copying the post_processor() from that function. INBOmd::inbo_rapport()
works both with and without BibTex. Working examples are
source/inbo_rapport and source/inbo_rapport_basic from
https://github.com/inbo/inbomd_examples. Note that you need some extra
work after installing INBOmd to inbo_rapport() to run. See the README at
https://github.com/inbo/INBOmd
I've created an issue https://github.com/rstudio/rmarkdown/issues/1138
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 21:18 GMT+02:00 Duncan Murdoch <murdoch.dun...@gmail.com
<mailto:murdoch.dun...@gmail.com>>:
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 <http://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@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
<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.dun...@gmail.com <mailto:murdoch.dun...@gmail.com>
<mailto:murdoch.dun...@gmail.com
<mailto:murdoch.dun...@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/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>
<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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