fix: audit workflows

.crow/weekly-audit-missing-alpine-322-arm64.yaml

@@ -20,6 +20,8 @@ steps:
         from_secret: REPO_RO_TOKEN
       GITHUB_PAT:
         from_secret: GITHUB_PAT
+      FORGEJO_TOKEN:
+        from_secret: FORGEJO_TOKEN
       PLATFORM: alpine-322
       ARCH: arm64
       R_LIBS_USER: /mnt/cache/R-pkgs

local/weekly-missing-binaries-audit.R

@@ -38,7 +38,38 @@ cat(sprintf("Platform: %s | Arch: %s | S3 codename: %s | OS family: %s\n",
             platform, arch, s3_codename, os_family))
 
 # ---------------------------------------------------------------------------
-# 1. CRAN release packages
+# 1. Query PostgreSQL for known build failures (before s3fs init to avoid
+#    C++ pointer conflicts between s3fs/curl and RPostgres/libpq)
+# ---------------------------------------------------------------------------
+cat("Connecting to PostgreSQL...\n")
+con <- DBI::dbConnect(
+  RPostgres::Postgres(),
+  dbname   = "build_metadata",
+  host     = "r-binaries.devxy.io",
+  port     = 15432,
+  user     = "rpkgs",
+  password = Sys.getenv("PGPASS"),
+  sslmode  = "require"
+)
+
+errored_pkgs <- DBI::dbGetQuery(
+  con,
+  sprintf(
+    "SELECT name, tag FROM single_builds WHERE error_occurred = TRUE AND platform = '%s' AND arch = '%s'",
+    platform, arch
+  )
+)
+DBI::dbDisconnect(con)
+
+errored_dt <- as.data.table(errored_pkgs)
+if (nrow(errored_dt) > 0) {
+  setnames(errored_dt, c("Package", "Version"))
+  setkey(errored_dt, Package, Version)
+}
+cat(sprintf("Found %d known build failures for %s/%s\n", nrow(errored_dt), platform, arch))
+
+# ---------------------------------------------------------------------------
+# 2. CRAN release packages (uses curl internally - must come after PG)
 # ---------------------------------------------------------------------------
 cat("Fetching CRAN package database...\n")
 cran_release <- tools::CRAN_package_db()
@@ -48,7 +79,7 @@ cran_dt <- data.table(
 )
 
 # ---------------------------------------------------------------------------
-# 2. S3 tarballs
+# 3. S3 tarballs
 # ---------------------------------------------------------------------------
 cat("Connecting to S3...\n")
 s3fs::s3_file_system(
@@ -82,7 +113,7 @@ s3_dt <- data.table(
 cat(sprintf("S3 contains %d tarballs for %s/%s\n", nrow(s3_dt), arch, s3_codename))
 
 # ---------------------------------------------------------------------------
-# 3. Find missing packages (CRAN release version not in S3)
+# 4. Find missing packages (CRAN release version not in S3)
 # ---------------------------------------------------------------------------
 setkey(cran_dt, Package, Version)
 setkey(s3_dt,   Package, Version)
@@ -90,7 +121,7 @@ missing_dt <- cran_dt[!s3_dt]
 cat(sprintf("%d CRAN release packages missing from S3\n", nrow(missing_dt)))
 
 # ---------------------------------------------------------------------------
-# 4. Remove excluded packages
+# 5. Remove excluded packages
 # ---------------------------------------------------------------------------
 script_dir <- tryCatch(
   dirname(normalizePath(
@@ -114,36 +145,6 @@ if (file.exists(excluded_path)) {
   cat(sprintf("No excluded-packages.json found at %s -- skipping exclusion step\n", excluded_path))
 }
 
-# ---------------------------------------------------------------------------
-# 5. Query PostgreSQL for known build failures
-# ---------------------------------------------------------------------------
-cat("Connecting to PostgreSQL...\n")
-con <- DBI::dbConnect(
-  RPostgres::Postgres(),
-  dbname   = "build_metadata",
-  host     = "r-binaries.devxy.io",
-  port     = 15432,
-  user     = "rpkgs",
-  password = Sys.getenv("PGPASS"),
-  sslmode  = "require"
-)
-on.exit(DBI::dbDisconnect(con), add = TRUE)
-
-errored_pkgs <- DBI::dbGetQuery(
-  con,
-  sprintf(
-    "SELECT name, tag FROM single_builds WHERE error_occurred = TRUE AND platform = '%s' AND arch = '%s'",
-    platform, arch
-  )
-)
-errored_dt <- as.data.table(errored_pkgs)
-if (nrow(errored_dt) > 0) {
-  setnames(errored_dt, c("Package", "Version"))
-  setkey(errored_dt, Package, Version)
-}
-
-cat(sprintf("Found %d known build failures for %s/%s\n", nrow(errored_dt), platform, arch))
-
 # ---------------------------------------------------------------------------
 # 6. Split into rebuildable vs known failures
 # ---------------------------------------------------------------------------