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Question: Issue with pandoc-citeproc when rendering the f1000 article Rmd file from BiocWorkFlowTools
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gravatar for Leonardo Collado Torres
5 months ago by
United States
Leonardo Collado Torres560 wrote:

Hi,

I am running into a pandoc-citeproc error when using BiocWorkflowTools' template Rmd file for an F1000 article. I updated both pandoc and pandoc-citeproc using brew, thinking that it could help with the error but it didn't. https://github.com/jgm/pandoc-citeproc/issues/265 could be related. Obviously, it doesn't seem to be a problem in the Bioc machines, though I couldn't figure out which pandoc and pandoc-citeproc versions you are using based on the BiocWorkflowTools vignette.

I don't see the error if I remove the "bibliography" line in the YAML. So I can keep writing my workflow for now and worry about the citations later.

Best,

Leo

 

> rmarkdown::draft("MyArticle.Rmd", template="f1000_article", package="BiocWorkflowTools")
> rmarkdown::render('MyArticle/MyArticle.Rmd')

processing file: MyArticle.Rmd
  |.........                                                        |  14%
  |...................                                              |  29%
label: firstCodeChunk
  |............................                                     |  43%
  |.....................................                            |  57%
  |..............................................                   |  71%
  |........................................................         |  86%
  |.................................................................| 100%
  ordinary text without R code

output file: MyArticle.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS MyArticle.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output MyArticle.tex --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocWorkflowTools/rmarkdown/templates/f1000_article/resources/template.tex --highlight-style tango --latex-engine pdflatex --variable documentclass=extarticle --variable fontsize=9pt --variable papersize=a4 --variable citationoptions=numbers --variable tables=yes --standalone --bibliography sample.bib --filter /usr/local/bin/pandoc-citeproc 
pandoc-citeproc: when expecting a product (:*:), encountered Object instead
pandoc: Error running filter /usr/local/bin/pandoc-citeproc
Filter returned error status 1
Error: pandoc document conversion failed with error 83
> system('pandoc -v')
pandoc 1.19.2.1
Compiled with pandoc-types 1.17.0.5, texmath 0.9, skylighting 0.1.1.4
Default user data directory: /Users/lcollado/.pandoc
Copyright (C) 2006-2016 John MacFarlane
Web:  http://pandoc.org
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose.
> system('pandoc-citeproc --version')
pandoc-citeproc 0.5
> options(width = 120)
> devtools::session_info()
Session info ----------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.0 (2017-04-21)
 system   x86_64, darwin15.6.0        
 ui       AQUA                        
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2017-06-15                  

Packages --------------------------------------------------------------------------------------------------------------
 package           * version date       source        
 backports           1.1.0   2017-05-22 CRAN (R 3.4.0)
 base              * 3.4.0   2017-04-21 local         
 BiocWorkflowTools   1.2.0   2017-04-25 Bioconductor  
 bookdown            0.4     2017-05-20 CRAN (R 3.4.0)
 compiler            3.4.0   2017-04-21 local         
 datasets          * 3.4.0   2017-04-21 local         
 devtools            1.13.2  2017-06-02 CRAN (R 3.4.0)
 digest              0.6.12  2017-01-27 CRAN (R 3.4.0)
 evaluate            0.10    2016-10-11 CRAN (R 3.4.0)
 graphics          * 3.4.0   2017-04-21 local         
 grDevices         * 3.4.0   2017-04-21 local         
 highr               0.6     2016-05-09 CRAN (R 3.4.0)
 htmltools           0.3.6   2017-04-28 CRAN (R 3.4.0)
 httr                1.2.1   2016-07-03 CRAN (R 3.4.0)
 knitr               1.16    2017-05-18 CRAN (R 3.4.0)
 magrittr            1.5     2014-11-22 CRAN (R 3.4.0)
 memoise             1.1.0   2017-04-21 CRAN (R 3.4.0)
 methods           * 3.4.0   2017-04-21 local         
 R6                  2.2.1   2017-05-10 CRAN (R 3.4.0)
 Rcpp                0.12.11 2017-05-22 CRAN (R 3.4.0)
 rmarkdown           1.5     2017-04-26 CRAN (R 3.4.0)
 rprojroot           1.2     2017-01-16 CRAN (R 3.4.0)
 stats             * 3.4.0   2017-04-21 local         
 stringi             1.1.5   2017-04-07 CRAN (R 3.4.0)
 stringr             1.2.0   2017-02-18 CRAN (R 3.4.0)
 tools               3.4.0   2017-04-21 local         
 utils             * 3.4.0   2017-04-21 local         
 withr               1.0.2   2016-06-20 CRAN (R 3.4.0)
 yaml                2.1.14  2016-11-12 CRAN (R 3.4.0)
> 
ADD COMMENTlink modified 5 months ago by Andrzej Oleś670 • written 5 months ago by Leonardo Collado Torres560
3
gravatar for Andrzej Oleś
5 months ago by
Andrzej Oleś670
EMBL Heidelberg, Germany
Andrzej Oleś670 wrote:

