build-cran-binaries/.crow/rebuild-abi-gap.yaml

# Rebuild specific packages into a per-R-minor slot.
#
# The per-minor scheme only ever covered packages that passed through the build
# pipeline after it existed. A package built into the flat slot before that, and
# never updated on CRAN since, is never reclassified and never gets a per-minor
# copy - so the union index serves its flat binary to every minor. When that
# binary references a symbol the client's R no longer exports, the install fails
# at dyn.load():
#
#   base64enc.so: undefined symbol: SETLENGTH
#
# base64enc calls SETLENGTH, its flat binary was built under R 4.4.3, and R 4.6
# does not export SETLENGTH. There was no way to rebuild one package into one
# minor from CI, only `just rebuild` from a workstation with the S3 and Postgres
# credentials to hand. This adds that path.
#
# `--sensitive-only` is deliberately NOT passed. That flag gates on the source
# classifier, which misses Rcpp: the repair therefore skipped Rcpp entirely,
# leaving its 4.5-built flat binary as the only copy and breaking every R 4.4
# client on the slot.
#
# Since bincraft v5.3.0 the destination is decided by the built binary's symbols
# in `upload_single_binary()`, so building unconditionally is safe: a package
# that needs a per-minor slot lands there, and one that does not lands in the
# flat slot. Skipping before the build is what removed that decision.
#
# Trigger with the slot and an explicit package list:
#
#   crow pipeline create devxy/build-cran-binaries \
#     --var rebuild_abi_gap=ubuntu-2604-amd64 \
#     --var ABI_PACKAGES="base64enc@0.1-6 lobstr@1.2.1" \
#     --var ABI_R_MINOR=4.6

variables:
  # A manual pipeline creation instantiates every file in .crow/, so the
  # default must match no matrix row.
  rebuild_abi_gap:
    description: "Rebuild target: a specific <os>-<arch>, 'all' for every slot, or 'none'."
    options:
      - none
      - all
      - alpine-323-amd64
      - alpine-323-arm64
      - alpine-324-amd64
      - alpine-324-arm64
      - redhat-8-amd64
      - redhat-8-arm64
      - redhat-9-amd64
      - redhat-9-arm64
      - redhat-10-amd64
      - redhat-10-arm64
      - ubuntu-2204-amd64
      - ubuntu-2204-arm64
      - ubuntu-2404-amd64
      - ubuntu-2404-arm64
      - ubuntu-2604-amd64
      - ubuntu-2604-arm64
    default: none
  ABI_PACKAGES:
    description: 'Space-separated package@version list, e.g. "base64enc@0.1-6 lobstr@1.2.1".'
    default: ''
  ABI_R_MINOR:
    description: 'The R minor to build into.'
    options:
      - '4.4'
      - '4.5'
      - '4.6'
    default: '4.6'

when:
  - event: manual
    evaluate: 'rebuild_abi_gap == "all" || rebuild_abi_gap == "${OS}-${ARCH}"'

skip_clone: true

labels:
  group: rpkgs-${ARCH}

matrix:
  include:
    - OS: alpine-323
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: alpine:3.23
    - OS: alpine-323
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: alpine:3.23
    - OS: alpine-324
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: alpine:3.24
    - OS: alpine-324
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: alpine:3.24
    - OS: redhat-8
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: redhat:8
    - OS: redhat-8
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: redhat:8
    - OS: redhat-9
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: redhat:9
    - OS: redhat-9
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: redhat:9
    - OS: redhat-10
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: redhat:10
    - OS: redhat-10
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: redhat:10
    - OS: ubuntu-2204
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: ubuntu:jammy
    - OS: ubuntu-2204
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: ubuntu:jammy
    - OS: ubuntu-2404
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: ubuntu:noble
    - OS: ubuntu-2404
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: ubuntu:noble
    - OS: ubuntu-2604
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: ubuntu:resolute
    - OS: ubuntu-2604
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: ubuntu:resolute

steps:
  - name: 'Rebuild packages into the per-minor slot'
    image: reg.devxy.io/rpkgs/build-env-${IMG}
    pull: true
    environment:
      OTEL_R_TRACES_EXPORTER: none
      OTEL_R_LOGS_EXPORTER: none
      OTEL_R_METRICS_EXPORTER: none
      RED_HAT_DEV_PW:
        from_secret: RED_HAT_DEV_PW
      B2_S3_ACCESS_KEY:
        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
      GIT_USER: pat-s
      # Pipeline variables are substituted into the YAML, not exported, so they
      # have to be bound here to be readable as env vars in the script below.
      ABI_PACKAGES: ${ABI_PACKAGES}
      ABI_R_MINOR: ${ABI_R_MINOR}
      UVR_CACHE_DIR: /tmp/uvr/cache
      UVR_PACKAGES_DIR: /tmp/uvr/packages
      CCACHE_DIR: /tmp/ccache
      NCPUS: 2
    commands:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      - mkdir -p $UVR_CACHE_DIR $UVR_PACKAGES_DIR $CCACHE_DIR
      - |
        set -eu
        if [ -z "$$ABI_PACKAGES" ]; then
          echo "ABI_PACKAGES is empty; nothing to rebuild." >&2
          exit 1
        fi
        RBIN=$(ls -d /opt/R/$${ABI_R_MINOR}*/bin 2>/dev/null | head -1)
        if [ -z "$$RBIN" ]; then
          echo "R $$ABI_R_MINOR is not installed in this image." >&2
          exit 1
        fi
        # Container-local library: this workflow mounts no shared cache volume,
        # so it cannot disturb the build pipeline's per-agent caches.
        LIB="/tmp/R-pkgs-$$ABI_R_MINOR"
        mkdir -p "$$LIB"
        export R_LIBS_USER="$$LIB"
        rm -rf "$$LIB"/00LOCK-*
        "$$RBIN/Rscript" local/install-bincraft.R
        UVR_R_BIN="$$RBIN/R" local/uvr-install.sh RPostgres
        rc=0
        for spec in $$ABI_PACKAGES; do
          pkg=$${spec%@*}
          ver=$${spec#*@}
          if [ "$$pkg" = "$$ver" ]; then
            echo "malformed spec '$$spec'; expected package@version" >&2
            rc=1
            continue
          fi
          echo "=== rebuilding $$pkg $$ver into $$ABI_R_MINOR ==="
          "$$RBIN/Rscript" local/build-one.R "$$pkg" "$$ver" || rc=1
        done
        exit $$rc
    backend_options:
      docker:
        resources:
          requests:
            memory: 5Gi
            cpu: 1000m