post_processor in rmarkdown not working

On 07/09/2017 2:04 PM, Duncan Murdoch wrote:

On 07/09/2017 10:11 AM, Thierry Onkelinx wrote:

Dear Duncan,

Thanks for chiming in. Could you explain how you set debug() on
post_processor()? I've tried adding debug(post_processor) to
rsos_article() or adding debug(post_processor) when after post_processor
was defined in the debugger. Neither work for me.

Not working for me either right now for some reason or other.  What I
was doing was manually running debug(post_processor) in the debugger
after single stepping past its definition.

What does show it is running is that at that same point I can execute

post_processor <- function() stop()

and it stops.

The end of the console log looks like this:


/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS
skeleton.utf8.md --to latex --from
markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash
--output skeleton.tex --template
/Library/Frameworks/R.framework/Versions/3.3/Resources/
library/INBOmd/rmarkdown/templates/rsos_article/resources/template.tex
--natbib --bibliography sample.bib
Latexmk: This is Latexmk, John Collins, 19 Jan. 2017, version: 4.52c.
Error in output_format$post_processor(yaml_front_matter, utf8_input,
output_file,  :
    unused arguments (yaml_front_matter, utf8_input, output_file, clean,
!quiet)
Called from: output_format$post_processor(yaml_front_matter, utf8_input,
output_file,
      clean, !quiet)

so we see pandoc being run, then Latexmk, then the post_processor call.
It seems a little odd that Latexmk is being run.  Is that something you
are doing, or is it pandoc asking for that?  If the latter, can you tell
pandoc not to do so?

I've done some debugging in rmarkdown::render.  Apparently if you need
Bibtex (as your example does), it runs Latexmk before the post-processor.

I don't know if there's a way around this...

Duncan Murdoch

All supporting files are available within the package. The code below
should be reproducible on your machine.

remove.packages("INBOmd")
devtools::install_github("inbo/INBOmd at post_processor")
setwd(system.file("rmarkdown/templates/rsos_article/skeleton", package =
"INBOmd"))
debug(INBOmd::rsos_article)
rmarkdown::render("skeleton.Rmd")

I'm not sure you would normally have write access in that directory, so
it may not be typical of what you'd see in a user directory.  I
certainly see something different when I copy the skeleton.Rmd file (and
nothing else) to my own temp directory.

The sign that post_processor() fails when the tex file still contains
\EndFirstPage resulting in the compilation error "Undefined control
sequence. l.128 \EndFirstPage"

That certainly indicates it isn't doing what you want, but it might be
running and doing something else.

Duncan Murdoch

I still get the error with the current version of the code. Running the
post_processor manually works.

eval(parse(
    text = readLines(
      "https://raw.githubusercontent.com/inbo/INBOmd/post_
processor/R/rsos_article.R"
    )[72:92]
))
post_processor(output_file = "skeleton.tex")
system("pdflatex skeleton.tex")

Best regards,


ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data. ~ John Tukey

2017-09-07 12:14 GMT+02:00 Duncan Murdoch <murdoch.duncan at gmail.com
<mailto:murdoch.duncan at gmail.com>>:

     On 06/09/2017 5:41 AM, Thierry Onkelinx wrote:

         Dear all,

         I'm trying to write a post_processor() for a custom rmarkdown
         format. The
         goal of the post_processor() is to modify the latex file before
         it is
         compiled. For some reason the post_processor() is not run. The
         post_processor() does work when I run it manually on the tex
file.

         Any suggestions on what I'm doing wrong? Below is the relevant
         snippet of
         the code. The full code is available at
         https://github.com/inbo/INBOmd/blob/post_processor/R/rsos_
article.R
         <https://github.com/inbo/INBOmd/blob/post_processor/R/rsos_
article.R>
         https://github.com/inbo/INBOmd/blob/post_processor/inst/
rmarkdown/templates/rsos_article/skeleton/skeleton.Rmd
         <https://github.com/inbo/INBOmd/blob/post_processor/inst/
rmarkdown/templates/rsos_article/skeleton/skeleton.Rmd>
         is an Rmd is a MWE that fails compile because the
         post_processor() is not
         run.


     I installed it and tried running it using

     debug(INBOmd::rsos_article)
     rmarkdown::render("skeleton.Rmd")

     then after post_processor was defined, I set it to debug as well,
     and could see that the post_processor was being run.

     I didn't get useful output, because the LaTeXing failed (I don't
     have the rsos.cls), but perhaps you've already fixed this problem,
     or perhaps it is intermittent?

     Duncan Murdoch

         Best regards,

         Thierry

             post_processor <- function(
               metadata, input_file, output_file, clean, verbose
             ) {
               text <- readLines(output_file, warn = FALSE)

               # set correct text in fmtext environment
               end_first_page <- grep("\\\\EndFirstPage", text) #nolint
               if (length(end_first_page) == 1) {
                 maketitle <- grep("\\\\maketitle", text) #nolint
                 text <- c(
                   text[1:(maketitle - 1)],
                   "\\begin{fmtext}",
                   text[(maketitle + 1):(end_first_page - 1)],
                   "\\end{fmtext}",
                   "\\maketitle",
                   text[(end_first_page + 1):length(text)]
                 )
                 writeLines(enc2utf8(text), output_file, useBytes = TRUE)
               }
               output_file
             }

             output_format(
               knitr = knitr_options(
                 opts_knit = list(
                   width = 60,
                   concordance = TRUE
                 ),
                 opts_chunk = opts_chunk,
                 knit_hooks = knit_hooks
               ),
               pandoc = pandoc_options(
                 to = "latex",
                 latex_engine = "xelatex",
                 args = args,
                 keep_tex = keep_tex
               ),
               post_processor = post_processor,
               clean_supporting = !keep_tex
             )



         ir. Thierry Onkelinx
         Instituut voor natuur- en bosonderzoek / Research Institute for
         Nature and
         Forest
         team Biometrie & Kwaliteitszorg / team Biometrics & Quality
         Assurance
         Kliniekstraat 25
         1070 Anderlecht
         Belgium

         To call in the statistician after the experiment is done may be
         no more
         than asking him to perform a post-mortem examination: he may be
         able to say
         what the experiment died of. ~ Sir Ronald Aylmer Fisher
         The plural of anecdote is not data. ~ Roger Brinner
         The combination of some data and an aching desire for an answer
         does not
         ensure that a reasonable answer can be extracted from a given
         body of data.
         ~ John Tukey

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