`tar_quarto()` always ends normally for quarto project even if there is error #103

psychelzh · 2022-08-22T02:12:14Z

Prework

Read and agree to the code of conduct and contributing guidelines.
Confirm that your issue is a genuine bug in tarchetypes and not a known limitation, usage error, or issue from another package that tarchetypes depends on. If you are unsure, please submit a discussion thread instead.
If there is already a relevant issue, whether open or closed, comment on the existing thread instead of posting a new issue.
Post a minimal reproducible example like this one so the maintainer can troubleshoot the problems you identify. A reproducible example is:
- Runnable: post enough R code and data so any onlooker can create the error on their own computer.
- Minimal: reduce runtime wherever possible and remove complicated details that are irrelevant to the issue at hand.
- Readable: format your code according to the tidyverse style guide.

Description

The pipeline will always ends normally even if quarto_render() errored. When setting quiet = TRUE, users will not notice that!

Reproducible example

The pipeline ends normally.

targets::tar_dir({  # tar_dir() runs code from a temporary directory.
  # Unparameterized Quarto document:
  lines <- c(
    "---",
    "title: report.qmd source file",
    "output_format: html",
    "---",
    "Assume these lines are in report.qmd.",
    "```{r}",
    "stop()",
    "```"
  )
  writeLines(lines, "report.qmd")
  writeLines(
    c("project:", "  type: website"),
    "_quarto.yml"
  )
  # Include the report in a pipeline as follows.
  targets::tar_script({
    library(tarchetypes)
    list(
      tar_quarto(report, path = ".")
    )
  }, ask = FALSE)
  targets::tar_make()
})
#> • start target report
#> • built target report
#> • end pipeline: 1.76 seconds

^{Created on 2022-08-22 with reprex v2.0.2}

But there is error (set quiet = FALSE):

targets::tar_dir({  # tar_dir() runs code from a temporary directory.
  # Unparameterized Quarto document:
  lines <- c(
    "---",
    "title: report.qmd source file",
    "output_format: html",
    "---",
    "Assume these lines are in report.qmd.",
    "```{r}",
    "stop()",
    "```"
  )
  writeLines(lines, "report.qmd")
  writeLines(
    c("project:", "  type: website"),
    "_quarto.yml"
  )
  # Include the report in a pipeline as follows.
  targets::tar_script({
    library(tarchetypes)
    list(
      tar_quarto(report, path = ".", quiet = F)
    )
  }, ask = FALSE)
  targets::tar_make()
})
#> • start target report
#> �[31m
#> 
#> processing file: report.qmd
#> �[39m  |                                                                              |                                                                      |   0%  |                                                                              |.......................                                               |  33%
#>   ordinary text without R code
#> 
#>   |                                                                              |...............................................                       |  67%
#> label: unnamed-chunk-1
#> �[31mQuitting from lines 7-8 (report.qmd) 
#> �[39m�[31mError in eval(expr, envir, enclos) : 
#> Calls: .main ... withVisible -> eval_with_user_handlers -> eval -> eval
#> �[39m
#> �[31mExecution halted
#> �[39m• built target report
#> • end pipeline: 1.81 seconds

^{Created on 2022-08-22 with reprex v2.0.2}

Expected result

Errors should be signalled.

The text was updated successfully, but these errors were encountered:

wlandau · 2022-08-22T11:51:33Z

The problem is that Quarto on Windows is apparently not forwarding errors back to R.

lines <- c(
  "---",
  "title: report",
  "output_format: html",
  "---",
  "```{r}",
  "stop(\"this is an error\")",
  "```"
)
writeLines(lines, "report.qmd")
tryCatch({
    quarto::quarto_render("report.qmd", as_job = FALSE, quiet = TRUE)
    message("missed error")
  },
  error = function(condition) message("caught error")
)
#> missed error

