps the ephemeral cache tier — RUN
+# --mount=type=cache mounts, local build context, git checkouts — at a
+# hardcoded 512 MB (shown as "488.3 MiB" in `buildx inspect`). Across our
+# 7-distro build matrix that fills instantly and forces re-downloads of
+# system + R packages every rebuild. The first rule below raises that tier.
+#
+# Limits are absolute (not %) on purpose: artemis and gaia have very
+# different free space (Hetzner ~42 GiB free vs Mac mini ~279 GiB), so a
+# percentage would mean wildly different real budgets. minFreeSpace = 20 GB
+# keeps the tight Hetzner host safe while staying modest on the Mac mini.
+
+[worker.oci]
+  gc = true
+
+  # Tier 1 — ephemeral caches (cache mounts, local context, git checkouts).
+  # Raised from the 512 MB default to 8 GB, retained for 7 days so weekly
+  # rebuilds reuse downloaded packages instead of re-fetching them.
+  [[worker.oci.gcpolicy]]
+    filters = [
+      "type==source.local",
+      "type==exec.cachemount",
+      "type==source.git.checkout",
+    ]
+    keepDuration = "168h"
+    maxUsedSpace = "8GB"
+
+  # Tier 2 — everything else (image layers, RUN exec results). Bounds the
+  # whole buildkit cache and always leaves 20 GB free on the host disk.
+  [[worker.oci.gcpolicy]]
+    all = true
+    reservedSpace = "2GB"
+    maxUsedSpace = "40GB"
+    minFreeSpace = "20GB"

justfile

@@ -10,8 +10,10 @@
 #   - buildx builders named `artemis` (amd64) and `gaia` (arm64), created with the
 #     docker-container driver (runs BuildKit on the remote host's docker daemon over
 #     SSH). The default `remote` driver does NOT work with an ssh:// docker host.
-#       docker buildx create --name artemis --driver docker-container ssh://<user@host-amd64>
-#       docker buildx create --name gaia    --driver docker-container ssh://<user@host-arm64>
+#     Pass --config docker/buildkitd.toml so BuildKit's GC keeps a usable cache
+#     (the default caps the cache-mount tier at 512 MB, forcing re-downloads).
+#       docker buildx create --name artemis --driver docker-container --config docker/buildkitd.toml ssh://<user@host-amd64>
+#       docker buildx create --name gaia    --driver docker-container --config docker/buildkitd.toml ssh://<user@host-arm64>
 #   - exported secrets: B2_S3_ACCESS_KEY, B2_S3_SECRET_KEY, PGPASS (GITHUB_PAT optional)
 #
 # Overridable (env or `just VAR=… rebuild …`):

local/build-all.R

@@ -64,10 +64,13 @@ sprintf("# of package versions for this job: %s", nrow(chunk))
 exclude <- jsonlite::fromJSON("local/excluded-packages.json")[["package"]]
 chunk <- chunk[!chunk$Package %in% exclude, ]
 
-# Skip package versions already built in a previous run.
+# Skip package versions already attempted in a previous run (built or errored).
 # pkgs_to_build.rds is a static snapshot from the install-deps step, so on a
 # restart it still lists everything an interrupted run already produced. The
 # metadata DB reflects that progress, so we re-derive the remaining set here.
+# We exclude *all* attempted versions, not just successful ones: a previously
+# errored version is skipped by build_binary_package() anyway, so leaving it in
+# the chunk only makes the job cycle through it one-by-one for no benefit.
 # Derive platform + arch from the running container, mirroring the codename ->
 # platform mapping bincraft uses internally. The OS/OS_VERSION selectors are
 # workflow-level CI variables that are not injected into the container
@@ -104,13 +107,13 @@ con <- DBI::dbConnect(
 )
 built <- DBI::dbGetQuery(
   con,
-  "SELECT name, tag FROM single_builds WHERE platform = $1 AND arch = $2 AND error_occurred = FALSE",
+  "SELECT name, tag FROM single_builds WHERE platform = $1 AND arch = $2",
   params = list(platform, arch)
 )
 DBI::dbDisconnect(con)
 before <- nrow(chunk)
 chunk <- chunk[!paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag), ]
-sprintf("Skipped %d already-built package versions; %d remaining for this job", before - nrow(chunk), nrow(chunk))
+sprintf("Skipped %d already-attempted package versions; %d remaining for this job", before - nrow(chunk), nrow(chunk))
 
