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CRAN notes that files cannot be checked without ‘pandoc’ being installed

In doing final checks on a CRAN package submission, this NOTE comes up:

* checking top-level files ... NOTE
Files ‘README.md’ or ‘NEWS.md’ cannot be checked without ‘pandoc’ being installed.

However, pandoc is definitely installed as I use it regularly, and this package makes frequent use of it in documentation using pkgdown.

> rmarkdown::pandoc_available()
[1] TRUE
> rmarkdown::pandoc_version()
[1] ‘1.19.2.1’

I want to avoid installing pandoc from source because the latest version of pandoc supercedes the version installed with other R packages and causes weird output.

There is a similar question from a few years back but the solutions there are to either:

  • Install pandoc from source or via the installr package, whereas I already have pandoc installed; and,
  • Place the two files into .Rbuildignore, however both should be accepted with CRAN submissions now.

This note only comes up when checked using devtools::release() and when using devtools::check(check_version = TRUE), which otherwise passes with no warnings or notes.

The RStudio install of Pandoc:

Sys.getenv('RSTUDIO_PANDOC')
[1] "/Applications/RStudio.app/Contents/MacOS/pandoc"

Which I had previously exported to my ~/.bash_profile:

export PATH="$PATH:/Applications/Rstudio.app/Contents/MacOS/pandoc"

Any ideas? 

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] cancensus_0.1.6

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14     rstudioapi_0.7   knitr_1.17       bindr_0.1       
 [5] xml2_1.1.1       magrittr_1.5     roxygen2_6.0.1   devtools_1.13.4 
 [9] R6_2.2.2         rlang_0.1.6      httr_1.3.1       stringr_1.2.0   
[13] dplyr_0.7.4      tools_3.4.3      hunspell_2.9     git2r_0.20.0    
[17] withr_2.1.1      htmltools_0.3.6  rversions_1.0.3  commonmark_1.4  
[21] rprojroot_1.2    yaml_2.1.14      digest_0.6.13    assertthat_0.2.0
[25] tibble_1.3.4     crayon_1.3.4     bindrcpp_0.2     curl_3.1        
[29] evaluate_0.10.1  memoise_1.1.0    glue_1.2.0       rmarkdown_1.8   
[33] stringi_1.1.5    compiler_3.4.3   backports_1.1.0  desc_1.1.1      
[37] jsonlite_1.5     pkgconfig_2.0.1
Solution

  • This happens because devtools::release calls devtools::check with check_version = TRUE.

    You can also run devtools::check(check_version = TRUE) to trigger the same note.

    I think for this part you would need pandoc on your PATH.

    (indeed, after adding the existing ...\RStudio\bin\pandoc to my PATH the note is gone)