^{Created on 2022-08-22 with reprex v2.0.2}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23 ucrt)
#>  os       Windows 10 x64 (build 19044)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United States.utf8
#>  ctype    English_United States.utf8
#>  tz       America/New_York
#>  date     2022-08-22
#>  pandoc   2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.3.0   2022-04-25 [1] CRAN (R 4.2.1)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.2.1)
#>  evaluate      0.16    2022-08-09 [1] CRAN (R 4.2.1)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.2.1)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.2.1)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.2.1)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.2.1)
#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.2.1)
#>  jsonlite      1.8.0   2022-02-22 [1] CRAN (R 4.2.1)
#>  knitr         1.39    2022-04-26 [1] CRAN (R 4.2.1)
#>  later         1.3.0   2021-08-18 [1] CRAN (R 4.2.1)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.2.1)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.2.1)
#>  processx      3.7.0   2022-07-07 [1] CRAN (R 4.2.1)
#>  ps            1.7.1   2022-06-18 [1] CRAN (R 4.2.1)
#>  quarto        1.2     2022-07-06 [1] CRAN (R 4.2.1)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.2.1)
#>  Rcpp          1.0.9   2022-07-08 [1] CRAN (R 4.2.1)
#>  reprex        2.0.2   2022-08-17 [1] CRAN (R 4.2.1)
#>  rlang         1.0.4   2022-07-12 [1] CRAN (R 4.2.1)
#>  rmarkdown     2.15    2022-08-16 [1] CRAN (R 4.2.1)
#>  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.2.1)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.1)
#>  stringi       1.7.8   2022-07-11 [1] CRAN (R 4.2.1)
#>  stringr       1.4.1   2022-08-20 [1] CRAN (R 4.2.1)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.2.1)
#>  xfun          0.32    2022-08-10 [1] CRAN (R 4.2.1)
#>  yaml          2.3.5   2022-02-21 [1] CRAN (R 4.2.1)
#> 
#>  [1] C:/Users/landau/AppData/Local/R/win-library/4.2
#>  [2] C:/Program Files/R/R-4.2.1/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

wlandau · 2022-08-22T11:55:22Z

See quarto-dev/quarto-r#48

psychelzh · 2022-08-23T00:58:29Z

Seemingly this is solved in quarto 1.1! Thank you very much.

quarto check:

[>] Checking Quarto installation......OK
      Version: 1.1.113
      Path: C:\Users\psych\AppData\Local\Programs\Quarto\bin\
      CodePage: 936

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....(None)

      Unable to locate an installed version of Python 3.
      Install Python 3 from https://www.python.org/downloads/

[>] Checking R installation...........OK
      Version: 4.2.1
      Path: C:/PROGRA~1/R/R-42~1.1
      LibPaths:
        - C:/Users/psych/AppData/Local/R/win-library/4.2
        - C:/Program Files/R/R-4.2.1/library
      rmarkdown: 2.14

[>] Checking Knitr engine render......OK

New reprex:

targets::tar_dir({  # tar_dir() runs code from a temporary directory.
    # Unparameterized Quarto document:
    lines <- c(
        "---",
        "title: report.qmd source file",
        "output_format: html",
        "---",
        "Assume these lines are in report.qmd.",
        "```{r}",
        "stop()",
        "```"
    )
    writeLines(lines, "report.qmd")
    writeLines(
        c("project:", "  type: website"),
        "_quarto.yml"
    )
    # Include the report in a pipeline as follows.
    targets::tar_script({
        library(tarchetypes)
        list(
            tar_quarto(report, path = ".")
        )
    }, ask = FALSE)
    targets::tar_make()
})
#> • start target report
#> ✖ error target report
#> • end pipeline: 2.03 seconds
#> Error : ! System command 'quarto.cmd' failed
#> ✖ Problem with the pipeline.
#> Error:
#> ! problem with the pipeline.

