Update lintr config and address newly found lints

[codecov-commenter]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (12f7eb6) 92.35% compared to head (a0c7564) 92.31%. Report is 5 commits behind head on main.

:exclamation: Current head a0c7564 differs from pull request most recent head f8a12b6. Consider uploading reports for the commit f8a12b6 to get more accurate results

Files	Patch %	Lines
R/io.R	71.42%	2 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #1158 +/- ## ========================================== - Coverage 92.35% 92.31% -0.04% ========================================== Files 46 46 Lines 2654 2655 +1 ========================================== Hits 2451 2451 - Misses 203 204 +1 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[github-actions[bot]]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if edf399cea742249e74d5a33668e0eb18c2c7a3cc is merged into main:

•   :ballot_box_with_check:cache_applying: 161ms -> 164ms [-1.46%, +4.78%]
•   :ballot_box_with_check:cache_recording: 541ms -> 538ms [-2.02%, +1.03%]
•   :ballot_box_with_check:without_cache: 1.03s -> 1.03s [-0.47%, +1.28%]

Further explanation regarding interpretation and methodology can be found in the documentation.