Render the Book

[karbalaei]

I`m new to GitHub, and I wanted to have an offline version of the Book on my computer. So, I cloned the OSCA, and in the book folder, I ran this code:

bookdown::render_book("index.Rmd") But I got an error message:

processing file: index.Rmd

output file: index.knit.md

processing file: contents.Rmd
  |.................                                   |  33% (unnamed-chunk-1)Quitting from lines 16-22 (contents.Rmd) 
Error in packageDescription("OSCA.intro")$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 contents.Rmd

I know this is not an issue, but I didn't know from whom I should ask my question.

Could someone please help me with this?

Thanks

[alanocallaghan]

Probably the easiest way for you to be able to build the books locally is to run BiocManager::install(c("OSCA", "OSCA.intro", "OSCA.workflows", "OSCA.multisample", "OSCA.advanced", "OSCA.trajectory")). That should fetch all the dependencies and ensure any commands like packageDescription("OSCA.intro")$Description return a valid output. It also may take a very long time to install everything, depending on how many dependencies you're missing.

What likely happened now is what happens if I try to run the same:

> packageDescription("OSCA.intro")$Description
Error in packageDescription("OSCA.intro")$Description : 
  $ operator is invalid for atomic vectors
In addition: Warning message:
In packageDescription("OSCA.intro") : no package 'OSCA.intro' was found

because

> packageDescription("OSCA.intro")
[1] NA
Warning message:
In packageDescription("OSCA.intro") : no package 'OSCA.intro' was found