Issues with Rmarkdown Knit project

R Markdown
#1

Hello everyone,

I am new to both RStudio and using a macOS. my windows pc crashed when I used Rstudio, so I decided to upgrade. However, I am having some difficulty while working in RStudio and Markdown. I am not entirely sure I have downloaded the software, every time I open it, it asks if I want to open an Internet file?
But when I try to use the Rmarkdown knit function this is the error message I receive:
sh: /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/pandoc: Bad CPU type in executable Error in strsplit(info, "\n")[[1]] : subscript out of bounds Calls: ... pandoc_available -> find_pandoc -> lapply -> FUN -> get_pandoc_version In addition: Warning message: In system(paste(shQuote(path), "--version"), intern = TRUE) : running command ''/Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/pandoc' --version' had status 126 Execution halted
Does anyone have any suggestions?
Thank you!

#2

You have the binary installed for Intel, and need Silicon. Or vice versa. Does the R.app work? Or from terminal R?

#3

Hi Technorat

I am able to use Rstudio, for basic vector addition, plots, etc. Every time I open R I get this comment:
“RStudio” is an app downloaded from the Internet. Are you sure you want to open it?
How can I check to see which one I have installed?

#4

From the terminal

which R

will show you the first version in your $PATH

What I did for Quarto/pandoc was to install those separately. q3uarto and pandoc. Then I created a ~/.Renviron file

───────┬──────────────────────────────────────────────────────────────
       │ File: .Renviron
───────┼──────────────────────────────────────────────────────────────
   1   │ PATH=/Users/ro/.nvm/versions/node/v18.9.1/bin:/opt/homebrew/C
       │ ellar/python@3.10/3.10.9/bin:/Applications/CMake.app/Contents
       │ /bin:/opt/homebrew/bin:/Users/ro/.cargo/bin:/Applications/Jul
       │ ia-1.8.app/Contents/Resources/julia/bin/julia:/usr/local/go/b
       │ in:/Users/ro/.fig/bin:/usr/local/mysql-8.0.28-macos11-x86_64/
       │ bin:/bin:/usr/bin:/usr/local/bin:/usr/sbin:/sbin:/Users/ro/.l
       │ ocal/bin
   2   │ R_INCLUDE_DIR=/Library/Frameworks/R.framework/Resources/inclu
       │ de
   3   │ R_LIBS_SITE=/Library/Frameworks/R.framework/Resources/library
       │
   4   │ R_LIBS_USER =/Library/Frameworks/R.framework/Resources/librar
       │ y
   5   │ RSTUDIO_PANDOC=/usr/local/bin/pandoc
   6   │ RSTUDIO_QUARTO=/usr/local/bin/quarto
   7   │
───────┴──────────────────────────────────────────────────────────────

where $PATH is taken from the terminal command

echo $PATH
I need some help in correctly installing R and Knitting the docs
#5

I uninstalled everything and used home-brew to install R and studio, when I was using home-brew I had to create the path for tinytex, but I am still receiving the same original error message. I used the Silicon for both Studio and R. R is working correctly but Studio still not working. any other ideas?

#6

Either unbrew these and install from CRAN directly for R and posit.com for RStudio (both are deb packages) or prepare to dig in for a long bout of testing out PATHS and various dotfiles. I’ve done my own Unix sysadm since 1983 and the friction from marching to my own drum became so great eventually that it takes a compelling case for me to even consider doing a nonstandard install.

#7

See this issue in RStudio repo

#8

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