pat-s
01b8ab43df
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## Problem
The rebuild now works — `AATtools 0.0.3` was detected as a source fallback, built, and published:
```
ℹ `upload_single_binary()`: Replacing the CRAN source published for AATtools 0.0.3 … with the binary.
✔ Successfully uploaded package AATtools with tag 0.0.3.
```
But clients still get the source, and will for about a year:
```
$ curl -sI .../src/contrib/AATtools_0.0.3.tar.gz
etag: "ea8127d953ca6a2f118ea49441772af6" # CRAN's source MD5
cdn-cache: HIT
cdn-cachedat: 08/09/2026 16:43:32 # predates the 18:12 upload
```
Two causes, both specific to a rebuild:
1. **The slot is never re-indexed.** `weekly-rebuild-missing` has no `upload_package_index` step, so the index keeps the old MD5 and — for anything that had been served from source — no `Built` stamp. This one self-heals at the next `process-updates` run.
2. **The tarball URL is never purged.** A normal update publishes new packages at *new* URLs, so `purge_cdn_cache.sh` only needs the five index files. A rebuild replaces an object *in place*, and the zone caches tarballs for `cache_expiration_time = 31919000` (~370 days). This does not self-heal.
Nothing about a stale package looks wrong from the outside, which is what makes it worth fixing rather than documenting.
## What this changes
**Re-index at the end of a rebuild**, flat and per-minor, mirroring the tail of `process-updates`. The codename is detected from the image's `/etc/os-release` (as `local/packages-to-build.R` already does) rather than adding `OS_ID` to all 18 matrix rows.
**Purge the zone afterwards**, via a new `scripts/purge_cdn_zone.sh`. One call to `POST /pullzone/{id}/purgeCache` covers every replaced object, and all three hostnames — `cran.devxy.io`, `cran.allianceswisspass.devxy.io`, `cran.rpkgs.com` — share pull zone `3857050`, confirmed from the `cdn-pullzone` response header.
Purging per URL was the alternative and is worse here: ~13.5k rate-limited calls per arch, where a single missed call leaves a package silently stale. The cost of the zone purge is a cold cache for everything else, which is why it stays out of the daily update path — `purge_cdn_cache.sh` is untouched.
The purge runs on failure too (`when: status: [success, failure]`): a rebuild that died part-way still replaced objects, and those are exactly the ones a stale edge keeps hiding.
## Verification
`crow lint .crow/` reports all ten configs valid; `bash -n` on the new script passes; prek hooks pass.
Not yet exercised against Bunny — it needs `BUNNYNET_API_KEY`, which is a CI secret. The failure mode is explicit rather than silent: any status other than 200/204 prints the response body and exits non-zero.
Reviewed-on: #160
207 lines
8.3 KiB
YAML
207 lines
8.3 KiB
YAML
# Consolidated weekly-rebuild-missing pipeline (all platforms, both arches).
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# One matrix row per OS/arch replaces the former per-platform files.
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# Routing is preserved 1:1:
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# - cron: each existing `weekly-rebuild-missing-<os>-<arch>` cron fires only
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# its matching matrix row (via the per-row `cron:` name filter).
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# - manual: `weekly_rebuild_missing` dropdown, default "all" (matches the
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# previous bare manual trigger that ran every os/arch); pick a
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# single <os>-<arch> to run just one.
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# Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64).
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variables:
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# Gates this pipeline. A manual pipeline creation instantiates every file in
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# .crow/, and a declared default is applied even when the run never passed
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# this variable, so the default must be a value that matches no matrix row.
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weekly_rebuild_missing:
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description: "Manual run target: a specific <os>-<arch>, 'all' for every os/arch, or 'none' to run nothing."
