feat: better tooling, linting, ci, readme

[sebffischer]

Summary:

• Improves the CI by:
  1. Adding spell checks
  2. Adding linter checks for C++ and R
• Improving the README by:
  1. Simplifying the quickstart example
  2. Adding more acknowledgements
• Adds a 'no-suggest' test which ensures that the test suite passes also in the absence of suggested packages
• Addressed linter issues
• Refactor the code for PJRTElementType class
• Add Makefile to format code easily

[sebffischer]

@dfalbel I am trying to setup a Cpp linter. I do this by running devtools::load_all() in the CI and then running clang-tidy and configure it to use compile_commands.json.

However, I still get these errors:

• 'xla/autotuning.pb.h' file not found (many more like this)
• Error: 'Rcpp.h' file not found

You can inspect the errors here

Do you understand why this happens? devtools::load_all() runs successfully

[sebffischer]

Here is data.table's CI file for clang-tidy: https://github.com/Rdatatable/data.table/blob/6e63f5b5a1eb14a374ecc24dc0459f1f15262864/.gitlab-ci.yml#L204

[dfalbel]

You probably need to configure the include paths for the linter as those files are in non-conventional include paths and it probably doesn't know how to parse Makevars to extract the correct paths.

[sebffischer]

I thought I am building compile_commands.json by running pkgdown::load_all() in the CI, but somehow the file is not created. Do I need to configure anything else (except putting Config/build/compilation-database: true into the description) in order to ensure that compile_commands.json is built?
`

[sebffischer]

So somehow the generation of the compilation database fails, weird:

[sebffischer]

This was a bug in pkgload, installing the dev version fixes it.

[sebffischer]

Now it's weird that g++ -std=gnu++17 is being used, but we require C++20

[sebffischer]

For some reason, the compile_commands.json is still off. The files are listed as C files, see the "file: pjrt.c" below.

{
     "command": "g++ -std=gnu++20 -I\"/opt/R/4.5.1/lib/R/include\" -DNDEBUG -DUSENEWAPI -Iproto -I/include -I../inst/include -I\"/home/runner/work/_temp/Library/Rcpp/include\" -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2   -c pjrt.cpp -o pjrt.o",
     "file": "pjrt.c",
     "directory": "/home/runner/work/pjrt/pjrt/src"
},

Compare this with my local compile_commands.json:

{
     "command": "clang++ -arch arm64 -std=gnu++20 -I\"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/include\" -DNDEBUG -I/opt/homebrew/Cellar/protobuf@21/21.12_1/include -DUSENEWAPI -Iproto -I/include -I../inst/include -I'/Users/sebi/Library/R/arm64/4.5/library/Rcpp/include' -I/opt/homebrew/include   -fvisibility=hidden -fPIC  -falign-functions=64 -Wall -g -O2   -c pjrt.cpp -o pjrt.o",
     "file": "pjrt.cpp",
     "directory": "/Users/sebi/r-xla/pjrt/src"
},

I think this then causes the cpp headers to not be found, which results in these error messages:

2025-09-04T07:21:18.1829074Z ##[error]'numeric' file not found
2025-09-04T07:21:18.2900471Z ##[error]'limits' file not found
2025-09-04T07:21:18.1746012Z ##[error]'memory' file not found
2025-09-04T07:21:18.1747137Z ##[error]'string' file not found
2025-09-04T07:21:18.1756819Z ##[error]'optional' file not found

[sebffischer]

There was a bug in pkgload for which I submitted a fix: r-lib/pkgload#318

[sebffischer]

@dfalbel have you used clang-tidy? If so, which checks would you recommend?