style: apply air and prettier formatting repo-wide

.crow/archive-missed-packages.yaml

@@ -6,7 +6,6 @@ when:
   - event: cron
     cron: archive-missed-packages
 
-
 matrix:
   include:
     - CODENAME: jammy

.crow/build-all-versions-amd64.yaml

@@ -39,7 +39,7 @@ depends_on:
 
 steps:
   - name: 'Build binaries'
-    image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}"
+    image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
     pull: true
     environment:
       RED_HAT_DEV_PW:
@@ -57,7 +57,7 @@ steps:
       # normal env vars
       GIT_USER: pat-s
       # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
-      R_PKG_CACHE_DIR: ""
+      R_PKG_CACHE_DIR: ''
       R_LIBS_USER: /mnt/cache/R-pkgs
       CCACHE_DIR: /mnt/cache/ccache
       NCPUS: 2

.crow/build-all-versions-arm64.yaml

@@ -54,7 +54,7 @@ depends_on:
 
 steps:
   - name: 'Build binaries'
-    image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}"
+    image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
     pull: true
     environment:
       RED_HAT_DEV_PW:

local/archive-missed-pkgs.R

@@ -11,16 +11,34 @@ s3fs::s3_file_system(
 arch = "arm64"
 os = "alpine321"
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib", arch, os))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib",
+  arch,
+  os
+))
 length(unique(sapply(strsplit(basename(files), "_"), function(x) x[1])))
-non_archived = unique(sapply(strsplit(basename(files), "_"), function(x) x[1])[duplicated(sapply(strsplit(basename(files), "_"), function(x) x[1]))])
+non_archived = unique(sapply(strsplit(basename(files), "_"), function(x) {
+  x[1]
+})[duplicated(sapply(strsplit(basename(files), "_"), function(x) x[1]))])
 # RInno is not built because it only exists for Windows
 non_archived = setdiff(non_archived, "RInno")
 # future::plan("sequential", workers = 8)
 future::plan("sequential", workers = 1)
 # future.apply::future_lapply(non_archived, function(x) archive_package(x, codename = os, arch = arch))
-lapply(non_archived, function(x) archive_package(x, codename = os, arch = arch, s3_region = "hel1", s3_endpoint = "https://hel1.your-objectstorage.com", s3_bucket = "devxy-r-package-binaries-hel1", s3_access_key_id = Sys.getenv("HETZNER_S3_ACCESS_KEY_K3S", s3_secret_access_key = Sys.getenv("HETZNER_S3_SECRET_KEY_K3S"))))
+lapply(non_archived, function(x) {
+  archive_package(
+    x,
+    codename = os,
+    arch = arch,
+    s3_region = "hel1",
+    s3_endpoint = "https://hel1.your-objectstorage.com",
+    s3_bucket = "devxy-r-package-binaries-hel1",
+    s3_access_key_id = Sys.getenv(
+      "HETZNER_S3_ACCESS_KEY_K3S",
+      s3_secret_access_key = Sys.getenv("HETZNER_S3_SECRET_KEY_K3S")
+    )
+  )
+})
 # archive_package()
 
-
 # grep("duckdb_", files, value = T)

local/check-NA.R

@@ -1,4 +1,3 @@
-
 ### Scope: Check whether there are any incomplete entries in PACKAGES.rds. These will result in NA when calling available.packages()
 foo = available.packages("https://cran.devxy.io/amd64/jammy/latest/src/contrib")
 sum((is.na(foo[, "Version"])))
@@ -17,7 +16,9 @@ foo = available.packages("https://cran.devxy.io/amd64/rhel9/latest/src/contrib")
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
-foo = available.packages("https://cran.devxy.io/amd64/alpine320/latest/src/contrib")
+foo = available.packages(
+  "https://cran.devxy.io/amd64/alpine320/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
@@ -40,6 +41,8 @@ foo = available.packages("https://cran.devxy.io/arm64/rhel9/latest/src/contrib")
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
-foo = available.packages("https://cran.devxy.io/arm64/alpine320/latest/src/contrib")
+foo = available.packages(
+  "https://cran.devxy.io/arm64/alpine320/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))

local/debug-packages-writing.R

@@ -2,42 +2,58 @@ library(future)
 future::plan(multisession)
 future::plan(sequential)
 time = Sys.time()
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib/Archive"), recurse = T)
+files <- s3fs::s3_dir_ls(
+  sprintf(
+    "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib/Archive"
+  ),
+  recurse = T
+)
 Sys.time() - time
 
