Re: [R] post_processor in rmarkdown not working

[Duncan Murdoch]

On 08/09/2017 3:56 AM, Thierry Onkelinx wrote:
That is strange. Another function in the same package 
(INBOmd::inbo_rapport) uses the same trick. 


I think the issue there is that the LaTeX code is valid before the 
post-processor is run, it just re-orders things.  So rmarkdown::render 
runs Pandoc, then LaTeX (via Latexmk), then the post-processor, then 
LaTeX again.


This suggests a solution to the rsos_article problem:  somehow make sure 
that the LaTeX is valid from the start, e.g. by defining dummy versions 
of the missing macros.


Duncan Murdoch


I actually started by
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 >:


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@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

Re: [R] post_processor in rmarkdown not working

[Thierry Onkelinx]

That is strange. Another function in the same package
(INBOmd::inbo_rapport) uses the same trick. I actually started by 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 :

> 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@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 

Re: [R] post_processor in rmarkdown not working

[Duncan Murdoch]

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@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 >:

 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/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)
 

Re: [R] post_processor in rmarkdown not working

[Duncan Murdoch]

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?






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;

   )[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 >:


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/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), 

Re: [R] post_processor in rmarkdown not working

[Duncan Murdoch]

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

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")


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] post_processor in rmarkdown not working

[Thierry Onkelinx]

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@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 :

> 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/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]]
>>
>> 

Re: [R] post_processor in rmarkdown not working

[Duncan Murdoch]

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/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]]

__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] post_processor in rmarkdown not working

[Thierry Onkelinx]

Dear Heinz,

Yes. The idea of the post_processor() is that 1) pandoc converts the .md to
.tex 2) the post_processors changes the .tex 3) the .tex is compiled into
.pdf Hence the post_processors need to read, change and overwrite the tex
output file.

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 9:08 GMT+02:00 Heinz Tuechler :

> Are you sure that you want to read in the output_file in
>
> text <- readLines(output_file, warn = FALSE)?
>
> best regards,
>
> Heinz
>
>
> Thierry Onkelinx wrote/hat geschrieben on/am 06.09.2017 11:41:
>
>> 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/inst/
>> rmarkdown/templates/rsos_article/skeleton/skeleton.Rmd
>> is an Rmd is a MWE that fails compile because the post_processor() is not
>> run.
>>
>> 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]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
> --
> Heinz Tüchler +436605653878
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posti
> ng-guide.html
> and provide commented, minimal, self-contained, reproducible code.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] post_processor in rmarkdown not working

[Heinz Tuechler]

Are you sure that you want to read in the output_file in

text <- readLines(output_file, warn = FALSE)?

best regards,

Heinz

Thierry Onkelinx wrote/hat geschrieben on/am 06.09.2017 11:41:

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/inst/rmarkdown/templates/rsos_article/skeleton/skeleton.Rmd
is an Rmd is a MWE that fails compile because the post_processor() is not
run.

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]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



--
Heinz Tüchler +436605653878

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.