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

[Simon Urbanek]

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



> On Jun 13, 2024, at 23:00, Spencer Graves <spencer.graves using prodsyse.com> wrote:
> 
> 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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