[help] I can no longer run targets pipeline with tar_quarto

[daranzolin]

Help

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

Description

I had a targets pipeline that has been running smoothly. But now every tar_*() command fails with a bizarre (empty?) error:

> tar_glimpse()
Error:
! targets::tar_glimpse() error

── Debugging ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
    • tar_errored()
    • tar_meta(fields = any_of("error"), complete_only = TRUE)
    • tar_workspace()
    • tar_workspaces()

── How to ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
    • Debug: https://books.ropensci.org/targets/debugging.html
    • Help: https://books.ropensci.org/targets/help.html

── Last error message ─────────────────────────────────────────────────────────────────────────────────────────────────────
    

── Last error traceback ───────────────────────────────────────────────────────────────────────────────────────────────────
    tryCatch(withCallingHandlers({ NULL saveRDS(do.call(do.call, c(readRDS("...
    tryCatchList(expr, classes, parentenv, handlers)
    tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), na...
    doTryCatch(return(expr), name, parentenv, handler)
    tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
    tryCatchOne(expr, names, parentenv, handlers[[1L]])
    doTryCatch(return(expr), name, parentenv, handler)
    withCallingHandlers({ NULL saveRDS(do.call(do.call, c(readRDS("C:\\Users...
    saveRDS(do.call(do.call, c(readRDS("C:\\Users\\<redacted>\\AppData\\Local\...
    do.call(do.call, c(readRDS("C:\\Users\\<redacted>\\AppData\\Local\\Temp\\R...
    (function (what, args, quote = FALSE, envir = parent.frame()) { if (!is....
    (function (targets_function, targets_arguments, options, envir = NULL, s...
    tryCatch(out <- withCallingHandlers(targets::tar_callr_inner_try(targets...
    tryCatchList(expr, classes, parentenv, handlers)
    tryCatchOne(expr, names, parentenv, handlers[[1L]])
    doTryCatch(return(expr), name, parentenv, handler)
    withCallingHandlers(targets::tar_callr_inner_try(targets_function = targ...
    targets::tar_callr_inner_try(targets_function = targets_function, target...
    eval(parse(file = script, keep.source = TRUE), envir = envir)
    eval(parse(file = script, keep.source = TRUE), envir = envir)
    tar_plan(tar_file(export_dir, path(Sys.getenv("S_DR_WFC"), "Raw_Data_Sys...
    lapply(commands, eval, envir = targets::tar_option_get("envir"))
    FUN(X[[i]], ...)
    FUN(X[[i]], ...)
    tar_quarto(test, path = "Reports/test.qmd")
    tar_quarto_raw(name = name, path = path, working_directory = working_dir...
    tar_quarto_files(path = path, profile = profile)
    if_any(fs::is_dir(path), tar_quarto_files_project(path), tar_quarto_file...
    tar_quarto_files_document(path)
    quarto::quarto_inspect(input = path)
    fromJSON(output)
    parse_and_simplify(txt = txt, simplifyVector = simplifyVector, simplifyD...
    parseJSON(txt, bigint_as_char)
    parse_string(txt, bigint_as_char)

However, if I comment out every tar_quarto() target in _targets.R, the pipeline runs again (except for the Quarto reports). Even more confusingly, a colleague can pull down the repo and run the pipeline with Quarto reports smoothly. We have the same targets and Quarto versions, but he is on R 4.4 whereas I am on R 4.2. Is there any other explanation for this?

[wlandau]

Do you have a reprex?

[daranzolin]

Sorry, the project is too large to reprex. It's just totally bizarre why, in _targets.R, this works fine:

...
test = quarto::quarto_render("Reports/test.qmd"),
...

But this crashes everything?

...
  tar_quarto(test, path = "Reports/test.qmd"),
...

tar_quarto() is doing something I can't see or understand.

[wlandau]

Looking again at the traceback, what happens with quarto::quarto_inspect(input = "Reports/test.qmd")? Looks like that could be the culprit.

[daranzolin]

Thanks Will, Interestingly quarto::quarto_inspect(input = "Reports/test.qmd") returned an error:

Error: lexical error: invalid character inside string.

But the string listed is from a different qmd file. Deleting that qmd appears to have solved everything: I can run the pipeline as usual again. That helped, thanks so much! quarto_inspect() will be handy going forward.