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fix(ci): refresh the apt index before uvr installs system dependencies (#161)

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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
This commit is contained in:
Patrick Schratz 2026-08-10 06:30:25 +00:00 • committed by Patrick Schratz
commit 6372f0f928
1 changed files with 19 additions and 0 deletions
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19
local/uvr-install.sh
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@ -87,4 +87,23 @@ cd "$project_dir"
# --no-install: resolve and lock only. The install happens in the sync below,
# which is the only command that honours --library.
"$uvr_bin" add --no-install "$@"
# TEMPORARY (drop once the images ship a uvr above v0.4.5): the sync below runs
# `apt-get install` for every resolved system dependency without refreshing the
# index first, and the ubuntu build images end their apt layers with
# `rm -rf /var/lib/apt/lists/*`. With no index apt cannot resolve a package that
# exists and is enabled, so `igraph needs: libglpk-dev` fails the whole build
# with `E: Unable to locate package libglpk-dev` on ubuntu 26.04.
#
# Fixed upstream in `e491b2e`, tagged one day after v0.4.5 (nbafrank/uvr#250),
# and the images pick it up via build-env-images#23 — but only after an image
# rebuild is triggered, which is why this runs here too.
#
# apt only: `apk add` fetches its index implicitly and dnf refreshes expired
# metadata on its own. Non-fatal, since a refresh failure still leaves whatever
# index is already there, and the install's own error is the more actionable one.
if command -v apt-get >/dev/null 2>&1; then
apt-get update -qq || echo "warning: apt-get update failed; continuing" >&2
fi
"$uvr_bin" sync --library "$target_lib" --install-system-deps