pat-s
930a4acd12bincraft v5.5.1 dropped lubridate, dplyr, purrr, data.table and others from its imports, so the pipelines' own calls now depend on whatever the build-env image's site library or the shared R_LIBS_USER cache happens to hold. The arm64 redhat:9 image has no progressr under R 4.4.3, which fails every process-cran-updates-redhat-9-arm64 run since v5.5.1. - Install progressr and lubridate for process-updates, which call them inline. - Install purrr for packages-to-build.R and data.table for the weekly audit. - Drop the unused dplyr and progressr library() calls from packages-to-build.R. - Install RPostgres in every pipeline that talks to the metadata DB, since bincraft silently skips the DB (and the per-minor index aborts) without it. - Reinstall bincraft in the prune re-index step, whose /tmp library does not survive from the prune step.
175 lines
5 KiB
YAML
175 lines
5 KiB
YAML
# Rebuild every flat object recorded as unable to load under some R minor.
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#
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# The list comes from `abi_flat_safety`, written by the flat-safety backfill
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# from the binaries themselves, so it names exactly the objects that fail at
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# dyn.load() somewhere rather than everything a source heuristic suspects. The
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# heuristic calls 93% of compiled packages risky; the binaries say 4.3%.
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#
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# Each object is rebuilt under every R minor installed in the image, with no
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# `--sensitive-only` gate. Since bincraft v5.3.0 the destination is decided by
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# the built binary's symbols in `upload_single_binary()`, so a package needing a
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# per-minor slot lands there and a portable one lands in the flat slot. Gating
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# on the source classifier is what let Rcpp slip through and break every R 4.4
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# client on the slot.
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#
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# crow pipeline create devxy/build-cran-binaries --var repair_unsafe=all
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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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repair_unsafe:
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description: "Repair 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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when:
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- event: manual
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evaluate: 'repair_unsafe == "all" || repair_unsafe == "${OS}-${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 objects recorded unsafe'
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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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R_LIBS_USER: /tmp/R-pkgs
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NCPUS: 2
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REPAIR_ARCH: ${ARCH}
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commands:
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- mkdir -p /tmp/R-pkgs
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- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
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- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
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- |
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set -eu
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CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e 'cat(bincraft::set_codename(NULL))')
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/opt/R/$R_VERSION/bin/Rscript local/list-unsafe-flat-objects.R \
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"$$REPAIR_ARCH" "$$CODENAME" > /tmp/unsafe.txt
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echo "objects to rebuild: $(wc -l < /tmp/unsafe.txt)"
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rc=0
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for RBIN in /opt/R/[0-9]*/bin/R; do
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RV=$(basename "$(dirname "$(dirname "$$RBIN")")")
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RMINOR=$(echo "$$RV" | cut -d. -f1-2)
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echo "=== rebuilding under R $$RV ==="
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LIB="/tmp/R-pkgs-$$RMINOR"
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mkdir -p "$$LIB"
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R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" local/install-bincraft.R || true
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R_LIBS_USER="$$LIB" UVR_R_BIN="$$RBIN" local/uvr-install.sh RPostgres || true
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while read -r pkg ver; do
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[ -z "$$pkg" ] && continue
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R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" \
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local/build-one.R "$$pkg" "$$ver" || rc=1
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done < /tmp/unsafe.txt
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done
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exit $$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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