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.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
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