 # Read pre-computed S3 listing from install-deps step
 # This avoids loading s3fs/reticulate/Python in the build container,
@@ -119,6 +122,10 @@ s3_cache <- readRDS("/mnt/cache/packages/s3_cache.rds")
 sprintf("S3 cache: %s files", length(s3_cache))
 
 n <- nrow(chunk)
+# Every `trim_every` packages, bound the pkgcache _metadata dir so a full-platform
+# run does not accumulate thousands of ~70 MB snapshots and fill the host disk.
+# No-op on amd64 (R_PKG_CACHE_DIR is empty / cache not persisted).
+trim_every <- 25L
 mapply(
   function(pkg, ver, sens, i) {
     cat(sprintf("[%d/%d] %s_%s (r_minor_sensitive=%s)\n", i, n, pkg, ver, sens))
@@ -144,6 +151,12 @@ mapply(
       upload = TRUE,
       store_build_metadata = TRUE
     )
+    if (i %% trim_every == 0L) {
+      removed <- trim_pkgcache_metadata()
+      if (removed > 0L) {
+        cat(sprintf("  [pkgcache trim] removed %d stale _metadata entries\n", removed))
+      }
+    }
   },
   chunk$Package,
   chunk$Version,

local/patches/fs/force-vendored-libuv.patch

@@ -0,0 +1,19 @@
+diff --git a/configure b/configure
+--- a/configure
++++ b/configure
+@@ -11,6 +11,15 @@
+ PKG_TEST_HEADER="<uv.h>"
+ PKG_LIBS="-luv"
+ 
++# bincraft patch: force the vendored static libuv so the resulting binary
++# is self-contained. fs configure otherwise links system libuv whenever
++# pkg-config finds libuv-devel (installed as a build-time sysreq), yielding
++# an fs.so with NEEDED libuv.so.1 that fails to dyn.load on machines lacking
++# runtime libuv (install.packages/renv do not install SystemRequirements).
++echo "Building static libuv (bincraft: forced vendored)" 1>&2
++cp -f src/Makevars.vendor src/Makevars
++exit 0
++
+ # Use pkg-config if available
+ if [ `command -v pkg-config` ]; then
+   PKGCONFIG_CFLAGS=`pkg-config --cflags --silence-errors ${PKG_CONFIG_NAME}`

local/patches/registry.json

@@ -8,5 +8,27 @@
     "makevars": {},
     "patch": "RcppParallel/disable-tbb.patch",
     "reason": "bundled Intel TBB build hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604); patch unsets USE_TBB and forces -DRCPP_PARALLEL_USE_TBB=0 so RcppParallel skips the bundled build and uses the TinyThread backend"
+  },
+  {
+    "package": "fs",
+    "versions": "*",
+    "platforms": ["*"],
+    "env": {},
+    "configure_args": [],
+    "makevars": {},
+    "patch": "fs/force-vendored-libuv.patch",
+    "reason": "fs 2.x configure links system libuv whenever pkg-config finds libuv-devel (installed as a build-time sysreq), producing an fs.so with NEEDED libuv.so.1. That binary fails to dyn.load on consumer machines lacking runtime libuv, because install.packages/renv do not install SystemRequirements (only pak does, and only in the build container). The patch short-circuits configure to copy src/Makevars.vendor and build the bundled static libuv (needs cmake) so the binary is self-contained on every platform. An env/pkg-config override was tried first but the rebuilt binary still linked libuv.so.1, so a source patch is used instead."
+  },
+  {
+    "package": "rstan",
+    "versions": "*",
+    "platforms": ["*"],
+    "env": {},
+    "configure_args": [],
+    "makevars": {
+      "CPPFLAGS": "-DTBB_INTERFACE_NEW -I/usr/local/include"
+    },
+    "patch": null,
+    "reason": "StanHeaders' init_threadpool_tbb.hpp unconditionally includes the legacy <tbb/tbb_stddef.h> (removed in oneTBB 2021+) for version detection, breaking compilation of Module.cpp against the bundled oneTBB. Pre-defining TBB_INTERFACE_NEW skips that include and selects the modern tbb/global_control.h + tbb/task_arena.h path that the bundled TBB provides (-I/usr/local/include preserves the default CPPFLAGS the override replaces)"
   }
 ]

local/r-minor-helpers.R

@@ -31,3 +31,42 @@ parse_build_args <- function(args) {
     ncpus = as.integer(pos[3L])
   )
 }
+
+# Bound the {pkgcache} metadata dir, which otherwise grows without limit: the
+# "patched" repo mints a new content hash on every PACKAGES change, so each build
+# writes a fresh ~70 MB _metadata/pkgs-<hash>.rds (+ patched-<hash>/) that is
+# never reused. Keep the `keep` newest entries by mtime; only remove entries
+# older than `min_age_secs`, so a concurrent split-job's in-flight files are
+# never deleted (each build uses a unique hash, so aged entries are
+# unreferenced). Stable repo dirs (CRAN-*, BioC*, INLA-*) and pkg/ downloads are
+# not matched and thus preserved. Returns the number of entries removed.
+trim_pkgcache_metadata <- function(cache_dir = Sys.getenv("R_PKG_CACHE_DIR"),
+                                   keep = 20L,
+                                   min_age_secs = 600) {
+  meta <- file.path(cache_dir, "R", "pkgcache", "_metadata")
+  if (!nzchar(cache_dir) || !dir.exists(meta)) {
+    return(0L)
+  }
+  entries <- c(
+    Sys.glob(file.path(meta, "patched-*")),
+    Sys.glob(file.path(meta, "pkgs-*.rds"))
+  )
+  if (length(entries) == 0L) {
+    return(0L)
+  }
+  info <- file.info(entries)
+  order_new_first <- order(info$mtime, decreasing = TRUE)
+  ranked <- entries[order_new_first]
+  ranked_mtime <- info$mtime[order_new_first]
+  if (length(ranked) <= keep) {
+    return(0L)
+  }
+  candidates <- ranked[(keep + 1L):length(ranked)]
+  candidate_age <- as.numeric(Sys.time()) - as.numeric(ranked_mtime[(keep + 1L):length(ranked)])
+  removable <- candidates[candidate_age >= min_age_secs]
+  if (length(removable) == 0L) {
+    return(0L)
+  }
+  unlink(removable, recursive = TRUE, force = TRUE)
+  length(removable)
+}

