fix(ci): install the R packages pipelines use instead of relying on the image (#238)

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

.crow/backfill-abi-classification.yaml

@@ -74,6 +74,7 @@ steps:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
       - mkdir -p /tmp/R-pkgs
       - /opt/R/4.5.3/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/4.5.3/bin/R local/uvr-install.sh RPostgres
       - |
         set -eu
         LIMIT=""

.crow/backfill-flat-safety.yaml

@@ -155,6 +155,7 @@ steps:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
       - mkdir -p /tmp/R-pkgs
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
       - |
         set -eu
         LIMIT=""

.crow/build-all-versions-install-deps.yaml

@@ -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:

.crow/build-all-versions.yaml

@@ -152,7 +152,7 @@ steps:
       # 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/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
+      - UVR_R_BIN=/opt/R/$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
       - |

.crow/process-updates.yaml

@@ -189,7 +189,7 @@ steps:
       - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft
       - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
-      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres progressr lubridate
       - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
       # rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run
       - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
@@ -205,7 +205,7 @@ steps:
           LIB="/mnt/cache/R-pkgs-$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="$LIB" UVR_R_BIN="$RBIN" local/uvr-install.sh RPostgres lubridate || true
           R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -- "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, patches = 'local/patches', r_minor_detection = 'classifier',r_minor_sensitive_only = TRUE, 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_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'verify-full', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true
           # Also build current packages whose required dependency tree needs a newer R.
           R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -- "$(dirname "$RBIN")/Rscript" local/build-newer-r.R "$R_VERSION"

.crow/prune-stale-flat-binaries.yaml

@@ -167,6 +167,7 @@ steps:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
       - mkdir -p /tmp/R-pkgs
       - /opt/R/4.5.3/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/4.5.3/bin/R local/uvr-install.sh RPostgres
       - |
         set -eu
         APPLY=""
@@ -208,6 +209,10 @@ steps:
           echo "Dry run: nothing was deleted, so there is nothing to re-index."
           exit 0
         fi
+        # /tmp is container-local, so the library installed by the prune step is gone here.
+        mkdir -p /tmp/R-pkgs
+        /opt/R/4.5.3/bin/Rscript local/install-bincraft.R
+        UVR_R_BIN=/opt/R/4.5.3/bin/R local/uvr-install.sh RPostgres
         /opt/R/4.5.3/bin/R -q -e 'library(bincraft); upload_package_index(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

.crow/rebuild-abi-gap.yaml

@@ -193,6 +193,7 @@ steps:
         export R_LIBS_USER="$$LIB"
         rm -rf "$$LIB"/00LOCK-*
         "$$RBIN/Rscript" local/install-bincraft.R
+        UVR_R_BIN="$$RBIN/R" local/uvr-install.sh RPostgres
         rc=0
         for spec in $$ABI_PACKAGES; do
           pkg=$${spec%@*}

.crow/reindex.yaml

@@ -158,6 +158,7 @@ steps:
       - mkdir -p /mnt/cache/R-pkgs
       - rm -rf /mnt/cache/R-pkgs/00LOCK-*
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
       # The codename is detected from the image's /etc/os-release.
       - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(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"))'
       - |

.crow/repair-unsafe-flat-objects.yaml

@@ -144,6 +144,7 @@ steps:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
       - mkdir -p /tmp/R-pkgs
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
       - |
         set -eu
         CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e 'cat(bincraft::set_codename(NULL))')
@@ -158,6 +159,7 @@ steps:
           LIB="/tmp/R-pkgs-$$RMINOR"
           mkdir -p "$$LIB"
           R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" local/install-bincraft.R || true
+          R_LIBS_USER="$$LIB" UVR_R_BIN="$$RBIN" local/uvr-install.sh RPostgres || true
           while read -r pkg ver; do
             [ -z "$$pkg" ] && continue
             R_LIBS_USER="$$LIB" "$(dirname "$$RBIN")/Rscript" \

.crow/weekly-audit-missing.yaml

@@ -137,7 +137,7 @@ steps:
       - mkdir -p /mnt/cache/packages /mnt/cache/R-pkgs
       - rm -rf /mnt/cache/R-pkgs/00LOCK-*
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
-      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2 jsonlite
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2 jsonlite data.table
       - /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")'
     backend_options:
       docker:

.crow/weekly-rebuild-missing.yaml

@@ -389,7 +389,7 @@ steps:
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
       - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
       - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
-      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2
       - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
       - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1
     backend_options:

.crow/weekly-rebuild-reindex.yaml

@@ -161,6 +161,7 @@ steps:
       - mkdir -p /mnt/cache/R-pkgs
       - rm -rf /mnt/cache/R-pkgs/00LOCK-*
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
       # The codename is detected from the image's /etc/os-release.
       - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(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"))'
       - |

local/packages-to-build.R

@@ -5,10 +5,8 @@ options(error = function() {
 })
 
 library(bincraft, quietly = TRUE)
-suppressPackageStartupMessages(library(dplyr))
 library(DBI, quietly = TRUE)
 library(purrr, quietly = TRUE)
-library(progressr, quietly = TRUE)
 suppressPackageStartupMessages(library(data.table))
 
 # Sys.setenv("OS" = "alpine")