pat-s
a84cca1949
## Why A dry run of the prune on `ubuntu-2404-amd64` (pipeline 12494): ``` Dry run: 3013 object(s) left in place. Re-run with --apply to delete. ``` 3013 objects on one slot. The recorded verdicts say roughly **230** of that slot's objects actually fail `dyn.load()` anywhere. The gap is the selector: the prune used `abi_cache_risky_packages()`, the source classifier, which calls **93%** of compiled packages risky where the binaries' own symbols say **4.3%**. Applying it would have deleted ~2800 working binaries and turned each into a source fallback for every client that cannot be routed by R minor. This is the same mistake #129 fixed in the index writer. The prune was written before the per-object verdicts existed (#200, before #128/#129) and was never brought forward. ## What changed - Selection comes from `abi_flat_safety`, every `NOT safe` row for the slot regardless of which minor it fails under, since the flat object is served to clients on all of them. - Matching is by **object**, `<package>_<version>`, not by package name. A package can have a safe flat binary at one version and an unsafe one at another; the old code deleted both. - The explicit `[pkg ...]` override is unchanged in behaviour and still matches by package name, which is what you want when naming a package by hand. - The refusal guard moves with the selector. An empty result now means the slot's flat-safety backfill never ran — the exact state rhel8 was found in today — and pruning nothing while reporting success would have hidden it. ## Not changed Still a dry run unless `PRUNE_APPLY=yes`, and still refuses to delete an object whose package CRAN no longer ships, since there would be no source to fall back to. ## Ordering note A prune converts each deleted binary into a source fallback. bincraft #131 fixes source fallbacks of *archived* versions being advertised as binaries, which breaks `uvr` outright. That should land before any large prune, or this will manufacture new instances of it. Reviewed-on: #211
252 lines
8 KiB
YAML
252 lines
8 KiB
YAML
# Remove flat-slot binaries recorded unable to load under some R minor, then
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# re-index.
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#
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# The list comes from `abi_flat_safety`, so it names the objects the binaries
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# themselves report as broken, not the ones a source heuristic suspects. That
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# distinction is the whole cost of the operation: the heuristic calls 93% of
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# compiled packages risky and would delete roughly 3000 objects per slot to fix
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# about 230.
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#
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# `upload_single_binary()` has written a non-portable package only to the
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# per-minor slot since v5.3.0, so this is a one-time cleanup of what was
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# uploaded before that. The flat slot is what every client that cannot be
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# routed by R minor receives, and such a binary was built under whichever R was
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# primary at the time, so it dies at load under any minor that dropped a symbol
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# it uses:
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#
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# base64enc.so: undefined symbol: SETLENGTH
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#
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# Deleting the flat object does not create a hole. The source fallback
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# republishes the CRAN source under the same key, so the package stays
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# installable everywhere and compiles against the client's own R, while routed
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# clients keep getting the per-minor binary.
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#
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# Dry run unless PRUNE_APPLY is 'yes'. Start with an explicit package list:
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#
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# crow pipeline create devxy/build-cran-binaries \
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# --var prune_flat=ubuntu-2604-amd64 \
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# --var PRUNE_PACKAGES="base64enc lobstr" \
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# --var PRUNE_APPLY=yes
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variables:
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# A manual pipeline creation instantiates every file in .crow/, so the default
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# must match no matrix row.
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prune_flat:
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description: "Prune target: a specific <os>-<arch>, 'all' for every slot, or 'none'."
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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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PRUNE_PACKAGES:
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description: 'Space-separated package names. Empty means every package the classifier cache calls risky.'
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default: ''
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PRUNE_APPLY:
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description: "Set to 'yes' to actually delete. Anything else is a dry run."
