Christophe Dervieux

> would it be possible to let the user type the two alternate codes directly (in html and in Latex) so that depending on the compilation output the correct code...

Yes the referencing and numbering is the hard part. It was the meaning behind original Yihui's comment I guess. It is easy for LaTeX but not to provide the same...

> Do you know if it's possible to specify this number manually? If not possible, then it's a deal breaker because not even manually we can make it work.. Unfortunately,...

I like this outline. Personal thoughts and feelings: * For the new chapter called blogdown, I see that as "Going Further" which is the usual path after "Getting Started". Having...

> a major point of confusion is "what DOES blogdown actually do" vs. Hugo/themes/GitHub/Netlify/etc. So I'd prefer to be ridiculously clear here. That make sense. It would indeed be more...

Oh cool. For the final solution, do you want still want it to be as part of R CMD check in package tests/ or is this a workaround and a...

Yes I’ll be able to explain this. I can work on mainly every ticket I opened so feel free to assign me with what you are not interested or not...

I'll reopen to consider for second edition. There was a question in https://github.com/yihui/knitr/issues/1939 and https://stackoverflow.com/questions/58694897/using-purl-to-source-a-rmd-file-from-within-a-rnw-file

If this is the culprit, then this is part of the cls file. We should check if the cls file is up to date. If so, it will be hard...

Template is from there right ? https://academic.oup.com/bioinformatics/pages/submission_online The template folder can be downloaded from there, and the `bioinfo.cls` files contains these lines. So I don't know if we can take...