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.gra...@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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