Code Profiling unable to produce html output

[Pweidemueller]

I'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 e.g. a selected line in a script by clicking Profile -> Profile Selected Line(s) the profiling runs but I get following error and not html output is generated:

sh: /Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc/pandoc: Not a directory
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 profvis 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 profvis to use the right path?

[wch]

What happens when you run:

library(profvis)
profvis({
  # code here
})

If that works, but Profile -> Profile Selected Line(s) does not, then it is probably an issue with the RStudio IDE, and you can file it here:
https://github.com/rstudio/rstudio/issues

[Pweidemueller]

Thank you for your fast reply! Unfortunately the error stays the same.

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

The error remains:

sh: /Users/pweide/opt/miniconda3/envs/r_env/bin/pandoc/pandoc: Not a directory
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

[wch]

I suspect this is a problem with the htmlwidgets package looking for pandoc in the wrong place.

If you run this:

p <- profvis({
  # Code here
})

htmlwidgets::saveWidget(p, "profile.html")

I think the same error will occur when you run saveWidget.

The error you're getting is coming from here:

https://github.com/ramnathv/htmlwidgets/blob/b3573236c4553019b30e595adcb4fbe693f4a834/R/pandoc.R#L280-L281

If I'm right about this, then I suggest filing an issue on the htmlwidgets repository.

[wch]

Also, you can probably reproduce the error by calling:

htmlwidgets:::find_pandoc()

[Pweidemueller]

Yes, both htmlwidgets::saveWidget(p, "profile.html") and htmlwidgets:::find_pandoc() reproduce the error.

When I try rmarkdown:::pandoc(), it actually finds the right directory. So your hunch might be right that it is an error in htmlwidgets package. I will ask my question there.

[hadley]

Closing since resolved in the linked issue.

[gsandrof66]

Hi everyone. I had the same problem. I solved it when I install xfun package and restart my environment.
install.packages("xfun")
I hope it helps.