index refers to wrong page when indexing words outside of the mainmatter

[ttimbers]

I initially opened a thread about this in the RStudio Community forum, but after further investigation, I think this might be a bug.

When using bookdown to render to pdf following the instructions in Write a Book with bookdown and Publish with Chapman & Hall, we have found (in two separate projects) that items that are indexed in the frontmatter are given the wrong page number - they get pointed to a page of the list of figures, but not to the preface.

So, including something like this in index.Rmd (which comes before the /mainmatter command):

Basic familiarity with version control\index{version control} and ...

Gets a page number of "x" - which is one of the pages of the list of figures. I have looked in this bookdown repo and see the same thing happens with the demo book:

There is an Index entry in the front matter (index.Rmd) for Git Book on line 54 that looks like this:

... and imported the GitBook\index{GitBook} style ...

Then in the pdf the index entry for Git Book is "ix", which is a list of figure page:

[ttimbers]

Just a gentle ping about this issue...

[cderv]

Hi @ttimbers,

Thanks for the ping. That is not an easy one to investigate as it is tied to how latex work. in fact, \index feature is not part of bookdown - it is brought by LaTeX by adding

  \usepackage{makeidx}
  \makeindex

in preamble using header includes and

  \printindex

where to place the index, usually in after body includes.

I tested with bookdown-demo book and I can"t seem to reproduce this issue. I saw it on the bookdown book too and I wonder if this is not something related to the special class to use for Chapman and Hall: krantz.cls

Are you using this documentclass too ? It seems you do https://github.com/UBC-DSCI/introduction-to-datascience/blob/master/pdf/krantz.cls

I don't really know where to look in bookdown for this. I wonder if someone maintaining the krants class could help us see if this maybe be from the class processing or not 🤔

Did you encounter this issue with another documentclass ?

[yihui]

For problems related to krantz.cls, usually there is only one person who can help---Shashi Kumar <texhelp@taylorandfrancis.com> (Chapman & Hall's TeX help desk).

[ttimbers]

Thanks @cderv and @yihui - I will reach out to Shashi!

[trevorcampbell]

@cderv and @yihui -- @ttimbers and I worked a bit with Shashi and we found that:

• if we manually compile bookdown.tex (output by bookdown) only once, then run makeindex, then compile again, the issue we noticed shows up -- the index entries in the preface / frontmatter don't point to the right pages
• if we manually compile bookdown.tex twice, then run makeindex, then compile again, the index entries all look correct

So basically it looks like krantz.cls is fine and that it boils down to how many times the latex is being compiled before running makeindex.

Is this something that bookdown controls when it calls pandoc (maybe some config params that it passes in?), or is it a bug in pandoc where it isn't properly recognizing how many times it needs to compile, or something else?

[trevorcampbell]

Ah, I think I may have found the issue -- it's in the tinytex repo

https://github.com/yihui/tinytex/blob/a339f67403637ff7f8d9ca062e359133b63554b0/R/latex.R#L226

run_engine() is only run once before making the index -- I think it may need to be run twice.

I'll test this out on our book, one moment...

[trevorcampbell]

Yup, that fixed it. I added a line after line 226 of latex.R in tinytex with an extra call to run_engine(), and our index entries look good now.

@yihui @cderv -- not sure if that's a reasonable fix or if there's something more clever to do, but at least we've nailed down the problem and a candidate fix. Please let us know how to proceed.

[cderv]

Wow thanks a lot for the investigation !

Does makeindex requires 2 render before in general case ? Or is this specific to our .tex file ? I don't know enough LaTeX to know this. Sorry it makes no sense.

@yihui is this something you would look for a fix in tinytex or specific to bookdown ?

It seems that it could happens with any tex file that requires makeindex 🤔 I wonder if there is something in the log file that would help know than latexmk() needs to still run once more.

@trevorcampbell I believe that if you set option tinytex.latexmk.emulation to FALSE (not using tinytex emulation of latexmk() but using latexmk program directly) this will work ? Probably that latexmk knows what to do ?

[yihui]

@yihui is this something you would look for a fix in tinytex or specific to bookdown ?

We should fix it in tinytex.

[trevorcampbell]

Does makeindex requires 2 render before in general case

Yes, I believe so (it's similar to hyperlinks in the main text)

It seems that it could happens with any tex file that requires makeindex thinking I wonder if there is something in the log file that would help know than latexmk() needs to still run once more.

Looking at the code right after the run_engine() call I pointed out, it seems there is already an if statement to check whether an .idx file was created. You could just put a call to run_engine() at the start of the if scope.

  # some problems only trigger warnings but not errors, e.g.,
  # https://github.com/yihui/tinytex/issues/311 fix them and re-run engine
  if (install_packages && check_extra(logfile)) run_engine()

  # generate index
  if (file.exists(idx <- aux_files['idx'])) {
    idx_engine = getOption('tinytex.makeindex', 'makeindex')
    install_cmd(idx_engine)
    system2_quiet(idx_engine, c(getOption('tinytex.makeindex.args'), shQuote(idx)), error = {
      stop("Failed to build the index via ", idx_engine, call. = FALSE)
    })
  }

I believe that if you set option tinytex.latexmk.emulation to FALSE

@cderv how do I do this? I assume I have to add something to the index.Rmd file?

We should fix it in tinytex.

I'll leave it in your capable hands :)

[yihui]

I just pushed the fix. You can test the development version of tinytex via

remotes::install_github('yihui/tinytex')

Thanks!

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