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"R CMD build" ...Error... "processing vignette ... failed with diagnostics:, Pandoc is required to build R Markdown vignettes but not available."

6 messages · Spencer Graves, Jeff Newmiller, Duncan Murdoch +1 more

Original
Spencer Graves
# 
Hello, All:


	  "R CMD build" fails for me, apparently because it cannot find pandoc, 
even though R in a command prompt finds it. This is with R 4.4.0 under 
macOS 14.5. I get the following in a Terminal:


___% R CMD build fda
* checking for file ?fda/DESCRIPTION? ... OK
* preparing ?fda?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ?BasisBasics.Rmd? using rmarkdown
Error: processing vignette 'BasisBasics.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. 
Please make sure it is installed.


	  "Pandoc 3.2 already installed", per the following interaction with R 
in said Terminal:
	

 > library(pandoc)
 > pandoc_install()
? Fetching Pandoc releases info from github...
? Pandoc 3.2 already installed.
   Use 'force = TRUE' to overwrite.
 >
 >
 > pandoc_is_active()
Error in pandoc_is_active() :
   argument "version" is missing, with no default
 > pandoc_is_active("system")
[1] FALSE
 > pandoc_locate()
[1] "~/Library/Application Support/r-pandoc/3.2"

	
	  sessionInfo() below.
	  Suggestions?
	  Thanks,
	  Spencer Graves


 > sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 

LAPACK: 
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; 
  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pandoc_0.2.0

loaded via a namespace (and not attached):
  [1] R6_2.5.1        utf8_1.2.4      gh_1.4.1        magrittr_2.0.3
  [5] rappdirs_0.3.3  glue_1.7.0      tibble_3.2.1    pkgconfig_2.0.3
  [9] gitcreds_0.1.2  lifecycle_1.0.4 cli_3.6.2       fansi_1.0.6
[13] vctrs_0.6.5     compiler_4.4.0  curl_5.2.1      pillar_1.9.0
[17] httr2_1.0.1     rlang_1.1.4     jsonlite_1.8.8  fs_1.6.4
Jeff Newmiller
# 
Don't assume the system environment variables defined at the R command prompt are the same as the environment variables defined at the shell prompt. Various R startup scripts often alter these variables within R. It looks from my obscured position like the pandoc install directory is present in your PATH directory from the shell.
On June 13, 2024 10:09:25 AM PDT, Spencer Graves <spencer.graves at prodsyse.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Spencer Graves
    

    

      
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On 6/13/24 12:27, Jeff Newmiller wrote:

            

      
      
      
    

        
echo $PATH
/opt/homebrew/bin:/opt/homebrew/sbin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Library/TeX/texbin


	  I do not find "pandoc" in this path.


	  What do you suggest I do to fix this?


	  Thanks,
	  Spencer Graves

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 2024-06-13 2:22 p.m., Spencer Graves wrote:

            

      
      
      
    

        
You can add it, and things should be fine.  I'd put it last, just in 
case there's anything else in that directory that might interfere with 
other things.  So you could do

   PATH=$PATH:~/Library/Application\ Support/r-pandoc/3.2 R CMD build ...

(or if you want, the equivalent that makes the PATH change permanent).

Duncan Murdoch

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Spencer Graves
    

    

      
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Hi, Duncan, Jeff et al.:


	  Thanks for the help. Can I edit "R CMD" so it modifies the path? If 
yes, how? If that's not feasible, can I create a script of my own that 
would first change the path and then call "R CMD"?


	  I asked Apple how to modify the path and was told they do not support 
that.


	  Thanks,
	  Spencer Graves

        
On 6/13/24 13:51, Duncan Murdoch wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Spencer,

Since you already have homebrew on your PATH you can simply run "brew install pandoc".

Otherwise you can just set the path while running R CMD:

PATH="~/Library/Application Support/r-pandoc/3.2:$PATH" R CMD build fda

As of where to set the PATH - it depends on where you run it from - if from Terminal then just set it in ~/.profile

Cheers,
Simon