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refactor: migrate package installation from pak to uvr

Browse source 
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
This commit is contained in:
Patrick Schratz 2026-07-31 12:16:32 +00:00
commit f3c18b6805
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GPG key ID: 62050D5BC68AB6DC
1 changed files with 327 additions and 245 deletions
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46
.crow/process-updates.yaml
View file

@ -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