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options:
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- 'no'
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- 'yes'
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default: 'no'
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when:
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- event: manual
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evaluate: 'prune_flat == "all" || prune_flat == "${OS}-${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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CODENAME: alpine322
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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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CODENAME: alpine322
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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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CODENAME: alpine323
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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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CODENAME: alpine323
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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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CODENAME: alpine324
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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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CODENAME: alpine324
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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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CODENAME: rhel8
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IMG: redhat:8
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- OS: redhat-8
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ARCH: arm64
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CODENAME: rhel8
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IMG: redhat:8
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- OS: redhat-9
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ARCH: amd64
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CODENAME: rhel9
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IMG: redhat:9
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- OS: redhat-9
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ARCH: arm64
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CODENAME: rhel9
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IMG: redhat:9
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- OS: redhat-10
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ARCH: amd64
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CODENAME: rhel10
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IMG: redhat:10
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- OS: redhat-10
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ARCH: arm64
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CODENAME: rhel10
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IMG: redhat:10
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- OS: ubuntu-2204
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ARCH: amd64
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CODENAME: jammy
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IMG: ubuntu:jammy
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- OS: ubuntu-2204
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ARCH: arm64
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CODENAME: jammy
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IMG: ubuntu:jammy
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- OS: ubuntu-2404
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ARCH: amd64
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CODENAME: noble
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IMG: ubuntu:noble
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- OS: ubuntu-2404
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ARCH: arm64
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CODENAME: noble
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IMG: ubuntu:noble
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- OS: ubuntu-2604
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ARCH: amd64
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CODENAME: resolute
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IMG: ubuntu:resolute
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- OS: ubuntu-2604
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ARCH: arm64
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CODENAME: resolute
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IMG: ubuntu:resolute
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steps:
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- name: 'Prune stale flat 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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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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GIT_USER: pat-s
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R_LIBS_USER: /tmp/R-pkgs
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# Pipeline variables are substituted into the YAML, not exported, so they
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# have to be bound here to be readable as env vars in the script below.
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PRUNE_ARCH: ${ARCH}
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PRUNE_CODENAME: ${CODENAME}
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PRUNE_PACKAGES: ${PRUNE_PACKAGES}
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PRUNE_APPLY: ${PRUNE_APPLY}
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commands:
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- mkdir -p /tmp/R-pkgs
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- /opt/R/4.5.3/bin/Rscript local/install-bincraft.R
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- |
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set -eu
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APPLY=""
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if [ "$$PRUNE_APPLY" = "yes" ]; then
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APPLY="--apply"
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fi
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/opt/R/4.5.3/bin/Rscript local/prune-stale-flat-binaries.R \
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"$$PRUNE_ARCH" "$$PRUNE_CODENAME" $$APPLY $$PRUNE_PACKAGES
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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: 3Gi
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cpu: 1000m
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# Deleting objects without re-indexing is worse than leaving them: the
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# published index keeps naming files that no longer exist, so every client
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# gets a 404 instead of a working source fallback. The re-index is what
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# republishes them as CRAN source, so it belongs in the same run.
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- name: 'Re-index the slot'
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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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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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R_LIBS_USER: /tmp/R-pkgs
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PRUNE_APPLY: ${PRUNE_APPLY}
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commands:
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- |
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set -eu
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if [ "$$PRUNE_APPLY" != "yes" ]; then
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echo "Dry run: nothing was deleted, so there is nothing to re-index."
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exit 0
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fi
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/opt/R/4.5.3/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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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/4.5.3/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: 3Gi
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cpu: 1000m
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# The edge caches indexes for ~370 days, so without this the deletion is
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# invisible to clients and they keep being handed the removed binary.
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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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BUNNYNET_API_KEY:
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from_secret: BUNNYNET_API_KEY
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# Same zones as reindex.yaml: the production pull zone id, the alliance
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# hostname and the staging zone, which shares the B2 origin.
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BUNNY_PULLZONES: '3857050 cran.allianceswisspass.devxy.io cran-rpkgs-test.b-cdn.net'
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PRUNE_APPLY: ${PRUNE_APPLY}
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commands:
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- |
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set -eu
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if [ "$$PRUNE_APPLY" != "yes" ]; then
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echo "Dry run: nothing changed at the origin, so no purge is needed."
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exit 0
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fi
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apk add --no-cache -q bash curl jq
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bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" $BUNNY_PULLZONES
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