With Pandoc 2.2.3-2 citations are not generated

[Karut]

Hi,

I just updated Pandoc from the version that comes with RStudio to Pandoc-2.2.3-2, because of this significant citations bug.

Now citations are not generated anymore, it says

'pandoc-citeproc: reference leucht_SixtyYearsPlaceboControlled_2017 not found'

I can insert citations without a problem, but they are not outputted. I tried generating new keys in Zotero, to no avail.

Can someone confirm this? I am running Papaja version v0.1.0.9709 and Rstudio Version 1.1.456.

Thank you!

[crsh]

Hi, thanks for the heads-up. Can you confirm that this is indeed related to papaja? Do citations work as expected in a regular pdf_document?

[Karut]

Yes, they do work here with the same .bib-file with a .rmarkdown to pdf file:

---
title: "Untitled"
author: "XY"
date: "6 August 2018"
output: pdf_document

citation_package: biblatex
bibliography  : "zotero_export.bib"
---

But not on a fresh rmarkdown file with the apa template. In addition to the citations not found I get this:

! Use of \@pr@videpackage doesn't match its definition.
\new@ifnextchar ...served@d = #1\def \reserved@a {
                                                  #2}\def \reserved@b {#3}\f...
l.54 \newcommand
                \LastLTentrywidth{1em} 

Edit: Output to Word works, but again no citations.

[crsh]

Okay, thanks. Are you using the development version (devtools::install_github("crsh/papaja@devel"))?

[crsh]

Oh, and one more question: Does this come up when you try to have biblatex take care of the citations? In your example above, I'd think that you would have to specify citation_package as part of the pdf_document list in the YAML front matter (see here).

[Karut]

Okay, thanks. Are you using the development version (devtools::install_github("crsh/papaja@devel"))?

I am getting this generic error. Do I have to uninstall the old version?

Downloading GitHub repo crsh/papaja@devel
from URL https://api.github.com/repos/crsh/papaja/zipball/devel
Installation failed: error in running command

In your example above, I'd think that you would have to specify citation_package as part of the >pdf_document

Isn't it though with _citationpackage: biblatex see post 3? I mean it works there so it must be specified correctly?

[Karut]

I am getting this generic error. Do I have to uninstall the old version?

Relevant issue, problem solved.

I am now on the developer version, but still no citations. Plus this: ! LaTeX Error: Missing \begin{document}.

[crsh]

Isn't it though with citation_package: biblatex see post 3? I mean it works there so it must be specified correctly?

If you follow the link in my previous post, you'll see that you need to specify the citation package as follows:

output:
  papaja::apa6_pdf:
    citation_package: biblatex

Even with the incorrect specification you are getting citations but they are created by pandoc-citeproc rather than biblatex.

I am now on the developer version, but still no citations. Plus this: ! LaTeX Error: Missing \begin{document}.

Could you provide a minimal working example (a R Markdown and BibTeX file) that I can use to diagnose the problem?

[Karut]

If you follow the link in my previous post, you'll see that you need to specify the citation package as follows

I thought you were talking about a simple R markdown to pdf file i.e. _output: pdfdocument where I could successful insert citations (as opposed to an apa6_pdf template). Sorry, if I misunderstood you.

Could you provide a minimal working example (a R Markdown and BibTeX file) that I can use to diagnose the problem?

Simple executing the untouched papaja example template gives me this error:

