Weird behavior in References

[Bruno T. Tomio]

There is a weird behavior in the references section appearing to me. I am just creating a new file, naming it "index" and knitting it.

After the section title, the number 10 appears in the first line (weird behavior). Please see it here:

Thanks a lot for your package! It's awesome.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.0.3    bookdown_0.21     htmltools_0.5.1.1 tools_4.0.3       yaml_2.2.1       
 [6] remotes_2.2.0     rmarkdown_2.7     knitr_1.31        xfun_0.21         digest_0.6.27    
[11] thesisdown_0.1.0  rlang_0.4.10      evaluate_0.14 

[Dr. Chester Ismay]

Very strange indeed. I'm not able to reproduce with

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

loaded via a namespace (and not attached):
 [1] compiler_4.0.3    bookdown_0.21     htmltools_0.5.1.1
 [4] tools_4.0.3       yaml_2.2.1        remotes_2.2.0    
 [7] rmarkdown_2.7     knitr_1.31        xfun_0.21        
[10] digest_0.6.27     packrat_0.5.0     thesisdown_0.1.0 
[13] rlang_0.4.10      evaluate_0.14    

I'm going to try on rstudio.cloud right now as well.

[Dr. Chester Ismay]

Getting the same 10 on rstudio.cloud with

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8    
 [5] LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C             
 [9] LC_ADDRESS=C           LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.0.3    here_1.0.1        bookdown_0.21     rprojroot_2.0.2   htmltools_0.5.1.1
 [6] tools_4.0.3       yaml_2.2.1        remotes_2.2.0     rmarkdown_2.7     knitr_1.31       
[11] xfun_0.21         digest_0.6.27     thesisdown_0.1.0  rlang_0.4.10      evaluate_0.14   

Investigating further now.

[Bruno T. Tomio]

Glad you could replicate it. Thanks! Just to add more information, I've tried other bib files. The weird behavior persisted.

[Dr. Chester Ismay]

Based on my cloning and building https://github.com/rstudio/bookdown-demo with template: template.tex and bookdown::pdf_book and also getting the 10 there on Linux, it looks like this is something in the template.tex file. Still digging...

[Dr. Chester Ismay]

It looks like I'll need to make one more change to the csl-refs code (Lines 119 - 130 of template.tex) to get this to work. The {rticles} package suggests replacing this with

$if(csl-refs)$
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
 {% don't indent paragraphs
  \setlength{\parindent}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
  % set entry spacing
  \ifnum #2 > 0
  \setlength{\parskip}{#2\baselineskip}
  \fi
 }%
 {}
\usepackage{calc} % for calculating minipage widths
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$

This is working for me on both Linux and Mac. Can you try it out and let me know if it works for you and then I'll update {thesisdown} to hopefully have this resolved?

[Bruno T. Tomio]

That works perfectly! Here is the image:

Thank you very much, @ismayc!

[Dr. Chester Ismay]

You're welcome! Thanks for bringing this up.

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