Pandoc error trying DISTILL

Job_Nmadu · December 8, 2020, 2:17pm

Always good to try out new methods and see it go. I tried HUGO severally and at one point or another, it bluffs. So I was excited to learn that DISTILL is an easy way to create personal website. Therefore I just tried the example for creating website from DISTILL help which resulted into the error message "pandoc document conversion failed with error 6"!!, I have tried all suggestions on Google (re-installed pandoc and rmarkdown) without success. Does anyone have ideas about this? I am using R4.03 and the RStudio is the very latest.

mattwarkentin · December 8, 2020, 3:03pm

Hi @Job_Nmadu,

Can you try running rmarkdown::pandoc_exec() in a fresh R session within RStudio and share what it returns?

Job_Nmadu · December 8, 2020, 6:16pm

rmarkdown::pandoc_exec()

"C:/Users/JOBNMA~1/AppData/Local/Pandoc/pandoc"

mattwarkentin · December 8, 2020, 6:29pm

Hmm, okay, this may be the issue. rmarkdown is probably using your system version of pandoc rather than the one that comes installed with RStudio.

Could you also run rmarkdown::find_pandoc() and Sys.getenv("RSTUDIO_PANDOC")?

Job_Nmadu · December 8, 2020, 6:36pm

rmarkdown::find_pandoc()
$version
[1] ‘2.11.2’

$dir
[1] "C:/Users/JOBNMA~1/AppData/Local/Pandoc"

Sys.getenv("RSTUDIO_PANDOC")
[1] "C:/Program Files/RStudio/bin/pandoc"

cderv · December 8, 2020, 6:51pm

It is indeed using a Pandoc version installed on your system, but that should work anyway.

Can you share the full console output you have for the pandoc command regarding this error ?

Thanks.

I tried HUGO severally and at one point or another, it bluffs.

Happy to here more about that too ! you can DM me to share your feedback, I would be very interested to know what frictions you had with blogdown

Job_Nmadu · December 8, 2020, 7:21pm

Not run:

library(distill)
create_website("mysite", "My Site")
Creating website directory mysite
Creating mysite/_site.yml
Creating mysite/index.Rmd
Creating mysite/about.Rmd
Rendering website...

Rendering: mysite/about.Rmd
|................. | 33%
ordinary text without R code

|................................. | 67%
label: setup (with options)
List of 1
$ include: logi FALSE

|..................................................| 100%
ordinary text without R code

"C:/Users/JOBNMA~1/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS about.utf8.md --to html5 --from markdown+autolink_bare_uris+tex_math_single_backslash --output about.html --lua-filter "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\RMARKD~1\RMARKD~1\lua\PAGEBR~1.LUA" --lua-filter "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\RMARKD~1\RMARKD~1\lua\LATEX-~1.LUA" --email-obfuscation none --standalone --variable toc-float=1 --highlight-style "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\distill\RMARKD~1\TEMPLA~1\DISTIL~1\RESOUR~1\ARROW~1.THE" --template "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\distill\RMARKD~1\TEMPLA~1\DISTIL~1\RESOUR~1\DEFAUL~1.HTM" "--metadata=link-citations:true" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f2056a84b02html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f2042b6ce4html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f2013a940a1html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f207c85aahtml" --include-before-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f20b1b20cehtml" --include-before-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f2044c92aa9html" --include-before-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f2019e0f7bhtml" --include-after-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f205df25a31html" --include-after-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f207761b05html" --include-after-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f20198c2117html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\rmarkdown-str3f2070ec7996.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpKwmp3W\file3f203547297bhtml"
Unknown highlight-style C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\distill\RMARKD~1\TEMPLA~1\DISTIL~1\RESOUR~1\ARROW~1.THE
Error: pandoc document conversion failed with error 6

