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

[Spencer Graves]

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


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

> 
> On June 13, 2024 10:09:25 AM PDT, Spencer Graves <spencer.graves using prodsyse.com> wrote:
>> 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()
>> ℹ 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
>>
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>