 
-
 archive <- llply(dirs, function(dir) {
-  files <- list.files(dir, recursive = FALSE, full.names = TRUE, pattern = "*.tar.gz")
+  files <- list.files(
+    dir,
+    recursive = FALSE,
+    full.names = TRUE,
+    pattern = "*.tar.gz"
+  )
   if (length(files) == 0) {
     print(paste0("Error: Empty directory: ", dir))
     return(NULL)
   }
   info <- file.info(files)
 
-  tryCatch({
+  tryCatch(
+    {
       rownames(info) <- paste0(basename(dirname(files)), "/", basename(files))
-  }, error = function(e) {
+    },
+    error = function(e) {
       print(paste0("Error: Exception catched for Archived directory: ", dir))
       print(e)
       return(NULL)
-  })
+    }
+  )
 
   info
 })
 
-tryCatch({
+tryCatch(
+  {
     rownames(info) <- paste0(basename(dirname(files)), "/", basename(files))
-}, error = function(e) {
+  },
+  error = function(e) {
     print(paste0("Error: Exception catched for Archived directory: ", dir))
     print(e)
     return(NULL)
-})
+  }
+)
 
 
-
+curl::curl_download(
-
+  "https://cran.devxy.io/amd64/rhel9/latest/src/contrib/PACKAGES.db",
-curl::curl_download("https://cran.devxy.io/amd64/rhel9/latest/src/contrib/PACKAGES.db", "PACKAGES.db")
+  "PACKAGES.db"
+)
 con = DBI::dbConnect(RSQLite::SQLite(), "PACKAGES.db")
 df = DBI::dbReadTable(con, "packages")
 
@@ -50,6 +66,14 @@ which(grepl("digest", df$Package))
 system("cat /tmp/PACKAGES | grep '^Package: digest' | wc -l")
 
 
-curl::curl_fetch_memory("https://cloud.r-project.org/src/contrib/Meta/archive.rds")
+curl::curl_fetch_memory(
-remotes = readRDS(url("https://cloud.r-project.org/src/contrib/Meta/archive.rds", "rb"))
+  "https://cloud.r-project.org/src/contrib/Meta/archive.rds"
-packages = readRDS(url("https://cran.devxy.io/arm64/noble/latest/src/contrib/PACKAGES.rds", "rb"))
+)
+remotes = readRDS(url(
+  "https://cloud.r-project.org/src/contrib/Meta/archive.rds",
+  "rb"
+))
+packages = readRDS(url(
+  "https://cran.devxy.io/arm64/noble/latest/src/contrib/PACKAGES.rds",
+  "rb"
+))

local/detect-duplicates.R

@@ -37,10 +37,13 @@ future.apply::future_lapply(
     files <- s3fs::s3_dir_ls(
       sprintf(
         "devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib",
-        arch, codename
+        arch,
+        codename
       )
     )
-    if (length(files) == 0) return(NULL)
+    if (length(files) == 0) {
+      return(NULL)
+    }
     files_b <- basename(files)
     pkg_names <- sapply(strsplit(files_b, "_"), `[`, 1)
     dupes <- unique(pkg_names[duplicated(pkg_names)])

local/fetch-rebuild-packages-from-issue.R

@@ -7,9 +7,15 @@ arch         <- Sys.getenv("ARCH")
 token <- Sys.getenv("FORGEJO_TOKEN")
 output_file <- Sys.getenv("REBUILD_PKG_LIST", "/tmp/rebuild_pkgs.txt")
 
-if (nchar(platform) == 0) stop("PLATFORM env var is not set")
+if (nchar(platform) == 0) {
-if (nchar(arch)     == 0) stop("ARCH env var is not set")
+  stop("PLATFORM env var is not set")
-if (nchar(token)    == 0) stop("FORGEJO_TOKEN env var is not set")
+}
+if (nchar(arch) == 0) {
+  stop("ARCH env var is not set")
+}
+if (nchar(token) == 0) {
+  stop("FORGEJO_TOKEN env var is not set")
+}
 
 os_family <- if (grepl("^ubuntu", platform)) {
   "Ubuntu"
@@ -21,12 +27,16 @@ os_family <- if (grepl("^ubuntu", platform)) {
   platform
 }
 
