[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]

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:
> On 2024-06-13 2:22 p.m., Spencer Graves wrote:
>>
>>
>> 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 $PATH
>> /opt/homebrew/bin:/opt/homebrew/sbin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Library/TeX/texbin
>>
>>
>>       I do not find "pandoc" in this path.
>>
>>
>>       What do you suggest I do to fix this?
> 
> You can add it, and things should be fine.  I'd put it last, just in 
> case there's anything else in that directory that might interfere with 
> other things.  So you could do
> 
>    PATH=$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
> 
>>
>>
>>       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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>>>
>>
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