Hi Leo,

there seems to be a problem with version compatibility between pandoc and pandoc-citeproc as described in the issue you linked. Apparently your pandoc-citeproc version is outdated, as on my linux machine I have a much more recent version of pandoc-citeproc 0.10.1 vs. yours 0.5 even though I use only pandoc 1.17.2. Did you try the solutions mentioned in https://github.com/jgm/pandoc-citeproc/issues/265?

Cheers,

Andrzej

ADD COMMENTlink modified 5 months ago • written 5 months ago by Andrzej Oleś670

Thanks Andrzej! I removed pandoc-citeproc and pandoc with brew and installed them via the binary file at https://github.com/jgm/pandoc/releases/latest. That lead to another error:

> rmarkdown::render('MyArticle/MyArticle.Rmd')

processing file: MyArticle.Rmd
  |.........                                                        |  14%
  |...................                                              |  29%
  |............................                                     |  43%
  |.....................................                            |  57%
  |..............................................                   |  71%
  |........................................................         |  86%
  |.................................................................| 100%
  ordinary text without R code

output file: MyArticle.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS MyArticle.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output MyArticle.tex --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocWorkflowTools/rmarkdown/templates/f1000_article/resources/template.tex --highlight-style tango --latex-engine pdflatex --variable documentclass=extarticle --variable fontsize=9pt --variable papersize=a4 --variable citationoptions=numbers --variable tables=yes --standalone --bibliography sample.bib --filter /usr/local/bin/pandoc-citeproc 
/usr/local/bin/pandoc +RTS -K512m -RTS MyArticle.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output MyArticle.tex --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocWorkflowTools/rmarkdown/templates/f1000_article/resources/template.tex --highlight-style tango --latex-engine pdflatex --variable documentclass=extarticle --variable fontsize=9pt --variable papersize=a4 --variable citationoptions=numbers --variable tables=yes --standalone --bibliography sample.bib --filter /usr/local/bin/pandoc-citeproc 
/bin/sh: pdflatex: command not found
Error: Failed to compile MyArticle.tex.

Which is weird. Anyhow, using RStudio's knit button it does work (it finds the correct pdflatex path). Actually, I don't get that error when using the terminal either. I only get it when using the R GUI.

/usr/local/bin/pandoc +RTS -K512m -RTS MyArticle.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output MyArticle.tex --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocWorkflowTools/rmarkdown/templates/f1000_article/resources/template.tex --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --variable documentclass=extarticle --variable fontsize=9pt --variable papersize=a4 --variable citationoptions=numbers --variable tables=yes --standalone --bibliography sample.bib --filter /usr/local/bin/pandoc-citeproc 
output file: MyArticle.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS MyArticle.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output MyArticle.tex --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocWorkflowTools/rmarkdown/templates/f1000_article/resources/template.tex --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --variable documentclass=extarticle --variable fontsize=9pt --variable papersize=a4 --variable citationoptions=numbers --variable tables=yes --standalone --bibliography sample.bib --filter /usr/local/bin/pandoc-citeproc 
Latexmk: This is Latexmk, John Collins, 19 Jan. 2017, version: 4.52c.

Output created: MyArticle.pdf

I also re-installed MacTex and added the bin files to my path, but that didn't seem to help with the pdflatex issue. In any case, I have a working solution now ^^.

## TeX -- ~/.bashrc file
export PATH="/Library/TeX/texbin:$PATH"

Best,

Leo

ADD REPLYlink written 5 months ago by Leonardo Collado Torres560
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