R bookdown, fontawesome5, render fails but file knits just fine in RStudio - r

Question

Experiencing an odd issue... using MacTeX 2018, current versions of all packages, R and RStudio ditto... I can knit a file containing fontawesome5 icons just fine in RStudio, however, render() is failing and I need to use render in a makefile to automate a build process... render() appears to set in motion a call to latexmk that appears to call tlmgr on fonts that already exist which then halts with a file not found error... any suggestions would be most welcome, hair successfully pulled out over this... thanks in advance!
Below is a minimal file needed to replicate (debug.Rmd in what follows):
---
output:
bookdown::pdf_document2:
toc: no
latex_engine: lualatex
header-includes:
- \usepackage{fontawesome5}
---
- \faIcon{phone}
If you remove \faIcon{phone} it renders fine and of course also builds fine in RStudio.
Here is the error message (session info follows)
Rscript -e 'rmarkdown::render("debug.Rmd",bookdown::pdf_document2(toc = FALSE))'
processing file: debug.Rmd
|.................................................................| 100%
ordinary text without R code
output file: debug.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS debug.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output debug.tex --template /Users/jracine/Library/R/rmarkdown/rmd/latex/default-1.17.0.2.tex --number-sections --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --variable 'geometry:margin=1in' --variable 'compact-title:yes' --variable tables=yes --standalone
tlmgr search --file --global '/fa5free0solid[.](tfm|afm|mf|otf)'
Trying to automatically install missing LaTeX packages...
tlmgr install fontawesome5
tlmgr: package repository http://ctan.mirror.colo-serv.net/systems/texlive/tlnet (verified)
tlmgr install: package already present: fontawesome5
tlmgr path add
tlmgr search --file --global '/fa5free0solid[.](tfm|afm|mf|otf)'
Output created: debug.pdf
Error in tools::file_path_as_absolute(output_file) :
file 'debug.pdf' does not exist
Calls: <Anonymous> -> <Anonymous>
Execution halted
Session Info:
Session info ------------------------------------------------------------------
setting value
version R version 3.5.0 (2018-04-23)
system x86_64, darwin17.5.0
ui X11
language (EN)
collate en_CA.UTF-8
tz America/Toronto
date 2018-06-24
Packages ----------------------------------------------------------------------
package * version date source
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base64enc 0.1-3 2015-07-28 CRAN (R 3.5.0)
bookdown 0.7.13 2018-06-18 Github (rstudio/bookdown#dda5f5a)
digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
evaluate 0.10.1 2017-06-24 CRAN (R 3.5.0)
glue 1.2.0 2017-10-29 CRAN (R 3.5.0)
graphics * 3.5.0 2018-04-23 local
grDevices * 3.5.0 2018-04-23 local
highr 0.7 2018-06-09 CRAN (R 3.5.0)
htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
knitr 1.20.6 2018-06-22 Github (yihui/knitr#2b3e617)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
markdown 0.8 2017-04-20 CRAN (R 3.5.0)
methods * 3.5.0 2018-04-23 local
mime 0.5 2016-07-07 CRAN (R 3.5.0)
Rcpp 0.12.17 2018-05-18 CRAN (R 3.5.0)
rmarkdown 1.10.2 2018-06-22 Github (rstudio/rmarkdown#1f5b299)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
stats * 3.5.0 2018-04-23 local
stringi 1.2.3 2018-06-12 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tinytex 0.5 2018-04-16 CRAN (R 3.5.0)
tools 3.5.0 2018-04-23 local
utils * 3.5.0 2018-04-23 local
xfun 0.2.5 2018-06-22 Github (yihui/xfun#b75336c)
yaml 2.1.19 2018-05-01 CRAN (R 3.5.0)
> rmarkdown::pandoc_version()
[1] ‘2.2.1’
> system('pdflatex --version')
pdfTeX 3.14159265-2.6-1.40.19 (TeX Live 2018)
kpathsea version 6.3.0
Copyright 2018 Han The Thanh (pdfTeX) et al.
There is NO warranty. Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.34; using libpng 1.6.34
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 4.00

Answer 1

Your Makefile is wrong. When you call
Rscript -e 'rmarkdown::render("debug.Rmd",bookdown::pdf_document2(toc = FALSE))'
you essentially overrode the settings in your YAML metadata (such as latex_engine) with bookdown::pdf_document2(toc = FALSE), which has the default latex_engine = 'pdflatex'. That is why your intermediate .tex output was compiled with pdflatex instead of lualatex.
Either call
Rscript -e 'rmarkdown::render("debug.Rmd")'
if bookdown::pdf_document2 is the only output format you need, or call
Rscript -e 'rmarkdown::render("debug.Rmd", "bookdown::pdf_document2")'
if you have multiple output formats set in YAML.
For the second argument of rmarkdown::render() (e.g., the output format), you should rarely need the form of an output format function that returns an output format (e.g., bookdown::pdf_document2(...)). In most cases, I believe the default (NULL, meaning the first format you set in YAML), or a character string (the name of the format you set in YAML) should be what you want.