pat-s
8140702b5fAlpine 3.22 is deprecated and is no longer a published slot.
It was never routed: `local.rpkgs_slots` in `cdn.tf` lists eight distros and
alpine322 is not among them, so `UNION_SLOTS` never gated per-minor rewriting
for it and every request fell through to the flat index.
The fleet-wide routing verification made that concrete.
Across all 16 published slots, both architectures, three R minors and both
contractual URL forms, 1056 of 1056 install-and-load checks passed.
Every failure in the run was alpine322, identical on amd64 and arm64, and
identical across `arch`, `generic` and `flat`.
That last part is the signature of an unrouted slot: on a routed slot the
contractual forms diverge from `flat`, because the divergence is the routing.
Its flat objects are R 4.5 builds, so R 4.4 and R 4.6 clients got
`LOAD_FAILED` while R 4.5 clients were fine.
This change will:
- Remove the alpine-322 matrix rows and dropdown options from every pipeline
that carried them, so `=all` no longer fans out to a slot nobody can reach.
- Remove `3.22` from the `OS_VERSION` dropdowns in `build-all-versions.yaml`
and `repair-built-stamp.yaml`, and move the latter's default to `3.23`.
- Update the stale `3.22` examples in `local/packages-to-build.R`.
The six alpine-322 cron jobs are deleted from the Crow server as well, since a
cron whose matrix row is gone would keep firing against nothing:
5 process-cran-updates-alpine-322-amd64 0 5/8 * * *
6 process-cran-updates-alpine-322-arm64 30 5/8 * * *
68 weekly-audit-missing-alpine-322-amd64 20 0 * * 0
69 weekly-audit-missing-alpine-322-arm64 30 0 * * 0
82 weekly-rebuild-missing-alpine-322-amd64 0 4 * * 0
83 weekly-rebuild-missing-alpine-322-arm64 10 4 * * 0
The published objects and indexes under `amd64/alpine322` and `arm64/alpine322`
are left in place; removing them from the bucket is a separate decision.
214 lines
6.3 KiB
YAML
214 lines
6.3 KiB
YAML
# Rebuild specific packages into a per-R-minor slot.
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#
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# The per-minor scheme only ever covered packages that passed through the build
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# pipeline after it existed. A package built into the flat slot before that, and
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# never updated on CRAN since, is never reclassified and never gets a per-minor
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# copy - so the union index serves its flat binary to every minor. When that
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# binary references a symbol the client's R no longer exports, the install fails
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# at dyn.load():
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#
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# base64enc.so: undefined symbol: SETLENGTH
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#
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# base64enc calls SETLENGTH, its flat binary was built under R 4.4.3, and R 4.6
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# does not export SETLENGTH. There was no way to rebuild one package into one
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# minor from CI, only `just rebuild` from a workstation with the S3 and Postgres
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# credentials to hand. This adds that path.
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#
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# `--sensitive-only` is deliberately NOT passed. That flag gates on the source
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# classifier, which misses Rcpp: the repair therefore skipped Rcpp entirely,
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# leaving its 4.5-built flat binary as the only copy and breaking every R 4.4
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# client on the slot.
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#
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# Since bincraft v5.3.0 the destination is decided by the built binary's symbols
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# in `upload_single_binary()`, so building unconditionally is safe: a package
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# that needs a per-minor slot lands there, and one that does not lands in the
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# flat slot. Skipping before the build is what removed that decision.
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#
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# Trigger with the slot and an explicit package list:
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#
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# crow pipeline create devxy/build-cran-binaries \
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# --var rebuild_abi_gap=ubuntu-2604-amd64 \
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# --var ABI_PACKAGES="base64enc@0.1-6 lobstr@1.2.1" \
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# --var ABI_R_MINOR=4.6
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variables:
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# A manual pipeline creation instantiates every file in .crow/, so the
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# default must match no matrix row.
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rebuild_abi_gap:
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description: "Rebuild 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-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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ABI_PACKAGES:
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description: 'Space-separated package@version list, e.g. "base64enc@0.1-6 lobstr@1.2.1".'
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default: ''
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ABI_R_MINOR:
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description: 'The R minor to build into.'
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options:
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- '4.4'
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- '4.5'
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- '4.6'
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default: '4.6'
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when:
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- event: manual
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evaluate: 'rebuild_abi_gap == "all" || rebuild_abi_gap == "${OS}-${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-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 packages into the per-minor 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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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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GIT_USER: pat-s
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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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ABI_PACKAGES: ${ABI_PACKAGES}
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ABI_R_MINOR: ${ABI_R_MINOR}
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UVR_CACHE_DIR: /tmp/uvr/cache
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UVR_PACKAGES_DIR: /tmp/uvr/packages
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CCACHE_DIR: /tmp/ccache
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NCPUS: 2
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commands:
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- mkdir -p $UVR_CACHE_DIR $UVR_PACKAGES_DIR $CCACHE_DIR
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- |
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set -eu
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if [ -z "$$ABI_PACKAGES" ]; then
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echo "ABI_PACKAGES is empty; nothing to rebuild." >&2
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exit 1
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fi
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RBIN=$(ls -d /opt/R/$${ABI_R_MINOR}*/bin 2>/dev/null | head -1)
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if [ -z "$$RBIN" ]; then
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echo "R $$ABI_R_MINOR is not installed in this image." >&2
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exit 1
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fi
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# Container-local library: this workflow mounts no shared cache volume,
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# so it cannot disturb the build pipeline's per-agent caches.
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LIB="/tmp/R-pkgs-$$ABI_R_MINOR"
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mkdir -p "$$LIB"
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export R_LIBS_USER="$$LIB"
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rm -rf "$$LIB"/00LOCK-*
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"$$RBIN/Rscript" local/install-bincraft.R
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rc=0
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for spec in $$ABI_PACKAGES; do
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pkg=$${spec%@*}
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ver=$${spec#*@}
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if [ "$$pkg" = "$$ver" ]; then
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echo "malformed spec '$$spec'; expected package@version" >&2
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rc=1
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continue
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fi
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echo "=== rebuilding $$pkg $$ver into $$ABI_R_MINOR ==="
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"$$RBIN/Rscript" local/build-one.R "$$pkg" "$$ver" || rc=1
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done
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exit $$rc
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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: 1000m
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