-issue_title <- sprintf("Missing package binaries for latest version (%s)", os_family)
+issue_title <- sprintf(
+  "Missing package binaries for latest version (%s)",
+  os_family
+)
 cat(sprintf("Searching for issue: %s\n", issue_title))
 
 search_url <- sprintf(
   "%s/repos/%s/issues?type=issues&state=open&q=%s&limit=50",
-  forgejo_base, repo,
+  forgejo_base,
+  repo,
   utils::URLencode(issue_title, reserved = TRUE)
 )
 search_resp <- request(search_url) |>
@@ -34,7 +44,9 @@ search_resp <- request(search_url) |>
   req_perform()
 
 issues <- resp_body_json(search_resp, simplifyVector = FALSE)
-match_idx <- which(vapply(issues, function(x) x$title, character(1)) == issue_title)
+match_idx <- which(
+  vapply(issues, function(x) x$title, character(1)) == issue_title
+)
 
 if (length(match_idx) == 0) {
   cat("No matching issue found - nothing to rebuild\n")
@@ -55,7 +67,10 @@ lines <- strsplit(body, "\n", fixed = TRUE)[[1]]
 plat_header <- sprintf("## %s", platform)
 plat_idx <- which(lines == plat_header)
 if (length(plat_idx) == 0) {
-  cat(sprintf("No section found for platform %s - nothing to rebuild\n", platform))
+  cat(sprintf(
+    "No section found for platform %s - nothing to rebuild\n",
+    platform
+  ))
   writeLines(character(0), output_file)
   q("no")
 }
@@ -64,7 +79,11 @@ if (length(plat_idx) == 0) {
 arch_pattern <- sprintf("^### %s ", arch)
 arch_idx <- which(grepl(arch_pattern, lines) & seq_along(lines) > plat_idx[1])
 if (length(arch_idx) == 0) {
-  cat(sprintf("No section found for arch %s under %s - nothing to rebuild\n", arch, platform))
+  cat(sprintf(
+    "No section found for arch %s under %s - nothing to rebuild\n",
+    arch,
+    platform
+  ))
   writeLines(character(0), output_file)
   q("no")
 }
@@ -82,6 +101,11 @@ pkg_lines <- section_lines[grepl("^- ", section_lines)]
 pkgs <- sub("^- ([^ ]+) \\(.*\\)$", "\\1", pkg_lines)
 pkgs <- pkgs[nchar(pkgs) > 0 & pkgs != "_None_"]
 
-cat(sprintf("Found %d rebuildable packages for %s/%s\n", length(pkgs), platform, arch))
+cat(sprintf(
+  "Found %d rebuildable packages for %s/%s\n",
+  length(pkgs),
+  platform,
+  arch
+))
 writeLines(pkgs, output_file)
 cat(sprintf("Wrote package list to %s\n", output_file))

local/label-removed-cran-packages.R

@@ -6,9 +6,13 @@ archived <- quickcode::archivedPkg() |>
   pull(name)
 
 # Query all distinct pkgs in the DB
-con <- DBI::dbConnect(RPostgres::Postgres(),
+con <- DBI::dbConnect(
-  dbname = "build_metadata", host = "r-binaries.devxy.io",
+  RPostgres::Postgres(),
-  port = 15432, user = "r_binaries", password = Sys.getenv("PGPASS"),
+  dbname = "build_metadata",
+  host = "r-binaries.devxy.io",
+  port = 15432,
+  user = "r_binaries",
+  password = Sys.getenv("PGPASS"),
   sslmode = "require"
 )
 
@@ -22,7 +26,9 @@ to_process <- pkgs_db[pkgs_db %in% archived]
 
 # for all matches, set 'removed = TRUE'
 sapply(to_process, function(.x) {
-  DBI::dbExecute(con, "UPDATE single_builds SET removed = 'TRUE' where name = $1",
+  DBI::dbExecute(
+    con,
+    "UPDATE single_builds SET removed = 'TRUE' where name = $1",
     params = list(.x)
   )
 })

local/missing-cran-packages-db.R

@@ -3,22 +3,34 @@ library(bincraft)
 library(dplyr)
 library(DBI)
 
-con <- DBI::dbConnect(RPostgres::Postgres(),
+con <- DBI::dbConnect(
-  dbname = "build_metadata", host = "r-binaries.devxy.io",
+  RPostgres::Postgres(),
-  port = 15432, user = "r_binaries", password = Sys.getenv("PGPASS"),
+  dbname = "build_metadata",
+  host = "r-binaries.devxy.io",
+  port = 15432,
+  user = "r_binaries",
+  password = Sys.getenv("PGPASS"),
   sslmode = "require"
 )
 
 `%nin%` <- Negate(`%in%`)
 
