Closed malcook closed 2 years ago
@malcook protobuf
is now bundled with cytolib
there is no longer a need to install it manually.
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...
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?