This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/TeX Live for SUSE Linux) (preloaded format=pdflatex 2018.6.22) 7 AUG 2018 14:48 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **test2.tex (./test2.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 51 language(s) loaded. (/usr/share/texmf/tex/latex/apa6/apa6.cls Document Class: apa6 2014/11/20 v2.14 APA formatting (6th edition) Class apa6 Info: Using default mode (jou) on input line 147. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size10.clo File: size10.clo 2014/09/29 v1.4h Standard LaTeX file (size option) ) \c@part=\count79 \c@section=\count80 \c@subsection=\count81 \c@subsubsection=\count82 \c@paragraph=\count83 \c@subparagraph=\count84 \c@figure=\count85 \c@table=\count86 \abovecaptionskip=\skip41 \belowcaptionskip=\skip42 \bibindent=\dimen102 ) (/usr/share/texmf/tex/latex/etoolbox/etoolbox.sty Package: etoolbox 2015/08/02 v2.2a e-TeX tools for LaTeX (JAW) \etb@tempcnta=\count87 ) Class apa6 Info: No bibliography package was specified; defaulting to (but not loading) Biblatex on input line 213. (/usr/share/texmf/tex/latex/lm/lmodern.sty Package: lmodern 2009/10/30 v1.6 Latin Modern Fonts LaTeX Font Info: Overwriting symbol fontoperators' in version normal' (Font) OT1/cmr/m/n --> OT1/lmr/m/n on input line 22. 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LaTeX Font Info: Overwriting math alphabet\mathtt' in version bold' (Font) OT1/cmtt/m/n --> OT1/lmtt/m/n on input line 38. ) (/usr/share/texmf/tex/latex/base/fontenc.sty Package: fontenc 2005/09/27 v1.99g Standard LaTeX package (/usr/share/texmf/tex/latex/base/t1enc.def File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file LaTeX Font Info: Redeclaring font encoding T1 on input line 48. )) (/usr/share/texmf/tex/latex/txfonts/txfonts.sty Package: txfonts 2008/01/22 v3.2.1 LaTeX Font Info: Redeclaring symbol fontoperators' on input line 21. LaTeX Font Info: Overwriting symbol font operators' in versionnormal' (Font) OT1/lmr/m/n --> OT1/txr/m/n on input line 21. LaTeX Font Info: Overwriting symbol font operators' in versionbold' (Font) OT1/lmr/bx/n --> OT1/txr/m/n on input line 21. 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LaTeX Font Info: Overwriting math alphabet \mathtt' in versionbold' (Font) OT1/txtt/m/n --> OT1/txtt/b/n on input line 51. LaTeX Font Info: Redeclaring symbol font letters' on input line 58. LaTeX Font Info: Overwriting symbol fontletters' in version normal' (Font) OML/lmm/m/it --> OML/txmi/m/it on input line 58. LaTeX Font Info: Overwriting symbol fontletters' in version bold' (Font) OML/lmm/b/it --> OML/txmi/m/it on input line 58. LaTeX Font Info: Overwriting symbol fontletters' in version bold' (Font) OML/txmi/m/it --> OML/txmi/bx/it on input line 59. \symlettersA=\mathgroup5 LaTeX Font Info: Overwriting symbol fontlettersA' in version bold' (Font) U/txmia/m/it --> U/txmia/bx/it on input line 67. LaTeX Font Info: Redeclaring symbol fontsymbols' on input line 77. LaTeX Font Info: Overwriting symbol font symbols' in versionnormal' (Font) OMS/lmsy/m/n --> OMS/txsy/m/n on input line 77. 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LaTeX Info: Redefining \not on input line 1043. ) apa6.cls: Using txfonts (/usr/share/texmf/tex/latex/geometry/geometry.sty Package: geometry 2010/09/12 v5.6 Page Geometry (/usr/share/texmf/tex/latex/graphics/keyval.sty Package: keyval 2014/10/28 v1.15 key=value parser (DPC) \KV@toks@=\toks14 ) (/usr/share/texmf/tex/generic/oberdiek/ifpdf.sty Package: ifpdf 2016/05/14 v3.1 Provides the ifpdf switch ) (/usr/share/texmf/tex/generic/oberdiek/ifvtex.sty Package: ifvtex 2016/05/16 v1.6 Detect VTeX and its facilities (HO) Package ifvtex Info: VTeX not detected. ) (/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional ) \Gm@cnth=\count88 \Gm@cntv=\count89 \c@Gm@tempcnt=\count90 \Gm@bindingoffset=\dimen103 \Gm@wd@mp=\dimen104 \Gm@odd@mp=\dimen105 \Gm@even@mp=\dimen106 \Gm@layoutwidth=\dimen107 \Gm@layoutheight=\dimen108 \Gm@layouthoffset=\dimen109 \Gm@layoutvoffset=\dimen110 \Gm@dimlist=\toks15 ) (/usr/share/texmf/tex/latex/graphics/graphicx.sty Package: graphicx 2014/10/28 v1.0g Enhanced LaTeX Graphics (DPC,SPQR) (/usr/share/texmf/tex/latex/graphics/graphics.sty Package: graphics 2016/05/09 v1.0r Standard LaTeX Graphics (DPC,SPQR) (/usr/share/texmf/tex/latex/graphics/trig.sty Package: trig 2016/01/03 v1.10 sin cos tan (DPC) ) (/usr/share/texmf/tex/latex/graphics-cfg/graphics.cfg File: graphics.cfg 2016/01/02 v1.10 sample graphics configuration ) Package graphics Info: Driver file: pdftex.def on input line 96. 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LaTeX Info: Redefining \bm on input line 208. ) \c@appendix=\count98 (/usr/share/texmf/tex/latex/tools/ftnright.sty Package: ftnright 2014/10/28 v1.1f footnote layout package (FMi) \rcol@footinsskip=\skip56 \ftn@amount=\dimen133 ) \auone@box=\box28 \autwo@box=\box29 \autot@box=\box30 \auone@boxwidth=\skip57 \autwo@boxwidth=\skip58 \autot@boxwidth=\skip59 ) (/usr/share/texmf/tex/latex/amsfonts/amssymb.sty Package: amssymb 2013/01/14 v3.01 AMS font symbols (/usr/share/texmf/tex/latex/amsfonts/amsfonts.sty Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support \@emptytoks=\toks16 LaTeX Font Info: Redeclaring symbol fontAMSa' on input line 59. LaTeX Font Info: Overwriting symbol font AMSa' in versionnormal' (Font) U/txsya/m/n --> U/msa/m/n on input line 59. LaTeX Font Info: Overwriting symbol font AMSa' in versionbold' (Font) U/txsya/bx/n --> U/msa/m/n on input line 59. LaTeX Font Info: Redeclaring symbol font AMSb' on input line 60. 