build-cran-binaries/.crow/build-all-versions.yaml

### Manual full rebuild of all CRAN binaries for one OS/arch.
# Set the variables below in the manual-run form (or via --var on the CLI).
# `target_arch` routes the matrix; OS/OS_VERSION/R_VERSION select the platform
# image and cache volume. Placement is via the group label (rpkgs-amd64/rpkgs-arm64).
# Skip list lives in local/excluded-packages.json (read by local/build-all.R).
variables:
  # Gates this pipeline. A manual pipeline creation instantiates every file in
  # .crow/, and a declared default is applied even when the run never passed
  # this variable, so the default must be a value that matches no matrix row.
  target_arch:
    description: 'Architecture to build, or "none" to run nothing.'
    options:
      - none
      - amd64
      - arm64
    default: none
  OS:
    description: 'Base OS image name.'
    options:
      - alpine
      - redhat
      - ubuntu
    default: alpine
  OS_VERSION:
    description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
    options:
      - '3.23'
      - '3.24'
      - '8'
      - '9'
      - '10'
      - 'jammy'
      - 'noble'
      - 'resolute'
    default: '3.24'
  R_VERSION:
    # The slot's *primary* R minor: what `local/build-all.R` builds into the
    # generic slot. The loop below already runs `--sensitive-only` for every
    # other installed minor, so filling a non-primary minor's gap needs this
    # left alone, not changed.
    #
    # 4.6.0 was briefly offered here (#183) and removed: selecting it for a
    # slot whose generic binaries are 4.5-built would publish 4.6 binaries
    # into the generic slot and break every 4.5 client.
    description: 'Primary R version under /opt/R.'
    options:
      - 4.5.3
      - 4.4.3
    default: 4.5.3

when:
  - event: manual
    evaluate: 'target_arch == "${ARCH}"'

skip_clone: true

labels:
  platform: linux/${ARCH}
  group: rpkgs-${ARCH}

# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local
# ~/.uvr defaults; amd64 deliberately does not persist them (as with the
# pkgcache dir it replaces), arm64 does.
matrix:
  include:
    - ARCH: amd64
      UVR_CACHE_DIR: ''
      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 1
    - ARCH: amd64
      UVR_CACHE_DIR: ''
      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 2
    - ARCH: amd64
      UVR_CACHE_DIR: ''
      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 3
    - ARCH: amd64
      UVR_CACHE_DIR: ''
      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 4
    - ARCH: arm64
      UVR_CACHE_DIR: /mnt/cache/uvr/cache
      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 1
    - ARCH: arm64
      UVR_CACHE_DIR: /mnt/cache/uvr/cache
      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 2
    - ARCH: arm64
      UVR_CACHE_DIR: /mnt/cache/uvr/cache
      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 3
    - ARCH: arm64
      UVR_CACHE_DIR: /mnt/cache/uvr/cache
      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 4

depends_on:
  - build-all-versions-install-deps

steps:
  - name: 'Build binaries'
    image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
    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
      # normal env vars
      GIT_USER: pat-s
      # set the location of uvr's caches, which persist the R package
      # dependencies needed to install the packages themselves
      UVR_CACHE_DIR: ${UVR_CACHE_DIR}
      UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR}
      R_LIBS_USER: /mnt/cache/R-pkgs
      CCACHE_DIR: /mnt/cache/ccache
      NCPUS: 2
      # Whole hours the build passes below may use, measured from the step's
      # start. The repo timeout is 50h; the remainder is left for archiving the
      # missed packages, so a long run ends cleanly instead of being killed.
      BUILD_BUDGET_HOURS: 44
    volumes:
      - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
    commands:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      - . local/compiler-cache.sh
      # One deadline shared by every build pass in this step, read by
      # local/build-all.R and local/build-newer-r.R before each package.
      - export BUILD_DEADLINE=$(( $(date +%s) + BUILD_BUDGET_HOURS * 3600 ))
      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      # The primary pass must not rely on build-all-versions-install-deps having
      # run on *this* agent: depends_on only orders the steps, but the cache
      # volume is per-agent, so a job landing on an agent where install-deps did
      # not run would otherwise use a stale bincraft (which resolves `platform`
      # to a zero-length value and breaks every metadata query and the sysdeps
      # install). Pin bincraft here, exactly like the R-minor pass below.
      - rm -rf /mnt/cache/R-pkgs/00LOCK-*
      - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
      # The dependency-prep job may run on another agent whose cache volume is
      # not visible here. Install the packages needed to recompute the snapshot
      # and query build metadata in every build job.
      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite purrr
      - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
      - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/build-all.R $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1
      - |
        PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2)
        for RBIN in /opt/R/[0-9]*/bin/R; do
          RV=$(basename "$(dirname "$(dirname "$RBIN")")")
          RMINOR=$(echo "$RV" | cut -d. -f1-2)
          [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue
          echo "=== R-minor-sensitive pass under R $RV ==="
          LIB="/mnt/cache/R-pkgs-$RMINOR"
          mkdir -p "$LIB"
          R_LIBS_USER="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true
          R_LIBS_USER="$LIB" UVR_R_BIN="$RBIN" local/uvr-install.sh RPostgres || true
          R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true
          # Also build current packages whose required dependency tree needs a newer R.
          R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$(dirname "$RBIN")/Rscript" local/build-newer-r.R "$R_VERSION" $SPLIT_INTO $SPLIT_INDEX
        done
      # archive missed packages; first arg is the codename (e.g. "alpine324"),
      # derived via bincraft like the upload step, not paste(OS, OS_VERSION).
      - /opt/R/$R_VERSION/bin/R -q -e "bincraft::process_unarchived_pkgs(bincraft::set_codename(NULL), Sys.getenv('ARCH'), 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'), workers = $NCPUS)"
    backend_options:
      docker:
        resources:
          requests:
            memory: 5Gi
            cpu: 1000m
          limits:
            memory: 20Gi
            cpu: 2000m
  - name: 'Upload package indexes'
    image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
    pull: true
    environment:
      OTEL_R_TRACES_EXPORTER: none
      OTEL_R_LOGS_EXPORTER: none
      OTEL_R_METRICS_EXPORTER: none
      B2_S3_ACCESS_KEY:
        from_secret: B2_S3_ACCESS_KEY
      B2_S3_SECRET_KEY:
        from_secret: B2_S3_SECRET_KEY
      # A per-minor index reads the ABI classifier cache and the flat-object
      # safety table from the build database, and is not republished without it.
      PGPASS:
        from_secret: PGPASS
      R_LIBS_USER: /mnt/cache/R-pkgs
    volumes:
      - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
    commands:
      - |
        CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e "cat(bincraft::set_codename(NULL))")
        /opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))"
        FAILED_MINORS=""
        for RBIN in /opt/R/[0-9]*/bin/R; do
          RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
          /opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', r_minor = '$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'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_port = 15432L, metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'verify-full')" || FAILED_MINORS="$FAILED_MINORS $RMINOR"
        done
        if [ -n "$FAILED_MINORS" ]; then
          echo "Could not republish the per-minor index for:$FAILED_MINORS" >&2
          exit 1
        fi
    backend_options:
      docker:
        resources:
          requests:
            memory: 5Gi
            cpu: 1000m
          limits:
            memory: 20Gi
            cpu: 2000m