Code Profiling unable to produce html output

[Pweidemueller]

I posted the original question in the profvis repository, because that is when the error first occurred, however the problem seems to be within the htmlwidgets package: r-lib/profvis#116 (comment)

'm using Rstudio with R version 3.6.2 on MacOS Catalina. I installed R through anaconda into a specified environment. Using the conda-forge distribution I installed theprofvis (version: 0.3.6) package.

When I try to profile following script, the profiling runs but I get an error and no html output is generated:

library(profvis)
p <- profvis({
  test_strings <- rep("test 134", 331582)
  Genes <- lapply(test_strings, function(x) unlist(strsplit(as.character(x), " "))[1])
})
htmlwidgets::saveWidget(p, "profile.html")

The error is the following:

sh: /Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc/pandoc: Not a directory
Error in strsplit(version_info, "\n")[[1]] : subscript out of bounds
In addition: Warning message:
In system(paste(shQuote(pandoc_path), "--version"), intern = TRUE) :
  running command ''/Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc/pandoc' --version' had status 126

When I check in my terminal where pandoc is located (which pandoc), I get following output:

/Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc

And checking for the version (pandoc --version), I get:

pandoc 2.9.2
Compiled with pandoc-types 1.20, texmath 0.12.0.1, skylighting 0.8.3.2
Default user data directory: /Users/pweide/.local/share/pandoc or /Users/pweide/.pandoc
Copyright (C) 2006-2019 John MacFarlane
Web:  https://pandoc.org
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose

So I'm wondering why htmlwidgets adds another pandoc to the path (/Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc) to identify the version? Obvisously /Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc/pandoc does not exist, hence the error.

How can I redirect htmlwidgets to use the right path?

[jcheng5]

What does Sys.getenv("RSTUDIO_PANDOC") give you?

[Pweidemueller]

> Sys.getenv("RSTUDIO_PANDOC")
[1] "/Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc"

[jcheng5]

I'm not sure how that's getting set, but it should be /Users/pweide/opt/miniconda3/envs/r_env/bin/ (i.e. the directory where the pandoc binary lives, not the pandoc binary itself

[Pweidemueller]

Hm, I see. For now I just set the variable inside my script
Sys.setenv(RSTUDIO_PANDOC="/Users/pweide/opt/miniconda3/envs/r_env/bin/")
But would be cool to find a solution to change the variable globally. I saw some possible solutions online.