pat-s
f3c18b6805bincraft 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
90 lines
3.6 KiB
Shell
Executable file
90 lines
3.6 KiB
Shell
Executable file
#!/bin/sh
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# Install R packages into the CI library with uvr (https://github.com/nbafrank/uvr).
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#
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# Usage:
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# local/uvr-install.sh httr2 jsonlite
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# local/uvr-install.sh forgejo::codefloe.com/rpkgs/bincraft@v4.4.3
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#
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# Replaces `pak::pak(...)`. uvr is project-scoped: `uvr add` refuses to run
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# outside a project and always writes to `.uvr/library/`, and only
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# `uvr sync --library` can target an existing library. The project is therefore
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# minted in a scratch directory under TMPDIR and thrown away afterwards; that
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# also keeps `uvr init`'s `.Rprofile` out of the repo checkout, where it would
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# hijack `.libPaths()` for every other R call in the pipeline.
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#
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# Pruning is a no-op here: uvr disables it whenever `--library` is passed,
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# precisely because such a target may be shared (`/mnt/cache/R-pkgs` holds
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# bincraft and its dependencies alongside whatever this script installs).
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#
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# System dependencies come from uvr's vendored r-system-requirements rules, so
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# `pak::sysreqs_db_update()` and `PKG_SYSREQS_PLATFORM` are no longer needed.
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#
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# Environment:
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# UVR_R_BIN R interpreter to install for; set by install-bincraft.R so
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# the per-R-minor passes target their own R, not the primary
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# R_VERSION fallback interpreter selector (/opt/R/<version>/bin/R)
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# UVR_TARGET_LIB target library; defaults to R_LIBS_USER, then to the
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# active R's .libPaths()[1] (which is where pak wrote)
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# UVR_INSTALL_DIR where the uvr binary lands (default /usr/local/bin)
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set -eu
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# renovate: datasource=github-releases depName=nbafrank/uvr
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UVR_PIN="v0.4.4"
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if [ "$#" -eq 0 ]; then
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echo "usage: $0 <pkg-spec>..." >&2
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exit 2
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fi
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# The build images keep R under /opt/R/<version> and off PATH. uvr resolves the
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# interpreter via PATH and never downloads one unless `uvr r install` is run, so
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# put the requested R first.
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r_bin="${UVR_R_BIN:-}"
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if [ -z "$r_bin" ] && [ -n "${R_VERSION:-}" ] && [ -x "/opt/R/${R_VERSION}/bin/R" ]; then
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r_bin="/opt/R/${R_VERSION}/bin/R"
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fi
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if [ -n "$r_bin" ]; then
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PATH="$(dirname "$r_bin"):$PATH"
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export PATH
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else
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r_bin="$(command -v R)"
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fi
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target_lib="${UVR_TARGET_LIB:-${R_LIBS_USER:-}}"
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if [ -z "$target_lib" ]; then
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target_lib="$("$r_bin" --no-echo --no-save -e 'cat(.libPaths()[1])')"
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fi
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if [ -z "$target_lib" ]; then
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echo "error: could not determine a target library; set UVR_TARGET_LIB" >&2
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exit 2
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fi
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mkdir -p "$target_lib"
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# Pin the manifest to the active R so the lockfile's R stays in step with the
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# library's R sentinel. Without that, uvr can decide the library is ABI-stale
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# and wipe it -- and this target is shared with bincraft. uvr only discovers R
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# via PATH/R_HOME (it does not scan /opt/R), so the R put on PATH above is the
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# only candidate this constraint can resolve to.
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# shellcheck disable=SC2016 # $major/$minor are R expressions, not shell vars
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r_full="$("$r_bin" --no-echo --no-save -e 'cat(paste(R.version$major, R.version$minor, sep = "."))')"
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install_dir="${UVR_INSTALL_DIR:-/usr/local/bin}"
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uvr_bin="${install_dir}/uvr"
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if [ ! -x "$uvr_bin" ]; then
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echo "Bootstrapping uvr ${UVR_PIN} into ${install_dir}"
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UVR_INSTALL_DIR="$install_dir" UVR_VERSION="$UVR_PIN" \
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sh -c 'curl -fsSL https://raw.githubusercontent.com/nbafrank/uvr/main/install.sh | sh'
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fi
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project_dir="${TMPDIR:-/tmp}/uvr-ci-$$"
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rm -rf "$project_dir"
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mkdir -p "$project_dir"
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trap 'rm -rf "$project_dir"' EXIT
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cd "$project_dir"
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"$uvr_bin" init --here --r-version "$r_full"
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# --no-install: resolve and lock only. The install happens in the sync below,
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# which is the only command that honours --library.
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"$uvr_bin" add --no-install "$@"
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"$uvr_bin" sync --library "$target_lib" --install-system-deps
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