-new_packages <- get_new_cran_packages(lubridate::interval(lubridate::today(), lubridate::today() - 2))$name
+new_packages <- get_new_cran_packages(lubridate::interval(
-removed_pkgs <- get_removed_cran_packages(lubridate::interval(lubridate::today(), lubridate::today() - 2))$name
+  lubridate::today(),
+  lubridate::today() - 2
+))$name
+removed_pkgs <- get_removed_cran_packages(lubridate::interval(
+  lubridate::today(),
+  lubridate::today() - 2
+))$name
 # filter windows packages
 # filter new packages from the last X days
-cran_pkgs <- unique(tools::CRAN_package_db() |>
+cran_pkgs <- unique(
+  tools::CRAN_package_db() |>
     filter(`OS_type` != "windows" | is.na(`OS_type`)) |>
     filter(`Package` %nin% new_packages) |>
-  pull(Package))
+    pull(Package)
+)
 
 arch <- "arm64"
 platform <- "redhat-8"
@@ -28,13 +40,24 @@ platform <- "alpine-321"
 platform <- "ubuntu-2204"
 platform <- "ubuntu-2404"
 
-data <- dbGetQuery(con, "SELECT name FROM single_builds WHERE platform = $1 AND arch = $2 and removed = FALSE;", params = list(platform, arch))
+data <- dbGetQuery(
-removed_pkgs = get_removed_cran_packages(lubridate::interval(lubridate::today(), lubridate::today() - 2))$name
+  con,
+  "SELECT name FROM single_builds WHERE platform = $1 AND arch = $2 and removed = FALSE;",
+  params = list(platform, arch)
+)
+removed_pkgs = get_removed_cran_packages(lubridate::interval(
+  lubridate::today(),
+  lubridate::today() - 2
+))$name
 pkgs_db <- unique(data$name)
 pkgs_db = setdiff(pkgs_db, removed_pkgs)
 
 pkgs <- setdiff(cran_pkgs, pkgs_db)
-formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs[1:length(pkgs)])))))
+formatted_pkgs <- gsub(
+  '"',
+  "'",
+  capture.output(dput(as.character(na.omit(pkgs[1:length(pkgs)]))))
+)
 formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ")
 
 cat(formatted_pkgs_one_line, "\n", sep = "")
@@ -44,7 +67,6 @@ clipr::write_clip(formatted_pkgs_one_line)
 
 # sapply(pkgs, function(x) which(grepl(sprintf("^%s$", x), cran_pkgs)))
 
-
 s3fs::s3_file_system(
   aws_access_key_id = Sys.getenv("HETZNER_S3_ACCESS_KEY_K3S"),
   aws_secret_access_key = Sys.getenv("HETZNER_S3_SECRET_KEY_K3S"),

local/missing-cran-packages.R

@@ -10,17 +10,37 @@ s3fs::s3_file_system(
 )
 s3fs::s3_dir_ls("s3://devxy-r-package-binaries")
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib")) # done
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib")) # done
+  "devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib"
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib")) # done
+)) # done
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib")) # done
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib")) # done
+  "devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib"
+)) # done
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib"
+)) # done
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib"
+)) # done
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib"
+)) # done
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib")) # done
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib")) # done
+  "devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib"
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib")) # done
+)) # done
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib")) # done
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib"
+)) # done
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib"
+)) # done
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib"
+)) # done
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib"
+))
 
 files_b = basename(files)
 files_b_split = sapply(strsplit(basename(files_b), "_"), function(x) x[1])
@@ -30,7 +50,11 @@ cran_pkgs <- tools::CRAN_package_db() |>
   pull(Package)
 
 pkgs = setdiff(cran_pkgs, files_b_split)
-formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs[1:900])))))
+formatted_pkgs <- gsub(
+  '"',
+  "'",
+  capture.output(dput(as.character(na.omit(pkgs[1:900]))))
+)
 formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ")
 
 cat(formatted_pkgs_one_line, "\n", sep = "")

local/missing-packages-in-index.R

@@ -7,42 +7,109 @@ s3fs::s3_file_system(
   region_name = "hel1",
 )
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/amd64/jammy/latest/src/contrib"
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib"))
+))
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib"
+))
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib"
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib"))
+))
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib"
+))
 