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LaTeX Font Info: Redeclaring math symbol \subseteqq on input line 152. LaTeX Font Info: Redeclaring math symbol \supseteqq on input line 153. LaTeX Font Info: Redeclaring math symbol \bumpeq on input line 154. LaTeX Font Info: Redeclaring math symbol \Bumpeq on input line 155. LaTeX Font Info: Redeclaring math symbol \lll on input line 156. LaTeX Font Info: Redeclaring math symbol \ggg on input line 158. LaTeX Font Info: Redeclaring math symbol \circledS on input line 160. LaTeX Font Info: Redeclaring math symbol \pitchfork on input line 161. LaTeX Font Info: Redeclaring math symbol \dotplus on input line 162. LaTeX Font Info: Redeclaring math symbol \backsim on input line 163. LaTeX Font Info: Redeclaring math symbol \backsimeq on input line 164. LaTeX Font Info: Redeclaring math symbol \complement on input line 165. LaTeX Font Info: Redeclaring math symbol \intercal on input line 166. LaTeX Font Info: Redeclaring math symbol \circledcirc on input line 167. LaTeX Font Info: Redeclaring math symbol \circledast on input line 168. LaTeX Font Info: Redeclaring math symbol \circleddash on input line 169. LaTeX Font Info: Redeclaring math symbol \lvertneqq on input line 171. LaTeX Font Info: Redeclaring math symbol \gvertneqq on input line 172. LaTeX Font Info: Redeclaring math symbol \nleq on input line 173. LaTeX Font Info: Redeclaring math symbol \ngeq on input line 174. LaTeX Font Info: Redeclaring math symbol \nless on input line 175. LaTeX Font Info: Redeclaring math symbol \ngtr on input line 176. LaTeX Font Info: Redeclaring math symbol \nprec on input line 177. LaTeX Font Info: Redeclaring math symbol \nsucc on input line 178. LaTeX Font Info: Redeclaring math symbol \lneqq on input line 179. LaTeX Font Info: Redeclaring math symbol \gneqq on input line 180. LaTeX Font Info: Redeclaring math symbol \nleqslant on input line 181. LaTeX Font Info: Redeclaring math symbol \ngeqslant on input line 182. LaTeX Font Info: Redeclaring math symbol \lneq on input line 183. LaTeX Font Info: Redeclaring math symbol \gneq on input line 184. LaTeX Font Info: Redeclaring math symbol \npreceq on input line 185. LaTeX Font Info: Redeclaring math symbol \nsucceq on input line 186. LaTeX Font Info: Redeclaring math symbol \precnsim on input line 187. LaTeX Font Info: Redeclaring math symbol \succnsim on input line 188. LaTeX Font Info: Redeclaring math symbol \lnsim on input line 189. LaTeX Font Info: Redeclaring math symbol \gnsim on input line 190. LaTeX Font Info: Redeclaring math symbol \nleqq on input line 191. LaTeX Font Info: Redeclaring math symbol \ngeqq on input line 192. LaTeX Font Info: Redeclaring math symbol \precneqq on input line 193. LaTeX Font Info: Redeclaring math symbol \succneqq on input line 194. LaTeX Font Info: Redeclaring math symbol \precnapprox on input line 195. LaTeX Font Info: Redeclaring math symbol \succnapprox on input line 196. LaTeX Font Info: Redeclaring math symbol \lnapprox on input line 197. LaTeX Font Info: Redeclaring math symbol \gnapprox on input line 198. LaTeX Font Info: Redeclaring math symbol \nsim on input line 199. LaTeX Font Info: Redeclaring math symbol \ncong on input line 200. LaTeX Font Info: Redeclaring math symbol \diagup on input line 201. LaTeX Font Info: Redeclaring math symbol \diagdown on input line 202. LaTeX Font Info: Redeclaring math symbol \varsubsetneq on input line 203. LaTeX Font Info: Redeclaring math symbol \varsupsetneq on input line 204. LaTeX Font Info: Redeclaring math symbol \nsubseteqq on input line 205. LaTeX Font Info: Redeclaring math symbol \nsupseteqq on input line 206. LaTeX Font Info: Redeclaring math symbol \subsetneqq on input line 207. LaTeX Font Info: Redeclaring math symbol \supsetneqq on input line 208. LaTeX Font Info: Redeclaring math symbol \varsubsetneqq on input line 209. LaTeX Font Info: Redeclaring math symbol \varsupsetneqq on input line 210. LaTeX Font Info: Redeclaring math symbol \subsetneq on input line 211. LaTeX Font Info: Redeclaring math symbol \supsetneq on input line 212. LaTeX Font Info: Redeclaring math symbol \nsubseteq on input line 213. LaTeX Font Info: Redeclaring math symbol \nsupseteq on input line 214. LaTeX Font Info: Redeclaring math symbol \nparallel on input line 215. LaTeX Font Info: Redeclaring math symbol \nmid on input line 216. LaTeX Font Info: Redeclaring math symbol \nshortmid on input line 217. LaTeX Font Info: Redeclaring math symbol \nshortparallel on input line 218. LaTeX Font Info: Redeclaring math symbol \nvdash on input line 219. LaTeX Font Info: Redeclaring math symbol \nVdash on input line 220. LaTeX Font Info: Redeclaring math symbol \nvDash on input line 221. LaTeX Font Info: Redeclaring math symbol \nVDash on input line 222. LaTeX Font Info: Redeclaring math symbol \ntrianglerighteq on input line 223 . LaTeX Font Info: Redeclaring math symbol \ntrianglelefteq on input line 224.

