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feat: provide guidance if tmp csv file is not found in Quarto rendering #1176

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feat: provide guidance if tmp csv file is not found in Quarto rendering #1176

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404c1e5
feat: provide guidance if tmp csv file is not found in Quarto rendering
avehtari Apr 8, 2026
5c8ef1b
fix: improve when to show the Quarto cache message
avehtari Apr 9, 2026
543980c
test: add test for Quarto cache message
avehtari Apr 9, 2026
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11 changes: 10 additions & 1 deletion R/csv.R
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Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,16 @@ read_cmdstan_csv <- function(files,
files <- file.path(temp_storage, basename(files))
}
format <- assert_valid_draws_format(format)
assert_file_exists(files, access = "r", extension = "csv")
csv_file_exists <- check_file_exists(files, access = "r", extension = "csv")
if (!isTRUE(csv_file_exists)) {
if (isTRUE(getOption("knitr.in.progress")) &&
is.null(getOption("cmdstanr_output_dir")) &&
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@jgabry jgabry Apr 9, 2026 •
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It occurs to me that this is checking the option value at read time but what matters is what the option value was at run time.

If between the first render of the document and the later rerender if the user has since set cmdstanr_output_dir then this message will be suppressed.

I have an idea for how we can handle this. I will make some commits when I have time.

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@jgabry jgabry Apr 9, 2026 •
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I just opened PR #1178, which takes a different approach to this that avoids this particular problem. Let me know what you think. One issue is that my version solves this problem but is more complicated. If we can figure out how to make your version work then I would prefer that to my version.

any(grepl("csv$", files))) {
stop(paste0(csv_file_exists, "\n If this error happened when using Quarto cache,\n see `cmdstanr_output_dir` in `?cmdstanr_global_options`"))
} else {
stop(csv_file_exists)
}
}
metadata <- NULL
warmup_draws <- list()
draws <- list()
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4 changes: 3 additions & 1 deletion R/options.R
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Expand Up @@ -27,7 +27,9 @@
#' * `cmdstanr_output_dir`: The directory where CmdStan should write its output
#' CSV files when fitting models. The default is a temporary directory. Files in
#' a temporary directory are removed as part of \R garbage collection, while
#' files in an explicitly defined directory are not automatically deleted.
#' files in an explicitly defined directory are not automatically deleted. Note
#' that Rmarkdown / Quarto cache does not store files in temporary directory,
#' and re-rendering with cache fails if explicit directory has not been defined.
#'
#' * `cmdstanr_verbose`: Should more information be printed
#' when compiling or running models, including showing how CmdStan was called
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12 changes: 9 additions & 3 deletions tests/testthat/test-csv.R
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Expand Up @@ -73,11 +73,17 @@ test_that("read_cmdstan_csv() fails for different variables", {
test_that("read_cmdstan_csv() fails if the file does not exist", {
csv_files <- c(test_path("resources", "csv", "model1-1-doesntexist.csv"))
expect_error(read_cmdstan_csv(csv_files),
"Assertion on 'files' failed: File does not exist: 'resources/csv/model1-1-doesntexist.csv'.")
"File does not exist: 'resources/csv/model1-1-doesntexist.csv'")
expect_error(read_cmdstan_csv(NULL),
"Assertion on 'files' failed: No file provided.")
"No file provided")
expect_error(read_cmdstan_csv(character(0)),
"Assertion on 'files' failed: No file provided.")
"No file provided")
# if knitr rendering and using temp directory, there is an additional message
old_opt <- options(knitr.in.progress = TRUE, cmdstanr_output_dir = NULL)
expect_error(read_cmdstan_csv(csv_files),
"File does not exist: 'resources/csv/model1-1-doesntexist.csv'\n If this error happened when using Quarto cache,\n see `cmdstanr_output_dir` in `?cmdstanr_global_options`",
fixed = TRUE)
options(old_opt)
})

test_that("read_cmdstan_csv() fails with empty csv file", {
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