Pass .libPaths() as R_LIBS to quarto subprocess
#228
Conversation
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It'd be worth double checking for other env vars that callr sets but processx doesn't. |
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Yeah I didn't want to just copy callr which aims to be more generic. Other env vars are the following > callr:::setup_context
function (options)
{
repos <- libpath <- system_profile <- user_profile <- load_hook <- NULL
make_path <- function(x) paste(x, collapse = .Platform$path.sep)
options <- within(options, {
profiles <- make_profiles(system_profile, user_profile,
repos, libpath, load_hook, env)
tmp_files <- c(tmp_files, profiles)
envs <- make_environ(profiles, libpath, env)
tmp_files <- c(tmp_files, envs)
save_env <- c("R_ENVIRON", "R_ENVIRON_USER", "R_PROFILE",
"R_PROFILE_USER", "R_LIBS", "R_LIBS_USER", "R_LIBS_SITE")
keep_set <- save_env %in% names(env)
save_set <- !keep_set & save_env %in% names(Sys.getenv())
save_nms <- paste0("CALLR_", save_env, "_BAK")
env[save_nms[keep_set]] <- env[save_env[keep_set]]
env[save_nms[save_set]] <- Sys.getenv(save_env[save_set])
env <- env[setdiff(names(env), save_nms[!keep_set & !save_set])]
if (is.na(env["R_ENVIRON"]))
env["R_ENVIRON"] <- envs[[1]]
if (is.na(env["R_ENVIRON_USER"]))
env["R_ENVIRON_USER"] <- envs[[2]]
if (is.na(env["R_PROFILE"]))
env["R_PROFILE"] <- profiles[[1]]
if (is.na(env["R_PROFILE_USER"]))
env["R_PROFILE_USER"] <- profiles[[2]]
if (is.na(env["R_LIBS"]))
env["R_LIBS"] <- make_path(libpath)
if (is.na(env["R_LIBS_USER"]))
env["R_LIBS_USER"] <- make_path(libpath)
if (is.na(env["R_LIBS_SITE"]))
env["R_LIBS_SITE"] <- make_path(.Library.site)
env["CALLR_IS_RUNNING"] <- "true"
})
call_user_hooks(options)
}So there is also
They could be helpful to modify startup behavior of R by Quarto inside So |
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That analysis makes sense to me! |
2 participants
Related to
This package is using
processx::run()and notcallr::r()to trigger the subprocess.Environment variables are inherited by default, but if
.libPaths()is modified during the R session before callingquarto_render(), this is unknown to the R process in Quarto processing.This PR insures that by default
.libPaths()is passed to the subprocess throughR_LIBSenvironment variable.This way, temporary install of the package, like with pkgdown or Quarto vignettes should not fail.