pat-s
4b7dc28cc8
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## Problem `weekly-rebuild-missing` runs one job per `<os>-<arch>` and walks that slot's list serially in a single `R -q -e` argument. That was cheap while every source fallback was skipped as "already built". Since bincraft #105/#106/#107 and #159 the gate works, and the lists are large: 8 917 source-served records on `amd64/alpine324`, 15 023 on `amd64/resolute`. Pipeline 10910 (`weekly_rebuild_missing:alpine-324-amd64`) ran for two days, reached `[8692/23885] cholera`, and was killed there. Two failures follow from that shape: - **No parallelism.** The work is embarrassingly parallel across packages; one job does all of it. - **No resumability and no clean stopping point.** The loop ends only by exhausting the list, so the only way to stop it is a kill. A restart re-walks from the first entry, paying a CRAN version resolution and an S3 `HEAD` per package before reaching new work. And a kill matches neither `success` nor `failure`, so the `Purge CDN cache` step never ran: the ~4 600 binaries 10910 did publish stayed hidden behind stale edge copies. ## What this changes **Three shards per slot.** Each of the 18 `OS`/`ARCH` rows gains `SPLIT_INTO`/`SPLIT_INDEX`, mirroring `build-all-versions.yaml`. Cron and manual routing are unchanged: both filters already match on `${OS}-${ARCH}`, so they now match all three shards of a slot. **`local/rebuild-missing.R`** replaces the ~1 500-character inline one-liner. The slice is interleaved rather than contiguous, because the list is alphabetical and cost clusters by name (`Rcpp*`, `Bioc*`, `rstan*`). **Resume by re-deriving state from the bucket.** One `s3_dir_info()` listing gives ETags for the slot; a package is outstanding iff its object's ETag equals CRAN's published `MD5sum`, i.e. it is still byte-identical to CRAN's source. That is `check_s3_root_package()` evaluated in bulk. No progress file, no volume, no DB cursor, and correct when a sibling shard or a `process-updates` run completes something concurrently. It reads ETags rather than the index's `Built` field the way `packages-to-build.R` does, because the index is no longer rewritten until the dependent pipeline runs and so cannot reflect the current run's progress. Unknown always means "already a binary", never "rebuild it": a multipart ETag, an unreadable CRAN index or an empty listing can never mass-schedule work. **A 20 h wall-clock budget** per shard. It exits 0, so the re-index and purge always fire and the remainder is picked up next run with no bookkeeping. **`.crow/weekly-rebuild-reindex.yaml`** takes over re-indexing and the purge, with `depends_on: [weekly-rebuild-missing]` and `runs_on: [success, failure]`. Three shards writing one slot's `PACKAGES` concurrently would race: `update_PACKAGES()` lists the live bucket, so an early lister that uploads last publishes an index missing its siblings' work. ## Verification `crow lint .crow/` passes on all 11 pipelines. `prek run` passes. 19 assertions in `local/tests/test-rebuild-missing.R`, 0 failures, covering the partition (disjoint, covering, deterministic, short lists, out-of-range index) and the outstanding filter (source ETag kept, binary ETag dropped, absent object kept, multipart and missing-from-CRAN treated as built). One of those tests caught a real bug before it shipped: an empty ETag table indexed to zero length rather than to `NA`, which recycled the result away and reported "nothing to build" — the dangerous direction. Fixed with an explicit `lookup()`. The filter run against the live `amd64/alpine324` index, using its `MD5sum` column as the ETag (established to match the objects): ``` index packages: 24343 outstanding (filter): 8950 no Built stamp: 8917 filter vs no-Built agreement: 8917 of 8917 outstanding but stamped Built: 33 (version drift vs CRAN) shard sizes: 2984/2983/2983 (sum 8950, unique 8950) ``` It reproduces the source-served set exactly. The extra 33 are packages whose slot version differs from CRAN's current one, so no object exists at the CRAN version key: correctly outstanding. ## Notes for review - The 20 h budget is a chosen default, exposed as `REBUILD_BUDGET_HOURS` in the pipeline. - `depends_on` is file-level, not row-level, so on a full cron run no slot is re-indexed until the slowest of all 54 jobs finishes. The budget bounds that at roughly a day. - An explicit cancel still skips the re-index. Recovery is to trigger `weekly-rebuild-reindex` on its own. - The purge runs on every re-index row rather than one designated slot: a cron fires only its own slot's row, so gating on a named slot would leave every other slot unpurged. - Out of scope: `build-all-versions` still cannot rebuild source fallbacks, because `local/build-all.R:113-122` drops every version with any `single_builds` row, which is precisely the source-fallback set. Design: `specs/2026-08-12-shard-weekly-rebuild-design.md` Reviewed-on: #163
441 lines
11 KiB
YAML
441 lines
11 KiB
YAML
# Consolidated weekly-rebuild-missing pipeline (all platforms, both arches).
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# Three matrix rows per OS/arch, one per shard of that slot's rebuild list.
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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 rows (via the per-row `cron:` name filter),
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# which is now all three shards of that slot.
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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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#
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# The shard picks up its own slice and re-derives what is still outstanding
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# from the bucket, so a restart resumes rather than replaying; see
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# local/rebuild-missing.R.
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#
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# Re-indexing and the CDN purge deliberately do NOT live here. Three shards
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# writing one slot's PACKAGES concurrently would race, so they moved to
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# .crow/weekly-rebuild-reindex.yaml, which depends on this pipeline.
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 1
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 2
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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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SPLIT_INTO: 3
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SPLIT_INDEX: 3
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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
|
|
B2_S3_SECRET_KEY:
|
|
from_secret: B2_S3_SECRET_KEY
|
|
PGPASS:
|
|
from_secret: PGPASS
|
|
REPO_RO_TOKEN:
|
|
from_secret: REPO_RO_TOKEN
|
|
GITHUB_PAT:
|
|
from_secret: GITHUB_PAT
|
|
FORGEJO_TOKEN:
|
|
from_secret: FORGEJO_TOKEN
|
|
GIT_USER: pat-s
|
|
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
|
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
|
R_LIBS_USER: /mnt/cache/R-pkgs
|
|
R_VERSION: ${R_VERSION}
|
|
CCACHE_DIR: /mnt/cache/ccache
|
|
PLATFORM: ${OS}
|
|
ARCH: ${ARCH}
|
|
NCPUS: 2
|
|
SPLIT_INTO: ${SPLIT_INTO}
|
|
SPLIT_INDEX: ${SPLIT_INDEX}
|
|
# Wall clock after which the shard stops cleanly instead of having to be
|
|
# killed. A kill matches neither `success` nor `failure`, so it would skip
|
|
# the dependent re-index and leave rebuilt binaries behind a stale edge.
|
|
REBUILD_BUDGET_HOURS: 20
|
|
commands:
|
|
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
|
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
|
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
|
|
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
|
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
|
|
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
|
|
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
|
|
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
|
|
- $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1
|
|
backend_options:
|
|
docker:
|
|
resources:
|
|
requests:
|
|
memory: 5Gi
|
|
cpu: 3000m
|
|
limits:
|
|
memory: 18Gi
|
|
cpu: 3000m
|