When preparing a release of phyloplace, I got an error from Singularity tests at Nextflow 25.10.4 that I let Claude analyze. He (it?) gave me this comment:

The singularity/conda CI matrix legs (which only run on release PRs targeting master, not regular dev PRs) are currently broken on our RunsOn AMI (runs-on-v2.2-ubuntu24-full-x64-20260717095855, built 2026-07-17). Singularity/Apptainer fails with Failed to create user namespace: Permission denied — Ubuntu 24.04 restricts unprivileged user-namespace creation via AppArmor by default (see apptainer/apptainer#2027), and this AMI doesn't carry a fix for it. It's runner-infra, not a pipeline bug — confirmed the exact same error also hits the latest-everything Nextflow leg, just silently, since that leg has continue-on-error set.

Since these legs are release-PR-only, it may have been broken silently for a while — worth checking if it's happening on other pipelines' release PRs too, and possibly worth a fix at the shared RunsOn AMI level rather than everyone patching their own nf-test.yml. I patched around it locally in phyloplace (sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0 before singularity runs) to unblock this release, but that's a per-repo workaround, not a real fix.

The tests seem to pass now, after Claude fixed it, see: github.com/nf-core/phyloplace/pull/65 I have no idea whether this is phyloplace specific or not.

4.0.3 had a faulty update for setup-apptainer. this doesn't break it in all pipelines but some run into this namespace error.

Ok, I'll let my work partner know and proceed with the release. Thanks!