 files_b = basename(files)
 files_b_split = sapply(strsplit(basename(files_b), "_"), function(x) x[1])
-files_b_split = setdiff(files_b_split, c("PACKAGES", "PACKAGES.gz", "PACKAGES.rds", "PACKAGES.db", "Archive"))
+files_b_split = setdiff(
+  files_b_split,
+  c("PACKAGES", "PACKAGES.gz", "PACKAGES.rds", "PACKAGES.db", "Archive")
+)
 # windows-only
-files_b_split = setdiff(files_b_split, c("PACKAGES", "PACKAGES.gz", "PACKAGES.rds", "PACKAGES.db", "Archive", "RInno", "KeyboardSimulator", "R2PPT", "RWinEdt", "blatr", "excel.link", "spectrino", "taskscheduleR", "MDSGUI", "BiplotGUI", "R2wd"))
+files_b_split = setdiff(
-pkgs_index = available.packages("https://cran.devxy.io/amd64/jammy/latest/src/contrib")[, "Package"]
+  files_b_split,
+  c(
+    "PACKAGES",
+    "PACKAGES.gz",
+    "PACKAGES.rds",
+    "PACKAGES.db",
+    "Archive",
+    "RInno",
+    "KeyboardSimulator",
+    "R2PPT",
+    "RWinEdt",
+    "blatr",
+    "excel.link",
+    "spectrino",
+    "taskscheduleR",
+    "MDSGUI",
+    "BiplotGUI",
+    "R2wd"
+  )
+)
+pkgs_index = available.packages(
+  "https://cran.devxy.io/amd64/jammy/latest/src/contrib"
+)[, "Package"]
 pkgs_index_b = basename(pkgs_index)
 if (length(files_b_split) != length(pkgs_index_b)) {
   pkgs_missing = setdiff(files_b_split, pkgs_index_b)
   message("Packages missing in index but present in S3:")
   pkgs_missing
-  formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs_missing[1:900])))))
+  formatted_pkgs <- gsub(
+    '"',
+    "'",
+    capture.output(dput(as.character(na.omit(pkgs_missing[1:900]))))
+  )
   formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ")
 
   cat(formatted_pkgs_one_line, "\n", sep = "")
 }
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/amd64/noble/latest/src/contrib"
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib"))
+))
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/rhel8/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/rhel9/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/amd64/alpine320/latest/src/contrib"
+))
 
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/arm64/jammy/latest/src/contrib"
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib"))
+))
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib"))
+files <- s3fs::s3_dir_ls(sprintf(
-files <- s3fs::s3_dir_ls(sprintf("devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib"))
+  "devxy-r-package-binaries-hel1/arm64/noble/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/rhel8/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib"
+))
+files <- s3fs::s3_dir_ls(sprintf(
+  "devxy-r-package-binaries-hel1/arm64/alpine320/latest/src/contrib"
+))

local/packages-without-any-binary.R

@@ -1,9 +1,13 @@
 ### Lists packages without any successful binaries, i.e. pkgs for which all builds errored (per platform & arch)
 library(DBI)
 library(dplyr)
-con <- DBI::dbConnect(RPostgres::Postgres(),
+con <- DBI::dbConnect(
-  dbname = "build_metadata", host = "r-binaries.devxy.io",
+  RPostgres::Postgres(),
-  port = 15432, user = "r_binaries", password = Sys.getenv("PGPASS"),
+  dbname = "build_metadata",
+  host = "r-binaries.devxy.io",
+  port = 15432,
+  user = "r_binaries",
+  password = Sys.getenv("PGPASS"),
   sslmode = "require"
 )
 
@@ -11,7 +15,10 @@ cran_pkgs <- tools::CRAN_package_db() |>
   filter(`Date/Publication` <= "2024-12-02") |>
   pull(Package)
 
-data <- dbGetQuery(con, "SELECT name,platform,arch,removed,error_occurred FROM single_builds;")
+data <- dbGetQuery(
+  con,
+  "SELECT name,platform,arch,removed,error_occurred FROM single_builds;"
+)
 
 pkgs <- data |>
   filter(platform == "alpine-320", arch == "arm64") |>
@@ -22,7 +29,11 @@ pkgs <- data |>
 
 pkgs = setdiff(cran_pkgs, pkgs)
 # Format, remove line breaks, and print as a single line
-formatted_pkgs <- gsub('"', "'", capture.output(dput(as.character(na.omit(pkgs[1:900])))))
+formatted_pkgs <- gsub(
+  '"',
+  "'",
+  capture.output(dput(as.character(na.omit(pkgs[1:900]))))
+)
 
 formatted_pkgs_one_line <- paste(formatted_pkgs, collapse = " ")
 

local/weekly-missing-binaries-audit.R

@@ -17,8 +17,12 @@ library(httr2, quietly = TRUE)
 platform <- Sys.getenv("PLATFORM")
 arch <- Sys.getenv("ARCH")
 