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options:
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- none
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- all
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- alpine-322-amd64
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- alpine-322-arm64
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- alpine-323-amd64
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- alpine-323-arm64
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- alpine-324-amd64
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- alpine-324-arm64
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- redhat-8-amd64
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- redhat-8-arm64
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- redhat-9-amd64
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- redhat-9-arm64
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- redhat-10-amd64
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- redhat-10-arm64
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- ubuntu-2204-amd64
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- ubuntu-2204-arm64
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- ubuntu-2404-amd64
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- ubuntu-2404-arm64
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- ubuntu-2604-amd64
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- ubuntu-2604-arm64
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default: none
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when:
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- event: cron
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cron: weekly-rebuild-missing-${OS}-${ARCH}
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- event: manual
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evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"'
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skip_clone: true
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labels:
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group: rpkgs-${ARCH}
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matrix:
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include:
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- OS: alpine-322
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: alpine:3.22
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- OS: alpine-322
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: alpine:3.22
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- OS: alpine-323
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: alpine:3.23
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- OS: alpine-323
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: alpine:3.23
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- OS: alpine-324
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: alpine:3.24
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- OS: alpine-324
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: alpine:3.24
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- OS: redhat-8
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: redhat:8
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- OS: redhat-8
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: redhat:8
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- OS: redhat-9
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: redhat:9
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- OS: redhat-9
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: redhat:9
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- OS: redhat-10
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: redhat:10
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- OS: redhat-10
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: redhat:10
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- OS: ubuntu-2204
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: ubuntu:jammy
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- OS: ubuntu-2204
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: ubuntu:jammy
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- OS: ubuntu-2404
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: ubuntu:noble
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- OS: ubuntu-2404
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: ubuntu:noble
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- OS: ubuntu-2604
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: ubuntu:resolute
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- OS: ubuntu-2604
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: ubuntu:resolute
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steps:
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- name: 'Rebuild missing binaries'
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image: reg.devxy.io/rpkgs/build-env-${IMG}
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pull: true
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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RED_HAT_DEV_PW:
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from_secret: RED_HAT_DEV_PW
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B2_S3_ACCESS_KEY:
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from_secret: B2_S3_ACCESS_KEY
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B2_S3_SECRET_KEY:
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from_secret: B2_S3_SECRET_KEY
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PGPASS:
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from_secret: PGPASS
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REPO_RO_TOKEN:
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from_secret: REPO_RO_TOKEN
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GITHUB_PAT:
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from_secret: GITHUB_PAT
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FORGEJO_TOKEN:
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from_secret: FORGEJO_TOKEN
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GIT_USER: pat-s
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UVR_CACHE_DIR: /mnt/cache/uvr/cache
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UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
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R_LIBS_USER: /mnt/cache/R-pkgs
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R_VERSION: ${R_VERSION}
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CCACHE_DIR: /mnt/cache/ccache
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PLATFORM: ${OS}
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ARCH: ${ARCH}
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NCPUS: 2
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commands:
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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- rm -rf /mnt/cache/R-pkgs/00LOCK-*
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- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
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- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
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- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
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- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
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- /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
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- $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1
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# A rebuild replaces objects in place, so the slot's index still advertises
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# the old MD5 and, for anything that had been served from source, no Built
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# stamp. Re-index here rather than waiting for the next process-updates
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# run, or the rebuilt binaries stay invisible to clients until then.
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# The codename is detected from the image's /etc/os-release.
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- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))'
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- |
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for RBIN in /opt/R/[0-9]*/bin/R; do
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RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
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/opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true
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done
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backend_options:
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docker:
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resources:
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requests:
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memory: 5Gi
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cpu: 3000m
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limits:
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memory: 18Gi
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cpu: 3000m
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- name: Purge CDN cache
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image: reg.devxy.io/docker.io/library/alpine:3.24
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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BUNNYNET_API_KEY:
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from_secret: BUNNYNET_API_KEY
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REPO_RO_TOKEN:
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from_secret: REPO_RO_TOKEN
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# All hostnames on the zone share this id, so one purge covers
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# cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com.
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BUNNY_PULLZONE: '3857050'
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commands:
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- apk add --no-cache -q bash curl git
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE"
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# A rebuild that died part-way still replaced objects, and those are exactly
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# the ones a stale edge would keep hiding, so purge either way.
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when:
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- status: [success, failure]
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