Unable to "Build Book" use the bookdown-demo

[richardgao1992]

Hello,

I just forked and cloned this repo, installed TinyTeX and tried building the book as instructed, however I encountered the following error (I got the same error before installing TinyTeX as well):
processing file: bookdown-demo.Rmd
|........ | 11%
inline R code fragments

|................ | 22%
label: unnamed-chunk-1 (with options)
List of 1
$ eval: logi FALSE

|....................... | 33%
ordinary text without R code

|............................... | 44%
label: unnamed-chunk-2 (with options)
List of 1
$ include: logi FALSE

Quitting from lines 32-36 (bookdown-demo.Rmd)
Error in parse(con) : 4:12: unexpected INCOMPLETE_STRING
3: title = "Welcome to the {tidyverse}",
4: author = "Hadley Wickham, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D'Agostino McGowan, Romain Fran
^
Calls: local ... -> readCitationFile -> -> parse
Execution halted
Error: bookdown::render_book() failed to render the output format 'bookdown::gitbook'.
Execution halted

Exited with status 1.

[yihui]

I can't reproduce this problem. Could you run bookdown::render_book() in the R console? If it throws the same error, please provide traceback() output.

[richardgao1992]

bookdown::render_book()
Rendering book in directory '.'

processing file: bookdown-demo.Rmd
|.......... | 11%
inline R code fragments

|................... | 22%
label: unnamed-chunk-1 (with options)
List of 1
$ eval: logi FALSE

|............................. | 33%
ordinary text without R code

|...................................... | 44%
label: unnamed-chunk-2 (with options)
List of 1
$ include: logi FALSE

Quitting from lines 32-36 (bookdown-demo.Rmd)
Error in parse(con) : 4:12: unexpected INCOMPLETE_STRING
3: title = "Welcome to the {tidyverse}",
4: author = "Hadley Wickham, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D'Agostino McGowan, Romain Fran
^

traceback()
31: parse(con)
30: tools:::.parse_CITATION_file(file, meta$Encoding)
29: readCitationFile(citfile, meta)
28: utils::citation(..., lib.loc = lib.loc)
27: citation(pkg, auto = FALSE)
26: FUN(X[[i]], ...)
25: lapply(x, function(pkg) {
if (pkg == "base")
return()
if (system.file("CITATION", package = pkg) == "")
return()
cites = citation(pkg, auto = FALSE)
cites = Filter(x = cites, function(cite) {
!isTRUE(grepl("R package version", cite$note))
})
s = make_unique(unlist(lapply(cites, function(cite) {
if (is.null(cite$year))
format(Sys.Date(), "%Y")
else cite$year
})))
mapply(cites, s, FUN = function(cite, suffix) {
if (isTRUE(grepl("R package version", cite$note)))
return()
entry = toBibtex(cite)
entry[1] = sub("\{,$", sprintf("{%s%s,", pkg, suffix),
entry[1])
...
24: knitr::write_bib(c(.packages(), "bookdown", "knitr", "rmarkdown"),
"packages.bib")
23: eval(expr, envir, enclos)
22: eval(expr, envir, enclos)
21: eval_with_user_handlers(expr, envir, enclos, user_handlers)
20: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
19: withCallingHandlers(withVisible(eval_with_user_handlers(expr,
envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
message = mHandler)
18: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,
envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
message = mHandler))
17: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,
envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
message = mHandler)))
16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
15: evaluate::evaluate(...)
14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include)
0L
else 2L
}, output_handler = knit_handlers(options$render, options))
13: in_dir(input_dir(), expr)
12: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include)
0L
else 2L
}, output_handler = knit_handlers(options$render, options)))
11: eng_r(options)
10: block_exec(params)
9: call_block(x)
8: process_group.block(group)
7: process_group(group)
6: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
5: process_file(text, output)
4: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3: rmarkdown::render(main, output_format, ..., clean = clean, envir = envir)
2: render_cur_session(files, main, config, output_format, clean,
envir, ...)
1: bookdown::render_book()

[yihui]

It looks like an encoding problem. The good news is that R 4.2.0 is coming soon, which should solve most encoding problems on Windows. For now, you can try the alpha version: https://cran.r-project.org/bin/windows/base/rtest.html

[cderv]

Seems also a encoding issue to me. R does not manage to process this lette ç in Romain François in this reference in the bib file.

@Article{tidyverse2019,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}

As a workaround, you can remove the bib file creation here, especially if you don't use it.

bookdown-demo/index.Rmd

Lines 32 to 35 in 5331ffc

	# automatically create a bib database for R packages
	knitr::write_bib(c(
	.packages(), 'bookdown', 'knitr', 'rmarkdown'
	), 'packages.bib')

And otherwise, remove this citation (which is probably included due to one of the tidyverse package).

For a full fix, we need to know if R 4.2 fix the issue for you or not. Thanks !