-if (nchar(platform) == 0) stop("PLATFORM env var is not set")
+if (nchar(platform) == 0) {
-if (nchar(arch)     == 0) stop("ARCH env var is not set")
+  stop("PLATFORM env var is not set")
+}
+if (nchar(arch) == 0) {
+  stop("ARCH env var is not set")
+}
 
 # Map platform names to S3 codenames
 s3_codename <- gsub("-", "", platform)
@@ -37,8 +41,13 @@ os_family <- if (grepl("^ubuntu", platform)) {
   platform
 }
 
-cat(sprintf("Platform: %s | Arch: %s | S3 codename: %s | OS family: %s\n",
+cat(sprintf(
-            platform, arch, s3_codename, os_family))
+  "Platform: %s | Arch: %s | S3 codename: %s | OS family: %s\n",
+  platform,
+  arch,
+  s3_codename,
+  os_family
+))
 
 # ---------------------------------------------------------------------------
 # 1. Query PostgreSQL for known build failures (before s3fs init to avoid
@@ -59,7 +68,8 @@ errored_pkgs <- DBI::dbGetQuery(
   con,
   sprintf(
     "SELECT name, tag FROM single_builds WHERE error_occurred = TRUE AND platform = '%s' AND arch = '%s'",
-    platform, arch
+    platform,
+    arch
   )
 )
 DBI::dbDisconnect(con)
@@ -69,7 +79,12 @@ 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))
+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)
@@ -93,13 +108,21 @@ s3fs::s3_file_system(
   refresh = TRUE
 )
 
-s3_path <- sprintf("devxy-rpkgs-binaries/%s/%s/latest/src/contrib", arch, s3_codename)
+s3_path <- sprintf(
+  "devxy-rpkgs-binaries/%s/%s/latest/src/contrib",
+  arch,
+  s3_codename
+)
 cat(sprintf("Listing S3 path: %s\n", s3_path))
 
 s3_pkgs <- tryCatch(
   s3fs::s3_dir_ls(s3_path, recurse = FALSE),
   error = function(e) {
-    cat(sprintf("WARNING: Could not list S3 path %s: %s\n", s3_path, conditionMessage(e)))
+    cat(sprintf(
+      "WARNING: Could not list S3 path %s: %s\n",
+      s3_path,
+      conditionMessage(e)
+    ))
     character(0)
   }
 )
@@ -117,7 +140,12 @@ if (length(parts) == 0) {
   )
 }
 
-cat(sprintf("S3 contains %d tarballs for %s/%s\n", nrow(s3_dt), arch, s3_codename))
+cat(sprintf(
+  "S3 contains %d tarballs for %s/%s\n",
+  nrow(s3_dt),
+  arch,
+  s3_codename
+))
 
 # ---------------------------------------------------------------------------
 # 4. Find missing packages (CRAN release version not in S3)
@@ -132,9 +160,15 @@ cat(sprintf("%d CRAN release packages missing from S3\n", nrow(missing_dt)))
 # ---------------------------------------------------------------------------
 script_dir <- tryCatch(
   dirname(normalizePath(
-    if (exists("ofile", envir = sys.frame(1), inherits = FALSE)) sys.frame(1)$ofile
+    if (exists("ofile", envir = sys.frame(1), inherits = FALSE)) {
-    else commandArgs(trailingOnly = FALSE)[grepl("--file=", commandArgs(trailingOnly = FALSE))] |>
+      sys.frame(1)$ofile
-      sub("--file=", "", x = _),
+    } else {
+      commandArgs(trailingOnly = FALSE)[grepl(
+        "--file=",
+        commandArgs(trailingOnly = FALSE)
+      )] |>
+        sub("--file=", "", x = _)
+    },
     mustWork = FALSE
   )),
   error = function(e) "local"
@@ -145,11 +179,21 @@ excluded_pkgs <- data.table(package = character(0), reason = character(0))
 if (file.exists(excluded_path)) {
   excluded_raw <- jsonlite::fromJSON(excluded_path)
   excluded_pkgs <- as.data.table(excluded_raw)
-  cat(sprintf("Loaded %d excluded packages from %s\n", nrow(excluded_pkgs), excluded_path))
+  cat(sprintf(
+    "Loaded %d excluded packages from %s\n",
+    nrow(excluded_pkgs),
+    excluded_path
+  ))
   missing_dt <- missing_dt[!Package %in% excluded_pkgs$package]
-  cat(sprintf("%d packages remain after removing exclusions\n", nrow(missing_dt)))
+  cat(sprintf(
+    "%d packages remain after removing exclusions\n",
+    nrow(missing_dt)
+  ))
 } else {
-  cat(sprintf("No excluded-packages.json found at %s -- skipping exclusion step\n", excluded_path))
+  cat(sprintf(
+    "No excluded-packages.json found at %s -- skipping exclusion step\n",
+    excluded_path
+  ))
 }
 
