refactor: migrate package installation from pak to uvr

bincraft dropped pak in favour of uvr, so the pipelines, helper scripts and images in this repo move with it. - add local/uvr-install.sh as the single replacement for pak::pak(); it bootstraps a pinned uvr, mints a throwaway project under TMPDIR and runs `uvr add --no-install` + `uvr sync --library`, because `uvr add` refuses to run outside a project and only `sync` honours --library - install bincraft via its Forgejo spec (forgejo::codefloe.com/rpkgs/ bincraft@<tag>) instead of a git:: URL, keeping the git ls-remote tag resolution - pass UVR_R_BIN/UVR_TARGET_LIB from install-bincraft.R so the per-R-minor passes target their own R and library - replace R_PKG_CACHE_DIR with UVR_CACHE_DIR/UVR_PACKAGES_DIR on the persistent volume, preserving the amd64-off/arm64-on split - drop trim_pkgcache_metadata() and its test; uvr's cache does not grow the way pkgcache's _metadata dir did - let uvr install system requirements from its vendored r-system-requirements rules, replacing pak::sysreqs_db_update() - migrate the shiny app image, the alpine reprex and the CRAN loading test; ship uvr-install.sh in the build-one image - track the uvr pin with renovate
2026-07-31 12:16:32 +00:00 · 2026-07-31 12:16:32 +00:00 · f3c18b6805
commit f3c18b6805
parent fe2289af56
7 changed files with 327 additions and 245 deletions
--- a/.crow/auto-apply-patches.yaml
+++ b/.crow/auto-apply-patches.yaml
@ -45,7 +45,7 @@ steps:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      - mkdir -p /mnt/cache/R-pkgs
      - rm -rf /mnt/cache/R-pkgs/00LOCK-*
-      - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))'
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
      - /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-pr --limit $PATCH_LIMIT
    backend_options:
      kubernetes:
--- a/.crow/build-all-versions-install-deps.yaml
+++ b/.crow/build-all-versions-install-deps.yaml
@ -10,22 +10,22 @@ variables:
      - arm64
    default: amd64
  OS:
-    description: "Base OS image name."
+    description: 'Base OS image name.'
    options:
      - alpine
      - redhat
      - ubuntu
    default: alpine
  OS_VERSION:
-    description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
+    description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
    options:
-      - "3.24"
-      - "8"
-      - "9"
-      - "10"
-      - "jammy"
-      - "noble"
-    default: "3.24"
+      - '3.24'
+      - '8'
+      - '9'
+      - '10'
+      - 'jammy'
+      - 'noble'
+    default: '3.24'
  R_VERSION:
    description: 'Primary R version under /opt/R.'
    options:
@ -66,23 +66,24 @@ steps:
        from_secret: B2_S3_SECRET_KEY
      PGPASS:
        from_secret: PGPASS
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
      R_LIBS_USER: /mnt/cache/R-pkgs
+      # Keep uvr's downloads and extracted-package entries on the persistent
+      # volume instead of the container-local ~/.uvr default.
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      CCACHE_DIR: /mnt/cache/ccache
    volumes:
      - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
    commands:
      # one-time full wipe to fix corrupted .so files from previous failed builds
      # - rm -rf /mnt/cache/R-pkgs
-      # Clear churny pkgcache metadata left by a prior crashed run (the "patched"
-      # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
-      # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs.
-      - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
-      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
+      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      # 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/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); source("local/install-bincraft.R"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
+      - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
+      - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
      - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))"
    backend_options:
      docker:
--- a/.crow/build-all-versions.yaml
+++ b/.crow/build-all-versions.yaml
@ -11,25 +11,25 @@ variables:
      - arm64
    default: amd64
  OS:
-    description: "Base OS image name."
+    description: 'Base OS image name.'
    options:
      - alpine
      - redhat
      - ubuntu
    default: alpine
  OS_VERSION:
-    description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
+    description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
    options:
-      - "3.22"
-      - "3.23"
-      - "3.24"
-      - "8"
-      - "9"
-      - "10"
-      - "jammy"
-      - "noble"
-      - "resolute"
-    default: "3.24"
+      - '3.22'
+      - '3.23'
+      - '3.24'
+      - '8'
+      - '9'
+      - '10'
+      - 'jammy'
+      - 'noble'
+      - 'resolute'
+    default: '3.24'
  R_VERSION:
    description: 'Primary R version under /opt/R.'
    options:
@ -47,38 +47,49 @@ labels:
  platform: linux/${ARCH}
  group: rpkgs-${ARCH}

+# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local
+# ~/.uvr defaults; amd64 deliberately does not persist them (as with the
+# pkgcache dir it replaces), arm64 does.
 matrix:
  include:
    - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 1
    - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 2
    - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 3
    - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
      SPLIT_INTO: 4
      SPLIT_INDEX: 4
    - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 1
    - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 2
    - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 3
    - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      SPLIT_INTO: 4
      SPLIT_INDEX: 4

