fix(ci): refresh the apt index before uvr installs system dependencies #161
2026-08-10
fix(ci): refresh the apt index before uvr installs system dependencies
uvr v0.4.5 runs `apt-get install` for every resolved system dependency without refreshing the package 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 with `E: Unable to locate package libglpk-dev` on ubuntu 26.04, taking every package depending on igraph with it. Refresh in `uvr-install.sh` rather than per pipeline: every build pipeline reaches it, directly or through `install-bincraft.R`, and the index it populates persists for the bincraft-driven syncs later in the same step. Guard on apt-get and keep it non-fatal. `apk add` fetches its index implicitly and dnf refreshes expired metadata on its own, so alpine and redhat need nothing here. Stopgap: build-env-images#23 fixes this in the image, but only reaches CI once an image rebuild is triggered.