[r/ci] Set options(pkgType = "binary") for MacOS

[mojaveazure]

Force binary-only installation for macOS. By setting as an option in ~/.Rprofile; this should affect both package installation and updating through utils::install.packages(), utils::update.packages(), and remotes::install_deps()

resolves #2254

[eddelbuettel]

What about the two packages we only have as source:

pbmc3k.tiledb,
pbmc3k.sce,

Maybe we need to toss them into a r-universe to have binaries too (and then Additional_repositories: point to that) ?

[codecov]

Codecov Report

Merging #2257 (ac0c159) into main (4a71f19) will increase coverage by 0.24%.
The diff coverage is n/a.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2257      +/-   ##
==========================================
+ Coverage   78.60%   78.85%   +0.24%     
==========================================
  Files         139      139              
  Lines       10704    10730      +26     
  Branches      215      215              
==========================================
+ Hits         8414     8461      +47     
+ Misses       2192     2171      -21     
  Partials       98       98              

Flag	Coverage Δ
libtiledbsoma	67.72% <ø> (ø)
python	90.84% <ø> (+0.61%)	⬆️
r	74.69% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	90.84% <ø> (+0.61%)	⬆️
libtiledbsoma	48.85% <ø> (ø)

[mojaveazure]

Yeah, just saw that. pbmc3k.sce is available on my universe, we can add pbmc3k.tiledb to a universe as well

Alternatively, a stanza à la

- name: Install dataset packages from source (macOS)
  if: ${{ matrix.os == 'macOS-latest' }}
  run: remotes::install_deps(dependencies = "Suggests", type = "source", upgrade = FALSE)
  shell: Rscript {0}

could work as well, without changing any package distribution machinery

[mojaveazure]

Note:

As the two pbmc3k dataset packages are source-only, I've added a new stanza to install these separately on macOS. This calls a separate R script apis/r/tools/install_missing_deps.R which

1. finds dependencies of tiledbsoma that were not installed due to the binary-only installation earlier
2. find the upstream dependencies of the missing packages that are source-only (because Bioconductor)

This stanza runs on macOS only

[johnkerl]

LGTM to me from the release-management point of view!! :) CI is green and I am happy

I defer to @eddelbuettel on the implementation details ...

[eddelbuettel]

I'll stay out of it. I provided a much simpler code example to @mojaveazure that attacked a simpler sub-task and that is what I might have done, but I didn't and I won't rewrite this. If it works it works.