post_processor in rmarkdown not working

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.

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")

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

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

         ? ? ? ? [[alternative HTML version deleted]]