instruction for installation of protobuf are outdated

[malcook]

Briefly describe what you hope to achieve: Install CytoExporeR on windows machine to work with latest R 4.2.0 (under RStudio 2022.02.2 with Rtools 4.2)

Outline the steps taken to attempt to reach this goal (paste code below): Following instructions at https://dillonhammill.github.io/CytoExploreR/index.html is not possible

since the instructions referenced have for some reason been removed

Can you please advise me how to proceed?

[DillonHammill]

@malcook protobuf is now bundled with cytolib there is no longer a need to install it manually.

[malcook]

Great.

I was able to complete install in fresh R/RStudio with the help of #119 (and your comment "GitHub versions of RGLab packages are no longer required. Either installation method is fine for RGLab packages but bioc_ver = "devel" is no longer necessary.")

You should probably want to change your instructions accordingly, possibly as follows

install.packages('markdown') # else vignette building fails.
install.packages("remotes")
install.packages("tidyverse") # or whatever portion you require - at least tibble
install.packages("devtools")
devtools::install_github("RGLab/cytoverse")
cytoverse::cytoverse_update(repo='github',branch='master',upgrades_approved=TRUE,build_manual=TRUE,build_vignettes=TRUE) # presumably from github since that is where cytoverse came from

Also, if it helps anyone, my install failed at this point:

...
* DONE (ggcyto)
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 403.
  API rate limit exceeded for 161.129.22.101. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

  Rate limit remaining: 0/60
  Rate limit reset at: 2022-04-29 19:37:40 UTC

  To increase your GitHub API rate limit
  - Use `usethis::create_github_token()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`. 

Following the advice given allowed me to rerun cytoverse_update which proceeded until failing due to absence of markdown package (which I've added to above instructions allowing cytoverse_update to now complete.

However, absence of pdflatex resulted in multiple warnings pdflatex not found! Not building PDF manual. So, you might want to advise users to run:

Sys.which("pdflatex")

and if it is undefined to install MiKTeX first (and then restart RStudio before proceeding with your package).

Also, during subsequent running of

# CytoExploreRData 
devtools::install_github("DillonHammill/CytoExploreRData")
# CytoExploreR 
devtools::install_github("DillonHammill/CytoExploreR")

I was repeatedly warned:

'\\ion\homedir$\mec\My Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

Not sure if that really matters going forward...