Fix some warnings and notes from PEcAn.MA package.

[nanu1605]

No description provided.

[infotroph]

This is good work. I left a few suggestions for edits -- some of them you can apply directly with the "commit suggestion" button if the edit I proposed looks correct to you (if you do this, make sure to pull the result back from GitHub to your local branch before making other edits), others will need more manual changes from you.

I'll be offline again for the rest of this week and should be back to more regular Internet access starting on the 16th.

[nanu1605]

Hi @infotroph @Aariq @mdietze, Should I manually update the docker/depends/pecan.depends.R to clear the PR checks?

[mdietze]

@nanu1605 the script itself includes the answer to your question

# autogenerated do not edit
# use scripts/generate_dependencies.R

[infotroph]

All of these commits are also included in #2965, so we should merge that and close this PR, but I'm leaving it open (marked as draft to prevent accidental merging) until then for easy reference to the review discussions.

[infotroph]

These changes have been merged as part of #2965