Ok, it turns out the problem was made up of some user errors and some bugs (?). Now that I have cleared up a bit, let me give an updated version of the problem:
Any LaTeX-related files only exist if I put bookdown::pdf_book:… before bookdown::gitbook:… in _output.yml, and once I do that, the .tex file re-renders, the .log refreshes, does not render PDF, and the .html file does not refresh.
If on the contrary, I put bookdown::gitbook:… before bookdown::pdf_book:… in _output.yml, then only the .html rerenders, and nothing happens to the LaTeX files.
.log
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex 2019.11.5) 14 FEB 2020 18:52
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**paper.tex
(./paper.tex
LaTeX2e <2019-10-01> patch level 1
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/size10.clo
File: size10.clo 2019/12/20 v1.4l Standard LaTeX file (size option)
)
...
LaTeX Info: Redefining \[ on input line 2859.
LaTeX Info: Redefining \] on input line 2860.
) (/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/ifxetex.sty
Package: ifxetex 2019/10/25 v0.7 ifxetex legacy package. Use iftex instead.
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty
Package: iftex 2019/11/07 v1.0c TeX engine tests
)) (/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/ifluatex.sty
Package: ifluatex 2019/10/25 v1.5 ifluatex legacy package. Use iftex instead.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty
Package: fontenc 2020/02/11 v2.0o Standard LaTeX package
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/t1enc.def
File: t1enc.def 2020/02/11 v2.0o Standard LaTeX file
LaTeX Font Info: Redeclaring font encoding T1 on input line 48.
)
LaTeX Font Info: Trying to load font information for T1+lmr on input line 11
2.
(/usr/local/texlive/2019/texmf-dist/tex/latex/lm/t1lmr.fd
File: t1lmr.fd 2009/10/30 v1.6 Font defs for Latin Modern
)
! Undefined control sequence.
l.115 \xdef\@fontenc@load@list{\@fontenc@load@list
Here is how much of TeX's memory you used:
2070 strings out of 492167
23632 string characters out of 6125389
81348 words of memory out of 5000000
6479 multiletter control sequences out of 15000+600000
6630 words of font info for 15 fonts, out of 8000000 for 9000
1141 hyphenation exceptions out of 8191
30i,0n,31p,262b,78s stack positions out of 5000i,500n,10000p,200000b,80000s
! ==> Fatal error occurred, no output PDF file produced!
Currently, I am using _render.R and Makefile from the bookdown repo as is, and other files are:
Summary
paper.Rmd:
---
title: "A Paper"
author: "loikein"
date: "Last update: `r (Sys.Date())`"
knit: "bookdown::render_book"
documentclass: article
bibliography: ["paper.bib"]
biblio-style: apalike
link-citations: yes
site: bookdown::bookdown_site
description: "A class paper."
bookdown:
book_filename: research-paper
---
# Test 44
Cite test: @kogan_technological_2017
# Reference {-}
_output.yml:
bookdown::gitbook:
split_by: none
config:
search: yes
download: ["pdf"]
sharing:
github: yes
facebook: no
bookdown::pdf_book:
keep_tex: yes
latex_engine: pdflatex
citation_package: biblatex
template: null
paper.bib:
@article{kogan_technological_2017,
title = {Technological Innovation, Resource Allocation, and Growth},
volume = {132},
issn = {0033-5533},
url = {https://academic.oup.com/qje/article/132/2/665/3076284},
doi = {10.1093/qje/qjw040},
abstract = {Abstract. We propose a new measure of the economic importance of each innovation. Our measure uses newly collected data on patents issued to U.S. firms in the},
language = {en},
number = {2},
urldate = {2020-02-12},
journal = {The Quarterly Journal of Economics},
author = {Kogan, Leonid and Papanikolaou, Dimitris and Seru, Amit and Stoffman, Noah},
month = may,
year = {2017},
pages = {665--712},
file = {Full Text PDF:/Users/loikein/Zotero/storage/QCX3WK8U/Kogan 等。 - 2017 - Technological Innovation, Resource Allocation, and.pdf:application/pdf;Snapshot:/Users/loikein/Zotero/storage/2BMMGFGK/3076284.html:text/html}
}