I want to compile a template quarto report in a temporary directory. In the real case, the template is in an R package, and therefore has to compiled in a temporary directory. But I get the following error:
# This will create a file named "template.qmd" in the current folder.
# Used in: the "template.qmd" is a parametrized report and in a package. The report
# will be compiled in a temporary directly which will be cleaned afterwards.
f <- c("---", "title: \"Test\"", "format: html", "---", "", "## Set a variable",
"", "```{r}", "OK <- FALSE", "```", "", "## Running Code depending on value of `OK`",
"", "```{r}", "#| eval: !expr OK", "print(\"OK is TRUE - otherwise you won't see anything here.\")",
"```", "")
writeLines(f, "template.qmd")
name <- "Test_Report"
output_format <- "html"
output_file <- paste0(name, ".html")
tmpdir <- tempfile()
dir.create(tmpdir)
template <- file.path(tmpdir, "template.qmd")
file.copy(
file.path(".", "template.qmd"),
template
)
report <- quarto::quarto_render(
input = template,
output_format = output_format,
output_file = output_file
)
# Here the error occurs:
#
# processing file: template.qmd
# |.............. | 20%
# ordinary text without R code
#
# |............................ | 40%
# label: unnamed-chunk-1
# |.......................................... | 60%
# ordinary text without R code
#
# |........................................................ | 80%
# label: unnamed-chunk-2 (with options)
# List of 1
# $ eval: logi FALSE
#
# |......................................................................| 100%
# ordinary text without R code
#
#
# output file: template.knit.md
#
# pandoc --output ../../../../../../../Users/rainerkrug/tmp/test/Test_Report.html
# to: html
# standalone: true
# section-divs: true
# html-math-method: mathjax
# wrap: none
# default-image-extension: png
#
# metadata
# document-css: false
# link-citations: true
# date-format: long
# lang: en
# title: Test
#
# pandoc: ../../../../../../../Users/rainerkrug/tmp/test/Test_Report.html: openFile: does not exist (No such file or directory)
# Error in `processx::run(quarto_bin, args, echo = TRUE)`:
# ! System command 'quarto' failed
# ---
# Exit status: 1
# stdout & stderr: <printed>
# ---
# Type .Last.error to see the more details.
# And I would like to continuye as follows:
file.copy(
file.path(tmpdir, output_file),
file.path(".", output_file),
)
unlink(tmpdir)
Session Info:
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 ps_1.7.2 digest_0.6.31 later_1.3.0 R6_2.5.1
[6] jsonlite_1.8.4 evaluate_0.19 rlang_1.0.6 cli_3.6.0 rstudioapi_0.14
[11] rmarkdown_2.19 tools_4.2.2 yaml_2.3.6 xfun_0.36 fastmap_1.1.0
[16] compiler_4.2.2 processx_3.8.0 htmltools_0.5.4 knitr_1.41 quarto_1.2
>
Is this a bug in quarto, or am I doing something obvious wrong?
There seems to be a bug in quarto / panda on Mac, as it works on Ubuntu. The problem is the argument output_file = output_file. As soon as it is present, the Mac implementation fails. I solved it wit the following:
f <- c("---", "title: \"Test\"", "format: html", "---", "", "## Set a variable",
"", "```{r}", "OK <- FALSE", "```", "", "## Running Code depending on value of `OK`",
"", "```{r}", "#| eval: !expr OK", "print(\"OK is TRUE - otherwise you won't see anything here.\")",
"```", "")
writeLines(f, "template.qmd")
name <- "Test_Report"
output_format <- "html"
output_file <- paste0(name, ".html")
tmpdir <- tempfile()
dir.create(tmpdir)
template <- file.path(tmpdir, paste0(name, ".qmd"))
file.copy(
file.path(".", "template.qmd"),
template
)
report <- quarto::quarto_render(
input = template,
output_format = output_format
)
fn <- c(paste0(name, ".html"), paste0(name, "_files"))
file.copy(
file.path(tmpdir, fn),
file.path("."),
recursive = TRUE
)
unlink(tmpdir)