failed to compile the book

[sherinesaber]

Hello, I came across this error while trying to compile basics. Any solution? Also, is there a working link for the book because this link http://bioconductor.org/books/3.16/OSCA.basic does not work?

bookdown::render_book("index.Rmd")

processing file: index.Rmd |....................................................| 100% (unnamed-chunk-2)Quitting from lines 27-32 (index.Rmd) Error in packageDescription("OSCA.basic")$Description : $ operator is invalid for atomic vectors Calls: local ... withVisible -> eval_with_user_handlers -> eval -> eval

Execution halted Error in Rscript_render(f, render_args, render_meta, add1, add2) : Failed to compile index.Rmd

[PeteHaitch]

The link http://bioconductor.org/books/3.16/OSCA.basic is working for me. What sort of error are you seeing and in what browser?

FYI https://osca.bioconductor.org/ is the recommended URL to use because it will redirect you to the current 'release' version of the book

[PeteHaitch]

The book is passing checks in release and devel on the Bioconductor build machines. It can be little tricky to setup to build locally but is doable (I'm on a new machine and can't test at the moment).

[sherinesaber]

Thank you for your fast reply. I was trying to access it through Safari. Only the introduction section works. Here is there error for the rest of the sections. They all work well on Chrome.

[PeteHaitch]

What's the exact URL you have open in that Safari window where it can't open the page? I just tried a number of OSCA sections in both Chrome and Safari and was unable to reproduce.

[alanocallaghan]

You should ensure all of your Bioc packages are up to date to ensure the book builds properly, something like BiocManager::install("OSCA.basic") should give you the right prompts

[PeteHaitch]

Please re-open if you have further information.