Entering edit mode
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)
>
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.
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 ^^.
Best,
Leo