setup-r-dependencies: switch back to classic sudo on runners with sudo-rs

[jeroen]

Alternative solution for #1094 (see also #1095).

sudo-rs, the default sudo on Ubuntu 25.10+ (and thus ubuntu-26.04 GitHub-hosted runners), does not support bare -E:

sudo: preserving the entire environment is not supported, '-E' is ignored

With the environment dropped, R_LIB_FOR_PAK is empty inside the sudo'd R process, so the pak installation fails.

Instead of changing the sudo invocation, this switches the sudo alternative back to classic sudo before installing pak:

sudo update-alternatives --set sudo /usr/bin/sudo.ws

This is guarded by a check that /usr/bin/sudo.ws exists, so it is a no-op on runners that ship classic sudo only.

Also adds ubuntu-26.04 and ubuntu-26.04-arm to the test matrix so this is exercised in CI.

Fixes #1094

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.33%. Comparing base (b7484da) to head (6d96816).
⚠️ Report is 3 commits behind head on v2-branch.

Additional details and impacted files

@@            Coverage Diff             @@
##           v2-branch    #1096   +/-   ##
==========================================
  Coverage      83.33%   83.33%           
==========================================
  Files              3        3           
  Lines             12       12           
==========================================
  Hits              10       10           
  Misses             2        2           

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[krlmlr]

A more sustainable fix might be to use targeted sudo --preserve-env=R_LIB_FOR_PAK or an extension to /etc/sudoers.d as implemented in https://github.com/cynkra/cynkratemplate/pull/88/changes#diff-a5460b4ed10f51fdbcfeb4d7e349088edf5c27f7c5ed9ae26e4038ab95e76708R113-R132 .

[krlmlr]

Of course, missed the earlier PR. The /etc/sudoers.d solution in https://github.com/cynkra/cynkratemplate/pull/88/changes#diff-a5460b4ed10f51fdbcfeb4d7e349088edf5c27f7c5ed9ae26e4038ab95e76708R113-R132 keeps sudo -E .

[gaborcsardi]

It seems pretty fragile to pass a subset of env vars. There is no security issue here, we should keep using -E.