^{Created on 2022-08-23 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23 ucrt)
#>  os       Windows 10 x64 (build 22000)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  Chinese (Simplified)_China.utf8
#>  ctype    Chinese (Simplified)_China.utf8
#>  tz       Asia/Taipei
#>  date     2022-08-23
#>  pandoc   2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  backports     1.4.1   2021-12-13 [1] CRAN (R 4.2.0)
#>  base64url     1.4     2018-05-14 [1] CRAN (R 4.2.1)
#>  callr         3.7.1   2022-07-13 [1] CRAN (R 4.2.1)
#>  cli           3.3.0   2022-04-25 [1] CRAN (R 4.2.1)
#>  codetools     0.2-18  2020-11-04 [2] CRAN (R 4.2.1)
#>  data.table    1.14.2  2021-09-27 [1] CRAN (R 4.2.1)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.2.1)
#>  evaluate      0.16    2022-08-09 [1] CRAN (R 4.2.1)
#>  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.2.1)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.2.1)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.2.1)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.2.1)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.2.1)
#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.2.1)
#>  igraph        1.3.4   2022-07-19 [1] CRAN (R 4.2.1)
#>  knitr         1.39    2022-04-26 [1] CRAN (R 4.2.1)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.2.1)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.2.1)
#>  pillar        1.8.0   2022-07-18 [1] CRAN (R 4.2.1)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.2.1)
#>  processx      3.7.0   2022-07-07 [1] CRAN (R 4.2.1)
#>  ps            1.7.1   2022-06-18 [1] CRAN (R 4.2.1)
#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.2.1)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.2.1)
#>  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       2.12.0  2022-06-28 [1] CRAN (R 4.2.1)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.2.1)
#>  reprex        2.0.1   2021-08-05 [1] CRAN (R 4.2.1)
#>  rlang         1.0.4   2022-07-12 [1] CRAN (R 4.2.1)
#>  rmarkdown     2.14    2022-04-25 [1] CRAN (R 4.2.1)
#>  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.2.1)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.1)
#>  stringi       1.7.8   2022-07-11 [1] CRAN (R 4.2.1)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.2.1)
#>  styler        1.7.0   2022-03-13 [1] CRAN (R 4.2.1)
#>  targets       0.13.1  2022-08-05 [1] CRAN (R 4.2.1)
#>  tibble        3.1.8   2022-07-22 [1] CRAN (R 4.2.1)
#>  tidyselect    1.1.2   2022-02-21 [1] CRAN (R 4.2.1)
#>  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.2.1)
#>  vctrs         0.4.1   2022-04-13 [1] CRAN (R 4.2.1)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.2.1)
#>  xfun          0.32    2022-08-10 [1] CRAN (R 4.2.1)
#>  yaml          2.3.5   2022-02-21 [1] CRAN (R 4.2.1)
#> 
#>  [1] C:/Users/psych/AppData/Local/R/win-library/4.2
#>  [2] C:/Program Files/R/R-4.2.1/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

psychelzh added the type: bug label Aug 22, 2022

psychelzh assigned wlandau Aug 22, 2022

wlandau added depends: external prerequisite and removed type: bug labels Aug 22, 2022

wlandau closed this as completed Aug 22, 2022

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`tar_quarto()` always ends normally for quarto project even if there is error #103

`tar_quarto()` always ends normally for quarto project even if there is error #103

psychelzh commented Aug 22, 2022

wlandau commented Aug 22, 2022

wlandau commented Aug 22, 2022

psychelzh commented Aug 23, 2022 •

edited

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tar_quarto() always ends normally for quarto project even if there is error #103

tar_quarto() always ends normally for quarto project even if there is error #103

Comments

psychelzh commented Aug 22, 2022

Prework

Description

Reproducible example

Expected result

wlandau commented Aug 22, 2022

wlandau commented Aug 22, 2022

psychelzh commented Aug 23, 2022 • edited Loading

`tar_quarto()` always ends normally for quarto project even if there is error #103

`tar_quarto()` always ends normally for quarto project even if there is error #103

psychelzh commented Aug 23, 2022 •

edited

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