pat-s
e77686affc
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Every `process-cran-updates-redhat-9-arm64` run since bincraft v5.5.1 fails with `there is no package called 'progressr'` (e.g. pipeline 14179). ## Cause bincraft v5.5.1 dropped `lubridate`, `dplyr`, `purrr`, `data.table`, `gert`, `gh` and `cranlike` from its imports. The pipelines call some of these directly, and so far got them from the build-env image's site library or the shared `R_LIBS_USER` cache. The arm64 `redhat:9` image has no `progressr` (and no `bincraft`) under R 4.4.3, and no `RPostgres`, `dplyr` or `purrr` under R 4.5.3. The amd64 image has all of them, which is why only this slot broke. ## Changes - `process-updates.yaml`: install `progressr` and `lubridate`, which the inline R calls use (`progressr::handlers`, `$INTERVAL`). - `build-all-versions*.yaml`: install `purrr` for `packages-to-build.R`. - `weekly-audit-missing.yaml`: install `data.table` for the audit script. - `local/packages-to-build.R`: drop the unused `dplyr` and `progressr` `library()` calls. - `reindex`, `weekly-rebuild-reindex`, `weekly-rebuild-missing`, `backfill-*`, `rebuild-abi-gap`, `repair-unsafe-flat-objects`, `prune-stale-flat-binaries`: install `RPostgres`, because bincraft quietly skips the metadata DB without it and the per-minor index build aborts. - `prune-stale-flat-binaries.yaml`: reinstall bincraft in the re-index step, since its `/tmp/R-pkgs` library doesn't survive from the prune step. ## Verification - `crow lint .crow/` passes; `prek` passes on the changed files. - The image contents were checked by exporting the arm64 and amd64 `build-env-redhat:9` images. - Not yet run in CI. Reviewed-on: #238
150 lines
4.1 KiB
YAML
150 lines
4.1 KiB
YAML
# Consolidated weekly-audit-missing pipeline (all platforms, both arches).
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# One matrix row per OS/arch replaces the former per-platform files.
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# Routing is preserved 1:1:
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# - cron: each existing `weekly-audit-missing-<os>-<arch>` cron fires only
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# its matching matrix row (via the per-row `cron:` name filter).
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# - manual: pick a target from the `weekly_audit_missing` dropdown;
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# "all" fans out every os/arch as parallel matrix workflows.
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# Arch placement is via the group label (rpkgs-amd64, rpkgs-arm64).
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variables:
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# Gates this pipeline. A manual pipeline creation instantiates every file in
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# .crow/, and a declared default is applied even when the run never passed
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# this variable, so the default must be a value that matches no matrix row.
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weekly_audit_missing:
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description: "Manual run target: a specific <os>-<arch>, 'all' to run every os/arch in parallel, or 'none' to run nothing."
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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: cron
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cron: weekly-audit-missing-${OS}-${ARCH}
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- event: manual
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evaluate: 'weekly_audit_missing == "all" || weekly_audit_missing == "${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: 4.5.3
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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: 4.5.3
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IMG: ubuntu:resolute
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steps:
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- name: 'Audit missing binaries'
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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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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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FORGEJO_TOKEN:
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from_secret: FORGEJO_TOKEN
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PLATFORM: ${OS}
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ARCH: ${ARCH}
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R_LIBS_USER: /mnt/cache/R-pkgs
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R_VERSION: ${R_VERSION}
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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 /mnt/cache/packages /mnt/cache/R-pkgs
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- rm -rf /mnt/cache/R-pkgs/00LOCK-*
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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 httr2 jsonlite data.table
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- /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")'
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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: 2Gi
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cpu: 2000m
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limits:
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memory: 4Gi
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cpu: 2000m
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