@ -107,8 +118,10 @@ steps:
        from_secret: GITHUB_PAT
      # normal env vars
      GIT_USER: pat-s
-      # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
-      R_PKG_CACHE_DIR: ${R_PKG_CACHE_DIR}
+      # set the location of uvr's caches, which persist the R package
+      # dependencies needed to install the packages themselves
+      UVR_CACHE_DIR: ${UVR_CACHE_DIR}
+      UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR}
      R_LIBS_USER: /mnt/cache/R-pkgs
      CCACHE_DIR: /mnt/cache/ccache
      NCPUS: 2
@ -116,12 +129,7 @@ steps:
      - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
    commands:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      # Clear churny pkgcache metadata left by a prior crashed run (the "patched"
-      # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
-      # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs. Within-run
-      # growth is bounded separately by trim_pkgcache_metadata() in build-all.R.
-      - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
-      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
+      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      # The primary pass must not rely on build-all-versions-install-deps having
      # run on *this* agent: depends_on only orders the steps, but the cache
      # volume is per-agent, so a job landing on an agent where install-deps did
--- a/.crow/process-updates.yaml
+++ b/.crow/process-updates.yaml
@ -49,109 +49,109 @@ matrix:
      R_VERSION: 4.5.3
      IMG: alpine:3.22
      OS_ID: alpine322
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
    - OS: alpine-322
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: alpine:3.23
      OS_ID: alpine322
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
    - OS: alpine-323
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: alpine:3.23
      OS_ID: alpine323
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
    - OS: alpine-323
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: alpine:3.23
      OS_ID: alpine323
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
    - OS: alpine-324
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: alpine:3.24
      OS_ID: alpine324
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
    - OS: alpine-324
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: alpine:3.24
      OS_ID: alpine324
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
    - OS: redhat-8
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: redhat:8
      OS_ID: rhel8
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: redhat-8
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: redhat:8
      OS_ID: rhel8
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: redhat-9
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: redhat:9
      OS_ID: rhel9
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: redhat-9
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: redhat:9
      OS_ID: rhel9
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: redhat-10
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: redhat:10
      OS_ID: rhel10
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: redhat-10
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: redhat:10
      OS_ID: rhel10
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: ubuntu-2204
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: ubuntu:jammy
      OS_ID: jammy
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: ubuntu-2204
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: ubuntu:jammy
      OS_ID: jammy
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: ubuntu-2404
      ARCH: amd64
      R_VERSION: 4.4.3
      IMG: ubuntu:noble
      OS_ID: noble
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: ubuntu-2404
      ARCH: arm64
      R_VERSION: 4.4.3
      IMG: ubuntu:noble
      OS_ID: noble
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: ubuntu-2604
      ARCH: amd64
      R_VERSION: 4.5.3
      IMG: ubuntu:resolute
      OS_ID: resolute
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
    - OS: ubuntu-2604
      ARCH: arm64
      R_VERSION: 4.5.3
      IMG: ubuntu:resolute
      OS_ID: resolute
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'

 steps:
  - name: 'Processing Updates'
@ -182,8 +182,10 @@ steps:
      NTFY_AUTH: TRUE
      NTFY_PASSWORD:
        from_secret: ntfy_token
-      # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      # set the location of uvr's caches, which persist the R package
+      # dependencies needed to install the packages themselves
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      R_LIBS_USER: /mnt/cache/R-pkgs
      R_VERSION: ${R_VERSION}
      CCACHE_DIR: /mnt/cache/ccache
@ -194,10 +196,10 @@ steps:
      INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3)
    commands:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/R-pkgs/pkgcache /mnt/cache/pkgcache/R/pkgcache
+      - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft
+      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
      - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
-      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      # rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run
      - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
      # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
--- a/.crow/weekly-audit-missing.yaml
+++ b/.crow/weekly-audit-missing.yaml
@ -142,7 +142,9 @@ steps:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      - mkdir -p /mnt/cache/packages /mnt/cache/R-pkgs
      - rm -rf /mnt/cache/R-pkgs/00LOCK-*
-      - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("git::https://codefloe.com/rpkgs/bincraft.git", "httr2", "jsonlite"))'
+      # bincraft is taken from the default branch here (not the latest release
+      # tag), matching what the pak call did before the uvr migration.
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh forgejo::codefloe.com/rpkgs/bincraft httr2 jsonlite
      - /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")'
    backend_options:
      docker:
--- a/.crow/weekly-patch-proposals.yaml
+++ b/.crow/weekly-patch-proposals.yaml
@ -35,7 +35,7 @@ steps:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
      - mkdir -p /mnt/cache/R-pkgs
      - rm -rf /mnt/cache/R-pkgs/00LOCK-*
-      - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))'
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
      - /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-issue
      - /opt/R/$R_VERSION/bin/Rscript local/proposal-tracking.R --open-issue
    backend_options:
--- a/.crow/weekly-rebuild-missing.yaml
+++ b/.crow/weekly-rebuild-missing.yaml
@ -141,7 +141,8 @@ steps:
      FORGEJO_TOKEN:
        from_secret: FORGEJO_TOKEN
      GIT_USER: pat-s
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
      R_LIBS_USER: /mnt/cache/R-pkgs
      R_VERSION: ${R_VERSION}
      CCACHE_DIR: /mnt/cache/ccache
@ -150,12 +151,12 @@ steps:
      NCPUS: 2
    commands:
      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
+      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
      - rm -rf /mnt/cache/R-pkgs/00LOCK-*
      - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
      - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
      - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
-      - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")'
+      - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
      - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
      - $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', 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 = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1
    backend_options: