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