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fix R CMD CHECK notes #272

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shajoezhu opened this issue Oct 14, 2024 · 2 comments · Fixed by #274
Closed

fix R CMD CHECK notes #272

shajoezhu opened this issue Oct 14, 2024 · 2 comments · Fixed by #274
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@pawelru
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@shajoezhu
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  • checking for hidden files and directories ... NOTE
    Found the following hidden files and directories:
    tests/testthat/_book/assets/www/.gitkeep
    tests/testthat/_book/assets/www/lock/.gitkeep
    tests/testthat/_data/.rbuildkeep
    These were most likely included in error. See section ‘Package
    structure’ in the ‘Writing R Extensions’ manual.
  • checking for portable file names ... NOTE
    Found the following non-portable file paths:
    tlg.catalog.pkg/tests/testthat/_book/_extensions/coatless/webr/qwebr-document-engine-initialization.js
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/css/latex-fontsize.css
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-brands-400.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-brands-400.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-regular-400.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-regular-400.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-solid-900.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-solid-900.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-v4compatibility.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/fa-v4compatibility.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/FontAwesome6Brands-Regular-400.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/FontAwesome6Brands-Regular-400.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/FontAwesome6Free-Regular-400.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/FontAwesome6Free-Regular-400.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/FontAwesome6Free-Solid-900.ttf
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts/FontAwesome6Free-Solid-900.woff2
    tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/shinylive/resources/css/shinylive-quarto.css
@shajoezhu shajoezhu added the sme label Oct 14, 2024
shajoezhu added a commit that referenced this issue Oct 14, 2024
@shajoezhu
close #272
16838fc
@pawelru
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pawelru commented Oct 14, 2024

All in all - I don't think these notes could be solved - or I don't have a good idea how to do this. May I ask you why this brought your attention. These should not fail our CI.

Please have a look at the current error:

ERROR: NotFound: No such file or directory (os error 2): lstat '/__w/tlg-catalog/tlg-catalog/tlg.catalog.pkg.Rcheck/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/css/all.css'

If you build-ignore some of the quarto extension files then these won't be added to the .tar.gz bundle. Then we are running tests on the .tar.gz bundle. During tests we are re-generating the whole book to compare the snapshots. If files are missing then quarto process complains.

That's just one mechanism. There is also a tests/testthat/_data/.rbuildkeep file which name indicates not to ignore it. During the tests - we are writting the files. We want to write it to some dir. The role of that dummy empty file is just to keep the dir not empty. If it's empty - you are going to see another note during R CMD BUILD (see last entry):

* checking for empty or unneeded directories
Removed empty directory ‘tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets/webfonts’
Removed empty directory ‘tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/fontawesome/assets’
Removed empty directory ‘tlg.catalog.pkg/tests/testthat/_book/_extensions/quarto-ext/shinylive/resources’
Removed empty directory ‘tlg.catalog.pkg/tests/testthat/_book/assets/www/lock’
Removed empty directory ‘tlg.catalog.pkg/tests/testthat/_book/assets/www’
Removed empty directory ‘tlg.catalog.pkg/tests/testthat/_data’

@shajoezhu
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these was raised as notes in our integration test

@pawelru pawelru mentioned this issue Oct 15, 2024
Merged
@pawelru pawelru changed the title update rbuildignore fix R CMD CHECK notes Oct 16, 2024
@pawelru pawelru self-assigned this Oct 16, 2024
pawelru added a commit that referenced this issue Oct 25, 2024
@pawelru @m7pr
move quarto render into cleanup script (#274)
f238d68 
fix #272

move `quarto render` into R CMD BUILD:
```
❯ R CMD BUILD .
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘tlg.catalog.pkg’:
* checking DESCRIPTION meta-information ... OK
* running ‘cleanup’                                                            <<<<------ HERE!
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘tlg.catalog.pkg_0.1.0.9029.tar.gz’
```

After `quarto render` we remove the symlink to the book.
As a result, we have refreshed files for snapshot tests and also we
don't have a book files that R CMD CHECK complains about.

---------

Co-authored-by: Marcin <[email protected]>
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move quarto render into cleanup script insightsengineering/tlg-catalog
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