diff --git a/.crow/archive-missed-packages.yaml b/.crow/archive-missed-packages.yaml index 71f808b..bd127d6 100644 --- a/.crow/archive-missed-packages.yaml +++ b/.crow/archive-missed-packages.yaml @@ -28,10 +28,6 @@ matrix: ARCH: amd64 - CODENAME: redhat-10 ARCH: arm64 - - CODENAME: alpine321 - ARCH: amd64 - - CODENAME: alpine321 - ARCH: arm64 - CODENAME: alpine322 ARCH: amd64 - CODENAME: alpine322 diff --git a/.crow/repair-built-stamp.yaml b/.crow/repair-built-stamp.yaml new file mode 100644 index 0000000..12e2644 --- /dev/null +++ b/.crow/repair-built-stamp.yaml @@ -0,0 +1,97 @@ +### Manual repair of a slot whose PACKAGES index advertises a broken `Built` +### stamp (e.g. `Built: R 4.5.0; NA; ...`). +# +# uvr matches the stamp's platform triple plus R minor to decide binary vs +# source, so an unusable triple turns a whole slot source-only. See +# local/repair-built-stamp.R for why this patches PACKAGES.db in place instead +# of forcing a full reparse. +# +# Run with `dry_run: true` first: it reports how many entries are broken per +# slot and changes nothing. Pick the R version the slot should advertise, which +# is the R_VERSION its entry in .crow/process-updates.yaml uses. +variables: + target_arch: + description: 'Architecture of the slot to repair.' + options: + - amd64 + - arm64 + default: arm64 + OS: + description: 'Base OS image name.' + options: + - alpine + - redhat + - ubuntu + default: alpine + OS_VERSION: + description: 'OS image tag. Must match OS (alpine: 3.22/3.23/3.24; redhat: 8/9/10; ubuntu: jammy/noble/resolute).' + options: + - '3.22' + - '3.23' + - '3.24' + - '8' + - '9' + - '10' + - 'jammy' + - 'noble' + - 'resolute' + default: '3.22' + R_VERSION: + description: 'R version whose stamp the slot should advertise.' + options: + - 4.5.3 + - 4.4.3 + default: 4.5.3 + dry_run: + description: 'Report what would change without writing anything.' + options: + - 'true' + - 'false' + default: 'true' + +when: + - event: manual + evaluate: 'target_arch == "${ARCH}"' + +skip_clone: true + +labels: + platform: linux/${ARCH} + group: rpkgs-${ARCH} + +matrix: + include: + - ARCH: amd64 + - ARCH: arm64 + +steps: + - name: 'Repair Built stamp' + image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' + pull: true + environment: + B2_S3_ACCESS_KEY: + from_secret: B2_S3_ACCESS_KEY + B2_S3_SECRET_KEY: + from_secret: B2_S3_SECRET_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + GIT_USER: pat-s + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' + - | + if [ "$dry_run" = "false" ]; then + /opt/R/$R_VERSION/bin/Rscript local/repair-built-stamp.R "$ARCH" --apply + else + /opt/R/$R_VERSION/bin/Rscript local/repair-built-stamp.R "$ARCH" + fi + backend_options: + docker: + resources: + requests: + memory: 2Gi + cpu: 1000m + limits: + memory: 8Gi + cpu: 2000m diff --git a/local/repair-built-stamp.R b/local/repair-built-stamp.R new file mode 100644 index 0000000..06f73be --- /dev/null +++ b/local/repair-built-stamp.R @@ -0,0 +1,175 @@ +#!/usr/bin/env Rscript + +### Rewrite a broken `Built` stamp across one arch/codename slot. +### +### A slot's index can end up advertising a stamp whose platform triple is +### unusable, e.g. `Built: R 4.5.0; NA; ...`. uvr picks binary vs source by +### matching that triple plus the R minor, so no client matches it and the whole +### slot silently reverts to source-only, which makes uvr compile everything and +### fail wherever a system `-dev` library is missing. +### +### Rewriting it is not a matter of re-running the normal index update. +### `upload_package_index()` reuses the slot's remote `PACKAGES.db`, and +### cranlike's `update_db()` only reparses files whose md5 changed, so entries +### already in the database keep the stamp they were written with. Dropping +### `PACKAGES.db` to force a full reparse does work, but for an S3 repo cranlike +### reads each package's metadata from the CRAN *source* mirror on GitHub, so a +### 25k-entry slot means 25k requests to raw.githubusercontent.com and a real +### risk of being rate-limited part-way through. +### +### Only the `Built` column is wrong, so correct it in place instead: patch the +### column in `PACKAGES.db`, put the database back, and let +### `upload_package_index()` re-emit `PACKAGES*` from it. `update_db()` always +### rewrites the index files even when nothing was reparsed, so no tarball is +### re-read and