Hi,
I cloned your repo and build the book.
I got this :
Seems ok to me.
This is the packages versions I have
sessioninfo::package_info("bookdown")
#> package * version date lib source
#> base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.5.0)
#> bookdown 0.11 2019-05-28 [1] CRAN (R 3.5.3)
#> digest 0.6.19 2019-05-20 [1] CRAN (R 3.5.3)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.5.3)
#> glue 1.3.1 2019-03-12 [1] CRAN (R 3.5.3)
#> highr 0.8 2019-03-20 [1] CRAN (R 3.5.3)
#> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1)
#> jsonlite 1.6 2018-12-07 [1] CRAN (R 3.5.1)
#> knitr 1.23 2019-05-18 [1] CRAN (R 3.5.3)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1)
#> markdown 1.0 2019-06-07 [1] CRAN (R 3.5.3)
#> mime 0.7 2019-06-11 [1] CRAN (R 3.5.3)
#> Rcpp 1.0.1 2019-03-17 [1] CRAN (R 3.5.3)
#> rmarkdown 1.13 2019-05-22 [1] CRAN (R 3.5.3)
#> stringi 1.4.3 2019-03-12 [1] CRAN (R 3.5.3)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.3)
#> tinytex 0.13 2019-05-14 [1] CRAN (R 3.5.3)
#> xfun 0.7 2019-05-14 [1] CRAN (R 3.5.3)
#> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.1)
#>
#> [1] C:/Users/chris/Documents/R/win-library/3.5
#> [2] C:/Program Files/R/R-3.5.3/library
You can check you have last knitr and rmarkdown also.
It seems I use pandoc 2.6 included with RStudio. Did not try pandoc 2.7.3...