LaTeX Font Info: Redeclaring math symbol \ntriangleleft on input line 225. LaTeX Font Info: Redeclaring math symbol \ntriangleright on input line 226. LaTeX Font Info: Redeclaring math symbol \nleftarrow on input line 227. LaTeX Font Info: Redeclaring math symbol \nrightarrow on input line 228. LaTeX Font Info: Redeclaring math symbol \nLeftarrow on input line 229. LaTeX Font Info: Redeclaring math symbol \nRightarrow on input line 230. LaTeX Font Info: Redeclaring math symbol \nLeftrightarrow on input line 231.

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LaTeX Font Info: Redeclaring math symbol \digamma on input line 259. LaTeX Font Info: Redeclaring math symbol \varkappa on input line 260. LaTeX Font Info: Redeclaring math symbol \Bbbk on input line 261. LaTeX Font Info: Redeclaring math symbol \hslash on input line 262. LaTeX Font Info: Redeclaring math symbol \backepsilon on input line 265. ) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty Package: amsmath 2016/03/10 v2.15b AMS math features \@mathmargin=\skip60 For additional information on amsmath, use the `?' option. (/usr/share/texmf/tex/latex/amsmath/amstext.sty Package: amstext 2000/06/29 v2.01 AMS text (/usr/share/texmf/tex/latex/amsmath/amsgen.sty File: amsgen.sty 1999/11/30 v2.0 generic functions \@emptytoks=\toks17 \ex@=\dimen134 )) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty Package: amsbsy 1999/11/29 v1.2d Bold Symbols LaTeX Info: Redefining \boldsymbol on input line 28. \pmbraise@=\dimen135 ) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty Package: amsopn 2016/03/08 v2.02 operator names ) \inf@bad=\count99 LaTeX Info: Redefining \frac on input line 199. \uproot@=\count100 \leftroot@=\count101 LaTeX Info: Redefining \overline on input line 297. \classnum@=\count102 \DOTSCASE@=\count103 LaTeX Info: Redefining \ldots on input line 394. LaTeX Info: Redefining \dots on input line 397. LaTeX Info: Redefining \cdots on input line 518. \Mathstrutbox@=\box31 \strutbox@=\box32 \big@size=\dimen136 LaTeX Font Info: Redeclaring font encoding OML on input line 634. LaTeX Font Info: Redeclaring font encoding OMS on input line 635. \macc@depth=\count104 \c@MaxMatrixCols=\count105 \dotsspace@=\muskip10 \c@parentequation=\count106 \dspbrk@lvl=\count107 \tag@help=\toks18 \row@=\count108 \column@=\count109 \maxfields@=\count110 \andhelp@=\toks19 \eqnshift@=\dimen137 \alignsep@=\dimen138 \tagshift@=\dimen139 \tagwidth@=\dimen140 \totwidth@=\dimen141 \lineht@=\dimen142 \@envbody=\toks20 \multlinegap=\skip61 \multlinetaggap=\skip62 \mathdisplay@stack=\toks21 LaTeX Info: Redefining [ on input line 2739. LaTeX Info: Redefining ] on input line 2740. ) (/usr/share/texmf/tex/generic/oberdiek/ifluatex.sty Package: ifluatex 2016/05/16 v1.4 Provides the ifluatex switch (HO) Package ifluatex Info: LuaTeX not detected. ) (/usr/share/texmf/tex/latex/base/fixltx2e.sty Package: fixltx2e 2015/06/22 v2.0b fixes to LaTeX (obsolete)

