fix(ci): install the R packages pipelines use instead of relying on the image (#238)
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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
This commit is contained in:
Patrick Schratz 2026-10-20 08:51:06 +00:00 • committed by Patrick Schratz
commit e77686affc

View file

@ -86,7 +86,7 @@ steps:
# Pin the same bincraft version the build steps use, so the precomputed
# snapshot and the per-agent library stay consistent across the pipeline.
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite purrr
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
- /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))"
backend_options: