pat-s
6372f0f928
Unblocks the ubuntu 26.04 builds without waiting for an image rebuild. ## What broke ``` i Installing R package dependencies ! Error in installing dependencies for package huge with tag 2.0.1: uvr sync --install-system-deps --library /mnt/cache/R-pkgs-4.4 failed (exit 1) ! WARN Missing system dependencies for 1 package(s) igraph needs: libglpk-dev > Running: apt-get install -y libglpk-dev E: Unable to locate package libglpk-dev ``` Neither the package name nor the sysreq mapping is wrong. `libglpk-dev` is `5.0-2build1` in `universe`, which `ubuntu:resolute` enables by default. What is missing is the apt index: uvr v0.4.5 runs `apt-get install` with no `apt-get update` before it, and every ubuntu build image ends its apt layers with `rm -rf /var/lib/apt/lists/*`, so the shipped image has no index at all. Not specific to 26.04 — jammy and noble fail identically for any sysreq the image's preinstall line doesn't already cover. 26.04 surfaced it first, through `igraph` and everything depending on it (`huge` was the first to fail). ## Fix `apt-get update` before the sync in `local/uvr-install.sh`. That one site covers every pipeline: `build-all-versions`, `build-all-versions-install-deps`, `weekly-rebuild-missing`, `weekly-audit-missing`, `trial-build-registry`, `auto-apply-patches` and `weekly-patch-proposals` all reach it, either directly or through `install-bincraft.R`. The index it populates persists for the rest of the step, so the bincraft-driven `uvr sync` calls that follow are covered too. Guarded on `apt-get` and non-fatal: `apk add` fetches its index implicitly and dnf refreshes expired metadata on its own, so alpine and redhat are unaffected and skip it. ## Why here as well as in the image The real fix is upstream `e491b2e`, which refreshes the index before the auto-install. It landed one day after v0.4.5 was tagged, so no release carries it ([nbafrank/uvr#250](https://github.com/nbafrank/uvr/issues/250)); [build-env-images#23](https://codefloe.com/rpkgs/build-env-images/pulls/23) pins the ubuntu image to a commit that has it. That only reaches CI after an image rebuild is triggered. This change takes effect on the next pipeline run. It also stays useful afterwards: a baked index goes stale within weeks, and a stale index turns the same install into a 404 on the `.deb`. ## Verified In `ubuntu:resolute`, with the image state reproduced exactly (R installed, then `rm -rf /var/lib/apt/lists/*` to empty the index again): | Check | Result | |---|---| | `apt-get install -y libglpk-dev`, empty index | `E: Unable to locate package libglpk-dev` — the reported failure, reproduced | | Same container after `apt-get update` | `Candidate: 5.0-2build1`, `Components: main universe restricted multiverse` | | `igraph` + `UVR_INSTALL_SYSREQS=1 uvr sync`, empty index, uvr with the refresh | `Setting up libglpk-dev:amd64 (5.0-2build1)`, `System dependencies installed.`, `Installed 11 package(s)` | | `sh -n` and `shellcheck local/uvr-install.sh` | pass | ## Reverting Delete the guarded block. It is marked TEMPORARY with the upstream reference, and can go once the images ship a uvr above v0.4.5. Reviewed-on: #161
109 lines
4.6 KiB
Shell
Executable file
109 lines
4.6 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="v0.4.5"
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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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# TEMPORARY (drop once the images ship a uvr above v0.4.5): the sync below runs
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# `apt-get install` for every resolved system dependency without refreshing the
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# index first, and the ubuntu build images end their apt layers with
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# `rm -rf /var/lib/apt/lists/*`. With no index apt cannot resolve a package that
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# exists and is enabled, so `igraph needs: libglpk-dev` fails the whole build
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# with `E: Unable to locate package libglpk-dev` on ubuntu 26.04.
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#
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# Fixed upstream in `e491b2e`, tagged one day after v0.4.5 (nbafrank/uvr#250),
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# and the images pick it up via build-env-images#23 — but only after an image
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# rebuild is triggered, which is why this runs here too.
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#
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# apt only: `apk add` fetches its index implicitly and dnf refreshes expired
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# metadata on its own. Non-fatal, since a refresh failure still leaves whatever
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# index is already there, and the install's own error is the more actionable one.
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if command -v apt-get >/dev/null 2>&1; then
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apt-get update -qq || echo "warning: apt-get update failed; continuing" >&2
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fi
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"$uvr_bin" sync --library "$target_lib" --install-system-deps
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