Package fixltx2e Warning: fixltx2e is not required with releases after 2015 (fixltx2e) All fixes are now in the LaTeX kernel. (fixltx2e) See the latexrelease package for details.

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2}\def \reserved@b {#3}\f...

l.54 \newcommand \LastLTentrywidth{1em} Here is how much of TeX's memory you used: 7038 strings out of 494041 98241 string characters out of 6158495 190429 words of memory out of 5000000 10327 multiletter control sequences out of 15000+600000 4403 words of font info for 15 fonts, out of 8000000 for 9000 475 hyphenation exceptions out of 8191 43i,0n,40p,772b,93s stack positions out of 5000i,500n,10000p,200000b,80000s

! ==> Fatal error occurred, no output PDF file produced! `

[crsh]

I thought you were talking about a simple R markdown to pdf file i.e. output: pdf_document where I could successful insert citations (as opposed to an apa6_pdf template). Sorry, if I misunderstood you.

No problem. But to be clear, the specification above is necessary regardless of whether you use apa6_pdf() or pdf_document() (i.e., also in simple R Markdown to PDF files). You are able to successfully insert citations because they are inserted by pandoc-citeproc (not by biblatex). You can see this if you simply omitting citation_package: biblatex; I'm pretty sure it has no effect.

Simple executing the untouched papaja example template gives me this error:

Thanks. Could you maybe also upload the generated TeX file? I currently don't have the most recent pandoc version installed but inspection of the TeX file may be helpful.

[Karut]

Here you go:

test.zip

[crsh]

Okay, that looks like all sorts of things are going wrong. Do you really have to use pandoc 2.2.3-2? As far as I can tell this is not even an official release, yet. If these problem persists in the next release I'll be happy to address it, but at this point I'm not sure whether this is a problem in the development snapshot of pandoc you are using or in papaja. For example, the TeX document contains the following:

\begin{longtable}[]{@{}l@{}}
\toprule
\endhead
\begin{minipage}[t]{0.05\columnwidth}\raggedright
title: The title shorttitle: Title author: - name: First
Author\textsuperscript{1} affiliation: \enquote{1} corresponding: yes
address: Postal address email:
\href{mailto:my@email.com}{\nolinkurl{my@email.com}} - name: ~\&
Ernst-August Doelle\textsuperscript{1,2} affiliation: \enquote{1,2}
affiliation: - id: \enquote{1} institution: Wilhelm-Wundt-University -
id: \enquote{2} institution: Konstanz Business School author\_note:
\textbar{}- Add complete departmental affiliations for each author here.
Each new line herein must be indented, like this line.\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.05\columnwidth}\raggedright
Enter author note here.\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.05\columnwidth}\raggedright
Correspondence concerning this article should be addressed to First
Author, Postal address. E-mail:
\href{mailto:my@email.com}{\nolinkurl{my@email.com}} abstract:
\textbar{} Enter abstract here. Each new line herein must be indented,
like this line. keywords: keywords wordcount: X bibliography:
r-references.bib figsintext: no figurelist: no tablelist: no
footnotelist: no lineno: yes mask: no class: man output:
papaja::apa6\_pdf\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}

For some reason it looks like the YAML front matter printed as a table in the body of the document. I doubt this is intended behavior and I see no obvious way in which papaja could cause this. Indeed, from this issue it sounds like this was a temporary bug in pandoc. Hence, I strongly suggest you use the latest pandoc release or downgrade to pandoc 2.2.1.

[Karut]

You are right, I was using a daily build of pandoc. I reverted to the earliest version of pandoc that includes the fix I needed (pandoc 2.2) and now it works! Only with the devel-version of papaja though, but thats fine with me. Finally, APA citations are working properly for me.

Thank you for looking into this. I also really appreciate that export to Word has improved substantially, thank you!

[crsh]

You are welcome. Thanks for reaching out about this issue. Bug reports are always appreciated.