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

bincraft 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.

.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")