tar_quarto_rep doesn't work on reports in subdirectories

[joelnitta]

Discussed in ropensci/targets#1046

^{Originally posted by joelnitta April 12, 2023}

Help

• I understand and agree to https://books.ropensci.org/targets/help.html.

Description

This is a slight modification of the example code for tar_quarto_rep() that puts the Qmd file in a subdirectory. It results in an error ERROR: --output option cannot specify a relative or absolute path

targets::tar_dir({ # tar_dir() runs code from a temporary directory.
# Parameterized Quarto:
lines <- c(
  "---",
  "title: 'report.qmd file'",
  "output_format: html_document",
  "params:",
  "  par: \"default value\"",
  "---",
  "Assume these lines are in a file called report.qmd.",
  "```{r}",
  "print(params$par)",
  "```"
)
dir.create("reports/")
writeLines(lines, "reports/report.qmd") # In tar_dir(), not the user's file space.
# The following pipeline will run the report for each row of params.
targets::tar_script({
  library(tarchetypes)
  list(
    tar_quarto_rep(
      report,
      path = "reports/report.qmd",
      execute_params = tibble::tibble(par = c(1, 2)),
      quiet = FALSE
    )
  )
}, ask = FALSE)
targets::tar_make()
# Then, run the targets pipeline as usual.
})
#> • start target report_params
#> • built target report_params [0.007 seconds]
#> • start branch report_c45b815a
#> �[91mERROR: --output option cannot specify a relative or absolute path�[39m
#> ✖ error branch report_c45b815a
#> • end pipeline [0.435 seconds]
#> Error:
#> ! Error running targets::tar_make()
#>   Error messages: targets::tar_meta(fields = error, complete_only = TRUE)
#>   Debugging guide: https://books.ropensci.org/targets/debugging.html
#>   How to ask for help: https://books.ropensci.org/targets/help.html
#>   Last error: ! ! System command 'quarto' failed

#> Backtrace:
#>     ▆
#>  1. └─targets::tar_make()
#>  2.   └─targets:::callr_outer(...)
#>  3.     ├─targets:::if_any(...)
#>  4.     └─targets:::callr_error(condition = out, fun = fun)
#>  5.       └─targets::tar_throw_run(message, class = class(condition))
#>  6.         └─targets::tar_error(...)
#>  7.           └─rlang::abort(message = message, class = class, call = tar_empty_envir)

^{Created on 2023-04-12 with reprex v2.0.2}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.3 (2023-03-15)
#>  os       macOS Big Sur ... 10.16
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Asia/Tokyo
#>  date     2023-04-12
#>  pandoc   2.19.2 @ /usr/local/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P backports     1.4.1   2021-12-13 [?] CRAN (R 4.2.0)
#>  P base64url     1.4     2018-05-14 [?] CRAN (R 4.2.0)
#>  P callr         3.7.2   2022-08-22 [?] CRAN (R 4.2.0)
#>  P cli           3.4.1   2022-09-23 [?] CRAN (R 4.2.0)
#>  P codetools     0.2-19  2023-02-01 [3] CRAN (R 4.2.3)
#>  P data.table    1.14.4  2022-10-17 [?] CRAN (R 4.2.1)
#>  P digest        0.6.30  2022-10-18 [?] CRAN (R 4.2.1)
#>  P evaluate      0.17    2022-10-07 [?] CRAN (R 4.2.1)
#>  P fansi         1.0.3   2022-03-24 [?] CRAN (R 4.2.0)
#>  P fastmap       1.1.0   2021-01-25 [?] CRAN (R 4.2.0)
#>  P fs            1.5.2   2021-12-08 [?] CRAN (R 4.2.0)
#>  P glue          1.6.2   2022-02-24 [?] CRAN (R 4.2.0)
#>  P highr         0.9     2021-04-16 [?] CRAN (R 4.2.0)
#>    htmltools     0.5.5   2023-03-23 [1] CRAN (R 4.2.0)
#>  P igraph        1.3.5   2022-09-22 [?] CRAN (R 4.2.0)
#>  P knitr         1.40    2022-08-24 [?] CRAN (R 4.2.0)
#>  P lifecycle     1.0.3   2022-10-07 [?] CRAN (R 4.2.0)
#>  P magrittr      2.0.3   2022-03-30 [?] CRAN (R 4.2.0)
#>  P pillar        1.8.1   2022-08-19 [?] CRAN (R 4.2.0)
#>  P pkgconfig     2.0.3   2019-09-22 [?] CRAN (R 4.2.0)
#>  P processx      3.8.0   2022-10-26 [?] CRAN (R 4.2.0)
#>  P ps            1.7.2   2022-10-26 [?] CRAN (R 4.2.0)
#>  P purrr         0.3.5   2022-10-06 [?] CRAN (R 4.2.0)
#>    R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.2.0)
#>    R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.2.0)
#>    R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.2.0)
#>    R.utils       2.12.2  2022-11-11 [1] CRAN (R 4.2.0)
#>  P R6            2.5.1   2021-08-19 [?] CRAN (R 4.2.0)
#>  P reprex        2.0.2   2022-08-17 [?] CRAN (R 4.2.0)
#>  P rlang         1.0.6   2022-09-24 [?] CRAN (R 4.2.0)
#>  P rmarkdown     2.17    2022-10-07 [?] CRAN (R 4.2.0)
#>    sessioninfo   1.2.2   2021-12-06 [3] CRAN (R 4.2.0)
#>  P stringi       1.7.8   2022-07-11 [?] CRAN (R 4.2.0)
#>  P stringr       1.4.1   2022-08-20 [?] CRAN (R 4.2.0)
#>    styler        1.8.1   2022-11-07 [1] CRAN (R 4.2.0)
#>  P targets       0.14.3  2023-03-08 [?] CRAN (R 4.2.0)
#>  P tibble        3.1.8   2022-07-22 [?] CRAN (R 4.2.0)
#>  P tidyselect    1.2.0   2022-10-10 [?] CRAN (R 4.2.0)
#>  P utf8          1.2.2   2021-07-24 [?] CRAN (R 4.2.0)
#>  P vctrs         0.5.0   2022-10-22 [?] CRAN (R 4.2.0)
#>  P withr         2.5.0   2022-03-03 [?] CRAN (R 4.2.0)
#>  P xfun          0.34    2022-10-18 [?] CRAN (R 4.2.1)
#>  P yaml          2.3.6   2022-10-18 [?] CRAN (R 4.2.1)
#> 
#>  [1] /Users/joelnitta/repos/ppg-import/renv/library/R-4.2/x86_64-apple-darwin17.0
#>  [2] /Users/joelnitta/repos/ppg-import/renv/sandbox/R-4.2/x86_64-apple-darwin17.0/84ba8b13
#>  [3] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#> 
#>  P ── Loaded and on-disk path mismatch.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

[wlandau]

This was an issue in tarchetypes which I fixed in 68e9ea1. Just in case, I tried your example again, and it turns out I also needed dde6288 to send the output files to the right place when the source document is also in a subdirectory.

[joelnitta]

Ah sorry I should have posted to {tarchetypes}. Installing the dev version of {tarchetypes} fixes it. Thanks!