 # ---------------------------------------------------------------------------
@@ -163,18 +207,28 @@ if (nrow(errored_dt) > 0) {
   rebuildable_dt <- missing_dt
 }
 
-cat(sprintf("Rebuildable: %d | Known failures: %d\n",
+cat(sprintf(
-            nrow(rebuildable_dt), nrow(known_failures_dt)))
+  "Rebuildable: %d | Known failures: %d\n",
+  nrow(rebuildable_dt),
+  nrow(known_failures_dt)
+))
 
 # ---------------------------------------------------------------------------
 # 7. Write rebuildable package names to cache RDS
 # ---------------------------------------------------------------------------
 cache_dir <- "/mnt/cache/packages"
-cache_file <- file.path(cache_dir, sprintf("weekly_rebuild_%s_%s.rds", platform, arch))
+cache_file <- file.path(
+  cache_dir,
+  sprintf("weekly_rebuild_%s_%s.rds", platform, arch)
+)
 
 if (dir.exists(cache_dir)) {
   saveRDS(rebuildable_dt$Package, cache_file)
-  cat(sprintf("Wrote %d rebuildable packages to %s\n", nrow(rebuildable_dt), cache_file))
+  cat(sprintf(
+    "Wrote %d rebuildable packages to %s\n",
+    nrow(rebuildable_dt),
+    cache_file
+  ))
 } else {
   cat(sprintf("Cache dir %s does not exist -- skipping RDS write\n", cache_dir))
 }
@@ -186,29 +240,47 @@ forgejo_token <- Sys.getenv("FORGEJO_TOKEN")
 if (nchar(forgejo_token) == 0) {
   cat("FORGEJO_TOKEN not set -- skipping issue update\n")
 } else {
-  issue_title <- sprintf("Missing package binaries for latest version (%s)", os_family)
+  issue_title <- sprintf(
+    "Missing package binaries for latest version (%s)",
+    os_family
+  )
 
   n_missing <- nrow(missing_dt)
   n_rebuild <- nrow(rebuildable_dt)
 
-  arch_lines <- sprintf("### %s (%d missing, %d to rebuild)", arch, n_missing, n_rebuild)
+  arch_lines <- sprintf(
+    "### %s (%d missing, %d to rebuild)",
+    arch,
+    n_missing,
+    n_rebuild
+  )
   if (nrow(rebuildable_dt) > 0) {
-    arch_lines <- c(arch_lines,
+    arch_lines <- c(
+      arch_lines,
       paste0("- ", rebuildable_dt$Package, " (", rebuildable_dt$Version, ")")
     )
   } else {
     arch_lines <- c(arch_lines, "_None_")
   }
   if (nrow(known_failures_dt) > 0) {
-    arch_lines <- c(arch_lines,
+    arch_lines <- c(
+      arch_lines,
       "",
       "#### Known build failures",
-      paste0("- ", known_failures_dt$Package, " (", known_failures_dt$Version, ")")
+      paste0(
+        "- ",
+        known_failures_dt$Package,
+        " (",
+        known_failures_dt$Version,
+        ")"
+      )
     )
   }
 
   build_excluded_footer <- function() {
-    if (nrow(excluded_pkgs) == 0) return(character(0))
+    if (nrow(excluded_pkgs) == 0) {
+      return(character(0))
+    }
     entries <- paste(
       paste0(excluded_pkgs$package, " (", excluded_pkgs$reason, ")"),
       collapse = ", "
@@ -221,7 +293,8 @@ if (nchar(forgejo_token) == 0) {
 
   search_url <- sprintf(
     "%s/repos/%s/issues?type=issues&state=open&q=%s&limit=50",
-    forgejo_base, repo,
+    forgejo_base,
+    repo,
     utils::URLencode(issue_title, reserved = TRUE)
   )
   search_resp <- httr2::request(search_url) |>
@@ -230,7 +303,9 @@ if (nchar(forgejo_token) == 0) {
 
   existing_issues <- httr2::resp_body_json(search_resp, simplifyVector = FALSE)
 
-  match_idx <- which(sapply(existing_issues, function(x) x$title) == issue_title)
+  match_idx <- which(
+    sapply(existing_issues, function(x) x$title) == issue_title
+  )
 
   today_str <- format(Sys.Date(), "%Y-%m-%d")
 