End(Not run)

cderv · December 8, 2020, 7:50pm

Thank you. I believe this is related to

github.com/rstudio/distill

Latest version of distill not working properly with pandoc

opened 02:40PM - 13 Nov 20 UTC

closed 11:49AM - 10 Dec 20 UTC

mondpanther

I am having a problem with distill after upgrading to version 1.0 Here is the e…rror message: Unknown highlight-style C:\Users\RALFMA1\DOCUME1\R\WIN-LI1\4.0\distill\RMARKD1\TEMPLA1\DISTIL1\RESOUR1\A11Y1.THE Error: pandoc document conversion failed with error 2 In addition: Warning message: In (function (category = "LC_ALL", locale = "") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Execution halted Can you help? Because of this I am not able to compile any distill documents anymore. I tried to re-install everything (r and rstudio, also wiped any traces of pandoc) but the error remains. The problem went away after I reverted to version 0.8

But I did not manage to reproduce.

It would be very much appreciated if your are willing to help me with this Latest version of distill not working properly with pandoc · Issue #214 · rstudio/distill · GitHub

As it is now the second times, I think we have an issue with Windows and Pandoc related to the custom theme used.

Maybe it is because of windows short path...

Job_Nmadu · December 8, 2020, 8:18pm

public_dir <- "C:/Users/Public/Documents/"

file.copy(distill:::distill_resource("a11y.theme"), public_dir)
[1] TRUE
theme_file <- list.files(public_dir, "a11y.theme", full.names = TRUE)
theme_file
[1] "C:/Users/Public/Documents/a11y.theme"

processing file: test.Rmd
|.................. | 25%
inline R code fragments

|................................... | 50%
label: setup (with options)
List of 1
$ include: logi FALSE

|.................................................... | 75%
ordinary text without R code

|......................................................................| 100%
label: unnamed-chunk-1

output file: test.knit.md

"C:/Users/JOBNMA~1/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS test.utf8.md --to html5 --from markdown+autolink_bare_uris+tex_math_single_backslash --output test.html --lua-filter "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\RMARKD~1\RMARKD~1\lua\PAGEBR~1.LUA" --lua-filter "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\RMARKD~1\RMARKD~1\lua\LATEX-~1.LUA" --email-obfuscation none --self-contained --standalone --variable toc-float=1 --highlight-style "C:/Users/Public/Documents/a11y.theme" --template "C:\Users\JOBNMA~1\DOCUME~1\R\WIN-LI~1\4.0\distill\RMARKD~1\TEMPLA~1\DISTIL~1\RESOUR~1\DEFAUL~1.HTM" "--metadata=link-citations:true" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c533adc2html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c69434960html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c22de6ba5html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c3bdeaf4html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c5547651html" --include-before-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c55676b61html" --include-before-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c3a9e282html" --include-before-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c19341130html" --include-after-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c3b24aahtml" --include-after-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c318d1e8fhtml" --include-after-body "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c4ba7b88html" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\rmarkdown-str152c45e14c47.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\JOBNMA~1\AppData\Local\Temp\RtmpcjxMlP\file152c76196b57html"

Output created: test.html
Warning message:
In (function (category = "LC_ALL", locale = "") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored

I am not so clear with the second part of this instruction.
4. Click the knit button. Does it work ? Paste the command line you have in the Rmarkdown pane below "output_file: test.knit.md"

cderv · December 8, 2020, 10:06pm

Thanks a lot ! That is exactly what I was looking for!

It seems this work for you by moving the theme file. So I believe this is an issue with WINDOWS and path with space. Can you confirm if you have a space in your username ?

