Argthtjtr

I just noticed that in clicking footnote links in the pdf makes the document jumps to the top instead to the footnote. Investigating why I identified the latex packages setspace and footmisc apparently causing the error.

Unfortunately I need both packages badly. The former to switch between onehalfspacing and singlespacing and the latter to get nice hanging footnotes.

Does anybody know a workaround?

MWE

(Note: Try un-commenting the outcommented lines. )

---

title: "Untitled"

date: "October 23, 2018"

output: pdf_document

linkcolor: blue

header-includes:

# - usepackage{setspace}

- usepackage{fancyhdr}

- usepackage{pdflscape}

- usepackage{dcolumn}

- usepackage{rotating, graphicx}

- usepackage{floatpag}

- usepackage{caption}

- usepackage[export]{adjustbox}

- usepackage{icomma}

- usepackage{tabularx}

- usepackage{lipsum}

- usepackage{csquotes}

# - usepackage[hang,flushmargin]{footmisc}

- usepackage{amsmath}

- usepackage{mathtools,extarrows}

- usepackage{changepage}

---



newpage

Lorem ipsum^[Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.] dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. 

Notes:

• MiKTeX 2.9.6850


• using outdated rmarkdown_1.8 intentionally (see this issue)

> sessionInfo()

R version 3.5.1 (2018-07-02)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1



Matrix products: default



locale:

[1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252   

[3] LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C                       

[5] LC_TIME=English_United States.1252 



attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     



loaded via a namespace (and not attached):

 [1] compiler_3.5.1  backports_1.1.2 rprojroot_1.3-2 htmltools_0.3.6 tools_3.5.1    

 [6] yaml_2.2.0      Rcpp_0.12.19    rmarkdown_1.8   knitr_1.20      digest_0.6.18  

[11] evaluate_0.12  

I ran into a similar problem (footnotes aren't links and thus not clickable anymore when using footmisc). Unfortunately I couldn't find any way to directly solve this in the .Rmd document itself. Instead I had to edit the Pandoc LaTeX template that's shipping with rmarkdown.

As @Mico explains in this answer on the TeX/LaTeX stack exchange site, the underlying problem is that the LaTeX package hyperref is called before footmisc while it has to be the other way round to avoid incompatibilities between the two. If you have a look into the default LaTeX template rmarkdown uses, you'll notice that hyperref is called way before the header-includes from the YAML front matter get injected. The only workaround for this I know of is to modify the LaTeX template, i.e. insert the line usepackage[hang,flushmargin]{footmisc} before the line where hyperref is called.

In order to do this follow these steps:

1. 
   

   Locate the original template file Pandoc uses when rmarkdown/knitr calls it.

   
   
   

   On Unix/Linux systems you'll find the original template file probably under the path ~/Library/R/3.5/library/rmarkdown/rmd/latex/ or /usr/lib/R/site-library/rmarkdown/rmd/latex/ (just replace the beginning of the path with what .libPaths() displays in your R console).

   
   
   

   At least in rmarkdown v1.10 the folder above contains 4 different LaTeX template files:

   
   
   
   
   
   • default-1.14.tex
   
   
   • default-1.15.2.tex
   
   
   • default-1.17.0.2.tex
   
   
   • default.tex
   
   
   
   

    
   default-1.17.0.2.tex seems the right choice if a halfway recent version of Pandoc is used (it's bundled with rmarkdown and will be used if no or only an antiquated Pandoc version can be found on your system; run rmarkdown::pandoc_version() to find out what version is actually in use).

   
   
   

   _{First I tried default.tex but it turned out to be pretty outdated and default-1.17.0.2.tex works just fine.}

   
   



2. Put that file's content into a fresh template.tex (or whatever you'd like to name it) file and insert your footmisc customization code before package hyperref is called (line 57).



3. 
   

   Put the path to the new template file into the YAML front matter under the key output.pdf_document.template:

   
   
   

   ---
   
   output:
   
     pdf_document:
   
       template: 'path/to/template.tex'
   
   ---
   
   

   
   

BTW: I didn't experience any problem regarding package setspace. But I in my case it's loaded before footmisc anyway due to setting linestretch in the YAML front matter (see the template for details about what triggers setspace to get loaded etc.).