chore: remove plans and specs design docs

Drop the internal plans/ and specs/ design documents, the README link to the patching spec and their markdownlint ignores.

local/archive-missed-pkgs.R

@@ -8,8 +8,8 @@ s3fs::s3_file_system(
   refresh = T
 )
 
-arch = "arm64"
-os = "alpine321"
+arch <- "arm64"
+os <- "alpine321"
 
 files <- s3fs::s3_dir_ls(sprintf(
   "devxy-r-package-binaries-hel1/%s/%s/latest/src/contrib",
@@ -17,11 +17,11 @@ files <- s3fs::s3_dir_ls(sprintf(
   os
 ))
 length(unique(sapply(strsplit(basename(files), "_"), function(x) x[1])))
-non_archived = unique(sapply(strsplit(basename(files), "_"), function(x) {
+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")
+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))

local/check-NA.R

@@ -1,22 +1,30 @@
 ### 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")
+foo <- available.packages(
+  "https://cran.devxy.io/amd64/jammy/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
-foo = available.packages("https://cran.devxy.io/amd64/noble/latest/src/contrib")
+foo <- available.packages(
+  "https://cran.devxy.io/amd64/noble/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
 
-foo = available.packages("https://cran.devxy.io/amd64/rhel8/latest/src/contrib")
+foo <- available.packages(
+  "https://cran.devxy.io/amd64/rhel8/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
-foo = available.packages("https://cran.devxy.io/amd64/rhel9/latest/src/contrib")
+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(
+foo <- available.packages(
   "https://cran.devxy.io/amd64/alpine320/latest/src/contrib"
 )
 sum((is.na(foo[, "Version"])))
@@ -24,24 +32,32 @@ which((is.na(foo[, "Version"])))
 
 # arm64
 
-foo = available.packages("https://cran.devxy.io/arm64/jammy/latest/src/contrib")
+foo <- available.packages(
+  "https://cran.devxy.io/arm64/jammy/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
-foo = available.packages("https://cran.devxy.io/arm64/noble/latest/src/contrib")
+foo <- available.packages(
+  "https://cran.devxy.io/arm64/noble/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
 
-foo = available.packages("https://cran.devxy.io/arm64/rhel8/latest/src/contrib")
+foo <- available.packages(
+  "https://cran.devxy.io/arm64/rhel8/latest/src/contrib"
+)
 sum((is.na(foo[, "Version"])))
 which((is.na(foo[, "Version"])))
 
-foo = available.packages("https://cran.devxy.io/arm64/rhel9/latest/src/contrib")
+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(
+foo <- available.packages(
   "https://cran.devxy.io/arm64/alpine320/latest/src/contrib"
 )
 sum((is.na(foo[, "Version"])))

local/debug-packages-writing.R

@@ -1,7 +1,7 @@
 library(future)
 future::plan(multisession)
 future::plan(sequential)
-time = Sys.time()
+time <- Sys.time()
 files <- s3fs::s3_dir_ls(
   sprintf(
     "devxy-r-package-binaries-hel1/arm64/rhel9/latest/src/contrib/Archive"
@@ -54,8 +54,8 @@ curl::curl_download(
   "https://cran.devxy.io/amd64/rhel9/latest/src/contrib/PACKAGES.db",
   "PACKAGES.db"
 )
-con = DBI::dbConnect(RSQLite::SQLite(), "PACKAGES.db")
-df = DBI::dbReadTable(con, "packages")
+con <- DBI::dbConnect(RSQLite::SQLite(), "PACKAGES.db")
+df <- DBI::dbReadTable(con, "packages")
 
 cranlike:::write_packages_files("/tmp", "PACKAGES.db")
 
@@ -69,11 +69,11 @@ system("cat /tmp/PACKAGES | grep '^Package: digest' | wc -l")
 curl::curl_fetch_memory(
   "https://cloud.r-project.org/src/contrib/Meta/archive.rds"
 )
-remotes = readRDS(url(
+remotes <- readRDS(url(
   "https://cloud.r-project.org/src/contrib/Meta/archive.rds",
   "rb"
 ))
-packages = readRDS(url(
+packages <- readRDS(url(
   "https://cran.devxy.io/arm64/noble/latest/src/contrib/PACKAGES.rds",
   "rb"
 ))

local/missing-cran-packages.R

@@ -42,14 +42,14 @@ 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 <- basename(files)
+files_b_split <- sapply(strsplit(basename(files_b), "_"), function(x) x[1])
 
 cran_pkgs <- tools::CRAN_package_db() |>
   filter(`Date/Publication` <= "2025-01-25") |>
   pull(Package)
 
-pkgs = setdiff(cran_pkgs, files_b_split)
+pkgs <- setdiff(cran_pkgs, files_b_split)
 formatted_pkgs <- gsub(
   '"',
   "'",

local/missing-packages-in-index.R

@@ -39,14 +39,14 @@ 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 <- 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")
 )
 # windows-only
-files_b_split = setdiff(
+files_b_split <- setdiff(
   files_b_split,
   c(
     "PACKAGES",
@@ -67,12 +67,12 @@ files_b_split = setdiff(
     "R2wd"
   )
 )
-pkgs_index = available.packages(
+pkgs_index <- available.packages(
   "https://cran.devxy.io/amd64/jammy/latest/src/contrib"
 )[, "Package"]
-pkgs_index_b = basename(pkgs_index)
+pkgs_index_b <- basename(pkgs_index)
 if (length(files_b_split) != length(pkgs_index_b)) {
-  pkgs_missing = setdiff(files_b_split, 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(