Stop advertising functions that don't fit in openxlsx2 API

[olivroy]

This PR aims to modify the function index https://janmarvin.github.io/openxlsx2/dev/reference/index.html, so that functions that don't fit in the openxlsx2 API are not advertised.

This will not create breakages, as all functions are still exported.

Adds a bunch of @keywords internal to the functions that don't fit in the API. (functions still exported, but not advertised)

Relocate wb_dims on top of rowcol_to_dims() dims_to_rowcols(), so it shows up first.

This PR is minimal. and a overhaul of examples, descriptions links, and deprecation warnings can be done elsewhere (wanted to keep it small)

Edit: this PR got a little larger, because wb_add_data() and write_data() were documented together. I separated the docs, to make sure that wb_add_data() was not marked with @keywords internal

Edit2 : I was not able to reproduce interactively, but when running R CMD Check in RStudio's build pane. I get the following error.

   Running the tests in 'tests/testthat.R' failed.
   Last 13 lines of output:
     Error in `basename(sheets$Target)`: object 'sheets' not found
     Backtrace:
         ▆
      1. └─openxlsx2::wb_load(xlsxFile) at test-write.R:135:2
      2.   └─base::basename(sheets$Target)

[JanMarvin]

And the R CMD check should be investigated too

[JanMarvin]

Thanks! since we have two interfaces, the lack of exports is something I'm constantly in fear of.

Do you still see the r cmd check, I haven't looked into this yet?

[olivroy]

HI @JanMarvin,

regarding the R CMD check, I don't really what is going on. It is failing because of tests only (i.e. only 1 ERROR) It is probably related to a setup on my computer, Windows, R 4.2.3, RStudio 2023.06.0

• This PR basically does nothing.
• It passes when I use Ctrl + Shift + T
• it passes when I run tests interactively. devtools::test()
• It just doesn't pass with RStudio Check command Ctrl + Shift + E
• I see the same thing on main on my machine.

Here is a snippet of the back trace I get.

── Warning ('test-class-comment.R:62:3'): load comments ────────────────────────
internal error in 'unz' code
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(fl) at test-class-comment.R:62:2
 2.   └─utils::unzip(file, exdir = xmlDir)
── Warning ('test-class-workbook-wrappers.R:222:3'): wb_add_drawing is a wrapper ──
internal error in 'unz' code
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(file = fl) at test-class-workbook-wrappers.R:222:2
 2.   └─utils::unzip(file, exdir = xmlDir)
── Warning ('test-class-workbook.R:328:3'): clone worksheet ────────────────────
internal error in 'unz' code
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(fl) at test-class-workbook.R:328:2
 2.   └─utils::unzip(file, exdir = xmlDir)
── Warning ('test-class-workbook.R:737:3'): changing sheet names works with named regions ──
zip file is corrupt
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(filename) at test-class-workbook.R:737:2
 2.   └─utils::unzip(file, exdir = xmlDir)
── Warning ('test-cloneWorksheet.R:9:3'): clone Worksheet with data ────────────
zip file is corrupt

I checked on R-devel, nothing seems related.

Only thing that was fixed in R 4.2.2

Files can now be extracted even from very large zip archives ([PR#18390](https://bugs.r-project.org/show_bug.cgi?id=18390), thanks to Martin Jakt).

Edit: other examples..

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-class-comment.R:62:3'): load comments ──────────────────────────
Error in `basename(sheets$Target)`: object 'sheets' not found
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(fl) at test-class-comment.R:62:2
 2.   └─base::basename(sheets$Target)
── Error ('test-class-workbook-wrappers.R:222:3'): wb_add_drawing is a wrapper ──
Error in `basename(sheets$Target)`: object 'sheets' not found
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(file = fl) at test-class-workbook-wrappers.R:222:2
 2.   └─base::basename(sheets$Target)
── Error ('test-class-workbook.R:328:3'): clone worksheet ──────────────────────
Error in `basename(sheets$Target)`: object 'sheets' not found
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(fl) at test-class-workbook.R:328:2
 2.   └─base::basename(sheets$Target)
── Error ('test-class-workbook.R:737:3'): changing sheet names works with named regions ──
Error in `basename(sheets$Target)`: object 'sheets' not found
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(filename) at test-class-workbook.R:737:2
 2.   └─base::basename(sheets$Target)
── Error ('test-cloneWorksheet.R:9:3'): clone Worksheet with data ──────────────
Error in `basename(sheets$Target)`: object 'sheets' not found
Backtrace:
    ▆
 1. └─openxlsx2::wb_load(file = file_name) at test-cloneWorksheet.R:9:2
 2.   └─base::basename(sheets$Target)
── Error ('test-cloneWorksheet.R:23:3'): clone empty Worksheet

[JanMarvin]

Hm, maybe a download didn't succeed? There isn't really a to big file in our tests. You could clone the git repo.

[olivroy]

Maybe a couple of skip_on_cran() could fix that? but if you never had these problems before, I think it is safe to assume it is related to my machine, and we can ignore until new information convinces us to do otherwise

[JanMarvin]

All good on my end

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1375 ]

[JanMarvin]

Thanks, merged!

[olivroy]

Great I am glad it passes on your end.. I really have no idea.. If I figure it out, I will let you know.

I found this link, but haven't looked at it yet! https://community.rstudio.com/t/devtools-test-passes-but-devtools-check-does-not/129885/7