@@ -238,7 +313,9 @@ if (nchar(forgejo_token) == 0) {
     # ---- Update existing issue ----
     issue_number <- existing_issues[[match_idx[1]]]$number
     old_body <- existing_issues[[match_idx[1]]]$body
-    if (is.null(old_body)) old_body <- ""
+    if (is.null(old_body)) {
+      old_body <- ""
+    }
 
     lines <- strsplit(old_body, "\n", fixed = TRUE)[[1]]
 
@@ -258,7 +335,11 @@ if (nchar(forgejo_token) == 0) {
     if (length(plat_idx) == 0) {
       # Platform section missing -- insert before --- footer
       footer_idx <- which(lines == "---")
-      insert_at  <- if (length(footer_idx) > 0) footer_idx[length(footer_idx)] else length(lines) + 1
+      insert_at <- if (length(footer_idx) > 0) {
+        footer_idx[length(footer_idx)]
+      } else {
+        length(lines) + 1
+      }
 
       new_plat_block <- c(sprintf("## %s", platform), "", arch_lines, "")
       lines <- c(
@@ -271,7 +352,11 @@ if (nchar(forgejo_token) == 0) {
 
       # End of platform section: next ## or --- at a higher level, or EOF
       next_section <- which(grepl("^## |^---", lines) & seq_along(lines) > pi)
-      plat_end     <- if (length(next_section) > 0) next_section[1] - 1 else length(lines)
+      plat_end <- if (length(next_section) > 0) {
+        next_section[1] - 1
+      } else {
+        length(lines)
+      }
 
       plat_lines <- lines[seq(pi, plat_end)]
       arch_local_idx <- which(plat_lines == arch_header)
@@ -288,7 +373,9 @@ if (nchar(forgejo_token) == 0) {
         ai <- pi + arch_local_idx[1] - 1 # absolute line index
 
         # End of arch subsection
-        next_arch <- which(grepl("^### |^## |^---", lines) & seq_along(lines) > ai)
+        next_arch <- which(
+          grepl("^### |^## |^---", lines) & seq_along(lines) > ai
+        )
         arch_end <- if (length(next_arch) > 0) next_arch[1] - 1 else plat_end
 
         lines <- c(
@@ -303,7 +390,11 @@ if (nchar(forgejo_token) == 0) {
     excl_hdr_idx <- which(lines == "## Excluded packages")
     if (length(excl_hdr_idx) > 0) {
       pre_dash <- which(lines == "---" & seq_along(lines) < excl_hdr_idx[1])
-      remove_from <- if (length(pre_dash) > 0) pre_dash[length(pre_dash)] else excl_hdr_idx[1]
+      remove_from <- if (length(pre_dash) > 0) {
+        pre_dash[length(pre_dash)]
+      } else {
+        excl_hdr_idx[1]
+      }
       lines <- lines[seq_len(remove_from - 1)]
     }
     footer <- build_excluded_footer()
@@ -313,7 +404,12 @@ if (nchar(forgejo_token) == 0) {
 
     new_body <- paste(lines, collapse = "\n")
 
-    patch_url <- sprintf("%s/repos/%s/issues/%d", forgejo_base, repo, issue_number)
+    patch_url <- sprintf(
+      "%s/repos/%s/issues/%d",
+      forgejo_base,
+      repo,
+      issue_number
+    )
     httr2::request(patch_url) |>
       httr2::req_headers(
         Authorization = paste("token", forgejo_token),
@@ -324,7 +420,6 @@ if (nchar(forgejo_token) == 0) {
       httr2::req_perform()
 
     cat(sprintf("Updated Forgejo issue #%d: %s\n", issue_number, issue_title))
-
   } else {
     # ---- Create new issue ----
     body_lines <- c(
@@ -352,7 +447,11 @@ if (nchar(forgejo_token) == 0) {
       httr2::req_perform()
 
     new_issue <- httr2::resp_body_json(create_resp)
-    cat(sprintf("Created Forgejo issue #%d: %s\n", new_issue$number, issue_title))
+    cat(sprintf(
+      "Created Forgejo issue #%d: %s\n",
+      new_issue$number,
+      issue_title
+    ))
   }
 }
 

renovate.json

@@ -1,11 +1,7 @@
 {
   "$schema": "https://docs.renovatebot.com/renovate-schema.json",
-  "extends": [
+  "extends": ["local>devxy/renovate-config"],
-    "local>devxy/renovate-config"
+  "ignorePaths": ["docker/**"],
-  ],
-  "ignorePaths": [
-    "docker/**"
-  ],
   "customManagers": [
     {
       "customType": "regex",