C:\Users\<user with space>\Documents ?

cderv · December 9, 2020, 11:16am

I manage to reproduce. This is a bug with rmarkdown and Pandoc

github.com/rstudio/rmarkdown

--highlight-style argument does not accept a shortpath name on WINDOWS

opened 11:10AM - 09 Dec 20 UTC

closed 05:36PM - 09 Dec 20 UTC

cderv

bug theme: pandoc

I isolated the bug to be with Windows and shortpath name transformation when the…re is a space in the path: It seems `--highlight-style` does not handle it. ## Reprex dummy proj for the example ``` r dir.create(tmp_dir <- tempfile(tmpdir = ".")) owd <- setwd(tmp_dir) ``` create a dummy md file ``` r xfun::write_utf8(c( "# A header" ), "test.md") ``` Get the distill theme file for example ``` r packageVersion("distill") #> [1] '1.1' theme_file <- distill:::distill_resource("arrow.theme") ``` create a copy in a directory with space ``` r dir.create(theme_dir <- "dir with space") file.copy(theme_file, theme_dir) #> [1] TRUE theme_file_copy <- file.path(theme_dir, basename(theme_file)) ``` helper function ``` r convert <- function(theme) { rmarkdown::pandoc_convert("test.md", to = 'html', output = "test.html", options = c("--highlight-style", theme), verbose = TRUE) } ``` With a path without space no issue ``` r convert(theme_file) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --highlight-style "C:/Users/chris/Documents/R/win-library/4.0/distill/rmarkdown/templates/distill_article/resources/arrow.theme" convert(rmarkdown::pandoc_path_arg(theme_file)) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --highlight-style "C:\Users\chris\Documents\R\win-library\4.0\distill\rmarkdown\templates\distill_article\resources\arrow.theme" ``` With a space in name, it is working well ``` r convert(theme_file_copy) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --highlight-style "dir with space/arrow.theme" ``` unless path is modified by `rmarkdown::pandoc_path_arg()` ``` r convert(rmarkdown::pandoc_path_arg(theme_file_copy)) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --highlight-style "DIRWIT~1\ARROW~1.THE" Unknown highlight-style DIRWIT~1\ARROW~1.THE #> Error: pandoc document conversion failed with error 6 ``` which use `utils::shortPathName` - this is cause the issue ``` r convert(utils::shortPathName(theme_file_copy)) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --highlight-style "DIRWIT~1\ARROW~1.THE" Unknown highlight-style DIRWIT~1\ARROW~1.THE #> Error: pandoc document conversion failed with error 6 ``` Clean ``` r setwd(owd) unlink(tmp_dir, recursive = TRUE) ``` <sup>Created on 2020-12-09 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0.9001)</sup> If a fix is to be made in our tool, this would be in **rmarkdown** not **distill**. I'll report upstream because it seems it is not causing any issue with other argument ``` r # dummy proj for the example dir.create(tmp_dir <- tempfile(tmpdir = ".")) owd <- setwd(tmp_dir) # create a dummy md file xfun::write_utf8(c( "---", "title: test", "---", "# A header" ), "test.md") # create a copy in a directory with space dir.create(sub_dir <- "dir with space") template_file <- file.path(sub_dir, "template.html") xfun::write_utf8(c( "$body$" ), template_file) # helper function convert <- function(template) { rmarkdown::pandoc_convert("test.md", to = 'html', output = "test.html", options = c("--template", template), verbose = TRUE) } # No issues convert(template_file) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --template "dir with space/template.html" convert(rmarkdown::pandoc_path_arg(template_file)) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --template "DIRWIT~1\TEMPLA~1.HTM" convert(utils::shortPathName(template_file)) #> "C:/Users/chris/scoop/apps/rstudio-daily/current/bin/pandoc/pandoc" +RTS -K512m -RTS test.md --to html4 --output test.html --template "DIRWIT~1\TEMPLA~1.HTM" # Clean setwd(owd) unlink(tmp_dir, recursive = TRUE) ``` Let's precise that it seems Pandoc on Windows no how to handle space in path, so maybe utils::shortPathName is nor more required. _Originally posted by @cderv in https://github.com/rstudio/distill/issues/214#issuecomment-741691386_

cderv · December 9, 2020, 6:01pm

@Job_Nmadu I pushed a fix in a PR if you want to try

You can install with

remotes::install_github("rstudio/distill#236")

Job_Nmadu · December 10, 2020, 10:36pm

Thanks very much. The fix has corrected the error code 6 in my device

system · December 17, 2020, 10:36pm

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