nothing is fetched from GitHub. +### +### The replacement comes from `bincraft::built_stamp()` under the R running +### this script, so run it under the R version the slot should advertise (the +### `R_VERSION` its entry in `.crow/process-updates.yaml` uses). That is what a +### healthy `upload_package_index()` run would have written. +### +### Usage, inside the platform's build image: +### Rscript local/repair-built-stamp.R [--apply] +### +### Without `--apply` it reports what it would change and touches nothing. + +suppressPackageStartupMessages({ + library(bincraft) +}) + +args <- commandArgs(trailingOnly = TRUE) +arch <- args[1L] +apply_changes <- "--apply" %in% args + +if (is.na(arch) || !nzchar(arch)) { + stop( + "Usage: Rscript local/repair-built-stamp.R [--apply]", + call. = FALSE + ) +} + +bucket <- "devxy-rpkgs-binaries" +endpoint <- "https://s3.eu-central-003.backblazeb2.com" +region <- "eu-central-003" + +codename <- bincraft::set_codename(NULL) +if (is.null(codename) || is.na(codename) || !nzchar(codename)) { + stop( + "Could not detect a codename from /etc/os-release; run this in a build image.", + call. = FALSE + ) +} + +# built_stamp() refuses an unusable platform, so a broken build image fails here +# rather than writing a second bad stamp over the first one. +stamp <- bincraft::built_stamp() +message(sprintf("Slot: %s/%s", arch, codename)) +message(sprintf("New stamp: %s", stamp)) + +s3fs::s3_file_system( + aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + aws_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), + endpoint = endpoint, + region_name = region, + refresh = TRUE +) + +base_dir <- file.path(bucket, arch, codename, "latest", "src", "contrib") + +# A stamp is broken when its platform component is absent or literally "NA". +broken_stamp_where <- paste( + "Built IS NULL", + "OR Built LIKE '%; NA;%'", + "OR Built LIKE '%; ;%'" +) + +# The generic slot plus every per-minor sub-slot, which carry the same stamp and +# are poisoned by the same run. +r_minors <- sub( + "^.*/R/([0-9]+\\.[0-9]+)\\.[0-9]+$", + "\\1", + list.dirs("/opt/R", recursive = FALSE) +) +r_minors <- unique(grep("^[0-9]+\\.[0-9]+$", r_minors, value = TRUE)) +slots <- c(base_dir, file.path(base_dir, r_minors)) + +repair_slot <- function(slot) { + db_remote <- file.path(slot, "PACKAGES.db") + if (!s3fs::s3_file_exists(db_remote)) { + message(sprintf(" %s: no PACKAGES.db, skipping", slot)) + return(invisible(NULL)) + } + + db_local <- tempfile(fileext = ".db") + s3fs::s3_file_download(db_remote, db_local, overwrite = TRUE) + + con <- DBI::dbConnect(RSQLite::SQLite(), db_local) + on.exit(DBI::dbDisconnect(con), add = TRUE) + + total <- DBI::dbGetQuery(con, "SELECT COUNT(*) AS n FROM packages")$n + broken <- DBI::dbGetQuery( + con, + sprintf("SELECT COUNT(*) AS n FROM packages WHERE %s", broken_stamp_where) + )$n + + message(sprintf(" %s: %s entries, %s broken", slot, total, broken)) + if (broken == 0L) { + return(invisible(NULL)) + } + if (!apply_changes) { + message(" (dry run, pass --apply to rewrite)") + return(invisible(NULL)) + } + + DBI::dbExecute( + con, + sprintf("UPDATE packages SET Built = ? WHERE %s", broken_stamp_where), + params = list(stamp) + ) + DBI::dbDisconnect(con) + on.exit() + + s3fs::s3_file_upload(db_local, db_remote, overwrite = TRUE) + message(sprintf(" rewrote %s entries and uploaded PACKAGES.db", broken)) + invisible(NULL) +} + +invisible(lapply(slots, repair_slot)) + +if (!apply_changes) { + message("Dry run complete; nothing was changed.") + quit(save = "no") +} + +# Re-emit PACKAGES/PACKAGES.gz/PACKAGES.rds from the corrected database. Nothing +# is reparsed, because no tarball's md5 changed. +message("Re-emitting index files from the corrected database...") +bincraft::upload_package_index( + codename = codename, + s3_endpoint = endpoint, + s3_region = region, + s3_bucket = bucket, + s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY") +) +for (minor in r_minors) { + try( + bincraft::upload_package_index( + codename = codename, + r_minor = minor, + s3_endpoint = endpoint, + s3_region = region, + s3_bucket = bucket, + s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY") + ), + silent = FALSE + ) +} + +message("Done. Verify with:") +message(sprintf( + " curl -sS https://cran.devxy.io/%s/%s/latest/src/contrib/PACKAGES | grep '^Built:' | sort | uniq -c", + arch, + codename +))