mikeblazanin / gcplyr

gcplyr is an R package that facilitates wrangling and analysis of microbial growth curve data

https://mikeblazanin.github.io/gcplyr/

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Vignettes: Broken on CRAN #112

Closed discoleo closed 1 year ago

discoleo commented 1 year ago

PDF Vignettes on CRAN

The "Analyse" vignette (and possibly others) are broken on CRAN. The pdf file (on CRAN) displays garbage text and the code-boxes do NOT display the code.

mikeblazanin commented 1 year ago

Hi @discoleo, all the vignette pdf's posted on CRAN look fine on my end. Could you provide more details on what pdf reader you're using?

discoleo commented 1 year ago

Vignette on CRAN: https://cran.r-project.org/web/packages/gcplyr/vignettes/analyze.pdf Creation Date: 2/2/2023, 9:24:51 PM Modification Date: 2/2/2023, 9:24:51 PM Creator: LaTeX via pandoc

Opened in the pdf-viewer inside the browser: Mozilla Firefox v.109;

other pdf files on CRAN are displayed correctly;
the vignettes on GitHub are also displayed correctly; link: https://raw.githubusercontent.com/mikeblazanin/gcplyr/master/vignettes/analyze.pdf
- opened pdf also in the browser (using download on GitHub);

mikeblazanin commented 1 year ago

This appears to be a firefox-specific issue with the CRAN-built vignette pdfs. vignettes look fine on Chrome or when downloaded on my machine too.

Perhaps could be fixed by changing the rbuildignore to ignore the pdf vignette files and instead include the html vignette files. Currently rbuildignore includes both the pdf and the html vignettes. As long as gitignore still doesn't list the pdf files maybe that will work?

discoleo commented 1 year ago

When downloading the pdf file from CRAN and opening the downloaded file:

file is displayed correctly in Microsoft Edge (Windows 10);
the locally-downloaded pdf is still displayed garbled in Firefox 109 (with the default Firefox pdf viewer); as opposed to this, the pdf file from GitHub is displayed correctly even in the Firefox pdf viewer;
could not find any details about the Firefox default pdf viewer;
however I did not see this issue with many other pdf files on CRAN;

mikeblazanin commented 1 year ago

This was an issue on Mozilla's side and has now been fixed by them: https://bugzilla.mozilla.org/show_bug.cgi?id=1816128

Presumably the next release of firefox will include this fix, but it can currently be accessed by using the nightly version of Firefox