local/tests/test-trim-pkgcache.R

@@ -0,0 +1,68 @@
+source(file.path("..", "r-minor-helpers.R"))
+
+# Build a fake _metadata dir under a temp R_PKG_CACHE_DIR. Each entry's mtime is
+# set to `age_secs` in the past so we can exercise the age gate deterministically.
+make_meta <- function(patched = 0L, pkgs = 0L, keep_repos = TRUE, age_secs = 3600) {
+  root <- tempfile("pkgcache-")
+  meta <- file.path(root, "R", "pkgcache", "_metadata")
+  dir.create(meta, recursive = TRUE)
+  old <- Sys.time() - age_secs
+  mk_dir <- function(p) { dir.create(p); Sys.setFileTime(p, old); p }
+  mk_file <- function(p) { writeLines("x", p); Sys.setFileTime(p, old); p }
+  for (i in seq_len(patched)) mk_dir(file.path(meta, sprintf("patched-%03d", i)))
+  for (i in seq_len(pkgs)) mk_file(file.path(meta, sprintf("pkgs-%03d.rds", i)))
+  if (keep_repos) {
+    mk_dir(file.path(meta, "CRAN-075c426938"))
+    mk_dir(file.path(meta, "BioCsoft-1ac964ed6c"))
+    mk_file(file.path(meta, "bioc-sysreqs.dcf.gz"))
+    mk_dir(file.path(root, "R", "pkgcache", "pkg")) # downloads, must survive
+  }
+  root
+}
+
+n_churn <- function(root) {
+  meta <- file.path(root, "R", "pkgcache", "_metadata")
+  length(Sys.glob(file.path(meta, "patched-*"))) +
+    length(Sys.glob(file.path(meta, "pkgs-*.rds")))
+}
+
+test_that("empty cache_dir is a no-op", {
+  expect_identical(trim_pkgcache_metadata("", keep = 5L, min_age_secs = 0), 0L)
+})
+
+test_that("missing _metadata dir is a no-op", {
+  expect_identical(
+    trim_pkgcache_metadata(tempfile("absent-"), keep = 5L, min_age_secs = 0),
+    0L
+  )
+})
+
+test_that("fewer than keep entries removes nothing", {
+  root <- make_meta(patched = 2L, pkgs = 2L)
+  expect_identical(trim_pkgcache_metadata(root, keep = 20L, min_age_secs = 0), 0L)
+  expect_identical(n_churn(root), 4L)
+})
+
+test_that("trims down to keep newest, leaving churn == keep", {
+  root <- make_meta(patched = 30L, pkgs = 30L) # 60 churn entries, all old
+  removed <- trim_pkgcache_metadata(root, keep = 20L, min_age_secs = 0)
+  expect_identical(removed, 40L)
+  expect_identical(n_churn(root), 20L)
+})
+
+test_that("entries younger than min_age_secs are protected", {
+  root <- make_meta(patched = 30L, pkgs = 0L, keep_repos = FALSE, age_secs = 60)
+  # keep=5 would drop 25, but all are 60s old < 600s gate -> nothing removed
+  expect_identical(trim_pkgcache_metadata(root, keep = 5L, min_age_secs = 600), 0L)
+  expect_identical(n_churn(root), 30L)
+})
+
+test_that("stable repo dirs and pkg downloads are never touched", {
+  root <- make_meta(patched = 30L, pkgs = 30L)
+  trim_pkgcache_metadata(root, keep = 0L, min_age_secs = 0)
+  meta <- file.path(root, "R", "pkgcache", "_metadata")
+  expect_true(dir.exists(file.path(meta, "CRAN-075c426938")))
+  expect_true(dir.exists(file.path(meta, "BioCsoft-1ac964ed6c")))
+  expect_true(file.exists(file.path(meta, "bioc-sysreqs.dcf.gz")))
+  expect_true(dir.exists(file.path(root, "R", "pkgcache", "pkg")))
+})