build-cran-binaries/.crow/repair-unsafe-flat-objects.yaml

# Rebuild every flat object recorded as unable to load under some R minor.
#
# The list comes from `abi_flat_safety`, written by the flat-safety backfill
# from the binaries themselves, so it names exactly the objects that fail at
# dyn.load() somewhere rather than everything a source heuristic suspects. The
# heuristic calls 93% of compiled packages risky; the binaries say 4.3%.
#
# Each object is rebuilt under every R minor installed in the image, with no
# `--sensitive-only` gate. Since bincraft v5.3.0 the destination is decided by
# the built binary's symbols in `upload_single_binary()`, so a package needing a
# per-minor slot lands there and a portable one lands in the flat slot. Gating
# on the source classifier is what let Rcpp slip through and break every R 4.4
# client on the slot.
#
#   crow pipeline create devxy/build-cran-binaries --var repair_unsafe=all

variables:
  # A manual pipeline creation instantiates every file in .crow/, so the default
  # must match no matrix row.
  repair_unsafe:
    description: "Repair target: a specific <os>-<arch>, 'all' for every slot, or 'none'."
    options:
      - none
      - all
      - alpine-322-amd64
      - alpine-322-arm64
      - 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

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

skip_clone: true

labels:
  group: rpkgs-${ARCH}

matrix:
  include:
    - OS: alpine-322
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: alpine:3.22
    - OS: alpine-322
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: alpine:3.22
    - 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 objects recorded unsafe'
    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
      R_LIBS_USER: /tmp/R-pkgs
      NCPUS: 2
      REPAIR_ARCH: ${ARCH}
    commands:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      - mkdir -p /tmp/R-pkgs
      - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
      - |
        set -eu
        CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e 'cat(bincraft::set_codename(NULL))')
        /opt/R/$R_VERSION/bin/Rscript local/list-unsafe-flat-objects.R \
          "$$REPAIR_ARCH" "$$CODENAME" > /tmp/unsafe.txt
        echo "objects to rebuild: $(wc -l < /tmp/unsafe.txt)"
        rc=0
        for RBIN in /opt/R/[0-9]*/bin/R; do
          RV=$(basename "$(dirname "$(dirname "$$RBIN")")")
          RMINOR=$(echo "$$RV" | cut -d. -f1-2)
          echo "=== rebuilding under R $$RV ==="
          LIB="/tmp/R-pkgs-$$RMINOR"
          mkdir -p "$$LIB"
          R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" local/install-bincraft.R || true
          while read -r pkg ver; do
            [ -z "$$pkg" ] && continue
            R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" \
              local/build-one.R "$$pkg" "$$ver" || rc=1
          done < /tmp/unsafe.txt
        done
        exit $$rc
    backend_options:
      docker:
        resources:
          requests:
            memory: 5Gi
            cpu: 1000m