refactor: migrate package installation from pak to uvr (#147)
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`bincraft` dropped pak in favour of uvr (5.0.x, "Dependencies and their system requirements are now installed with `uvr` instead of pak during `build_binary_package()`"), so the pipelines, helper scripts and images in this repo move with it.

## Approach

uvr is project-scoped in a way pak is not: `uvr add` refuses to run outside a project and always installs into `.uvr/library/`, and only `uvr sync` honours `--library`. So there is no one-line `pak::pak(...)` equivalent. `local/uvr-install.sh` encapsulates the dance — bootstrap a pinned uvr, mint a throwaway project under `TMPDIR`, `uvr add --no-install`, then `uvr sync --library <target>`. Keeping the project outside the checkout also keeps `uvr init`'s `.Rprofile` from hijacking `.libPaths()` for every other R call in the pipeline.

This matches what bincraft itself does (`uvr sync --install-system-deps --library <lib>`), and bincraft requires `uvr` on `PATH`, which the bootstrap provides: every pipeline that calls `bincraft::` runs `install-bincraft.R` (and therefore the bootstrap) first.

## Changes

| File | Change |
| --- | --- |
| `local/uvr-install.sh` | **New.** The single replacement for `pak::pak(...)`. Bootstraps uvr `v0.4.4`, resolves the R interpreter from `UVR_R_BIN`/`R_VERSION`/`PATH`, pins the manifest to that R's exact version, and syncs into `UVR_TARGET_LIB`/`R_LIBS_USER`. |
| `local/install-bincraft.R` | Installs `forgejo::codefloe.com/rpkgs/bincraft@<tag>` instead of a `git::` URL; keeps the `git ls-remote` tag resolution. Exports `UVR_R_BIN`/`UVR_TARGET_LIB` from `R.home()`/`.libPaths()[1]` so the per-R-minor passes target their own R and library. |
| `.crow/auto-apply-patches.yaml`, `.crow/weekly-patch-proposals.yaml`, `.crow/weekly-audit-missing.yaml`, `.crow/weekly-rebuild-missing.yaml`, `.crow/build-all-versions-install-deps.yaml` | `pak::pak(...)` → `UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh ...`. The explicit `UVR_R_BIN` matters in `build-all-versions-install-deps.yaml`, which has no `R_VERSION` in its step environment. |
| `.crow/build-all-versions.yaml`, `.crow/process-updates.yaml`, `.crow/weekly-rebuild-missing.yaml` | `R_PKG_CACHE_DIR` → `UVR_CACHE_DIR` + `UVR_PACKAGES_DIR` on the same `/mnt/cache` volume, preserving the amd64-off/arm64-on split. Drops the `rm -rf .../pkgcache/_metadata/...` cleanup. |
| `local/r-minor-helpers.R`, `local/build-all.R`, `local/tests/test-trim-pkgcache.R` | Removes `trim_pkgcache_metadata()`, its every-25-packages call and its tests. uvr's cache does not mint a fresh ~70 MB snapshot per `PACKAGES` change. |
| `.crow/build-all-versions-install-deps.yaml` | Drops `pak::sysreqs_db_update()`; uvr resolves sysreqs from its vendored `r-system-requirements` rules via `--install-system-deps`. |
| `docker/Containerfile-shiny-app` | Bootstraps uvr and drives both dependency installs through one uvr project with `UVR_LIBRARY` pointed at the image's R library. |
| `docker/build-one.Dockerfile` | Ships `uvr-install.sh` at `/work/local/` so `install-bincraft.R` finds it. |
| `docker/reprex/alpine.sh` | Replaces `pak::local_install_deps()` with DESCRIPTION parsing + `uvr add`. |
| `local/test-package-loading.R` | Installs via the helper instead of `pak::pkg_install()`. |
| `README.md` | Documents uvr for sysreq inference, archived-version installs and cache clearing. |
| `renovate.json` | Tracks the `UVR_PIN` in `uvr-install.sh` via `github-releases`. |

## Behaviour notes

- **`weekly-audit-missing` still takes bincraft from the default branch**, not the latest release tag, matching what the `git::` pak call did. Called out in a comment rather than silently changed.
- **The uvr pin is repo-wide.** bincraft resolves `uvr` from `PATH` and pins no version of its own, so `UVR_PIN` in `uvr-install.sh` governs the whole pipeline.
- **Persistent caches now also benefit bincraft**, which reads `UVR_CACHE_DIR`/`UVR_PACKAGES_DIR` from the inherited pipeline environment.
- **`uvr sync` will not prune the shared library.** Pruning is disabled whenever `--library` is passed (`do_prune = prune && library_override.is_none()`), so `/mnt/cache/R-pkgs` keeps bincraft and its dependencies. The wipe-on-ABI-mismatch path is *not* similarly guarded, which is why the helper pins the manifest to the active R's exact version.
- **`plans/` and `specs/` are untouched** — they are dated records of decisions made in June 2026 and describe bincraft's then-pak-based internals; rewriting them would misstate history.

## Verification

`shellcheck`, all pre-commit hooks (on this commit's file range) and the `local/tests/` suite (100 assertions) pass.

Not yet exercised in CI: the build-env images do not ship `uvr`, so the per-step `curl install.sh` bootstrap is untested against a real image. Worth a manual `build-all-versions-install-deps` run before merging.

Reviewed-on: #147
This commit is contained in:
Patrick Schratz 2026-07-31 12:19:26 +00:00 committed by Patrick Schratz
commit ee15c50f53
7 changed files with 326 additions and 245 deletions

View file

@ -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:

View file

@ -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:

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@ -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

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

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@ -142,7 +142,8 @@ 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/$R_VERSION/bin/R -q -e 'pak::pak(c("git::https://codefloe.com/rpkgs/bincraft.git", "httr2", "jsonlite"))'
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")'
backend_options:
docker:

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@ -35,7 +35,7 @@ steps:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /mnt/cache/R-pkgs
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
- /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))'
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
- /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-issue
- /opt/R/$R_VERSION/bin/Rscript local/proposal-tracking.R --open-issue
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@ -141,7 +141,8 @@ steps:
FORGEJO_TOKEN:
from_secret: FORGEJO_TOKEN
GIT_USER: pat-s
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
UVR_CACHE_DIR: /mnt/cache/uvr/cache
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
R_LIBS_USER: /mnt/cache/R-pkgs
R_VERSION: ${R_VERSION}
CCACHE_DIR: /mnt/cache/ccache
@ -150,12 +151,12 @@ steps:
NCPUS: 2
commands:
- git clone -q https://pat-s:$$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
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