bookdown::pdf_book output does not generate bold, italics, and font specified

I am setting bookdown::pdf_book as the output using bookdown. Unfortunately the pdf generated does not show bold/italic text. On top of that, when I specify font type in preamble.tex to "charter" or "bookman" nothing will change.

The .tex file generated along pdf contains all the latex commands to bold/italiczed text and if I compile my pdf straight from this file, I will get everything correct.

What is causing this? How should I start looking for the cause

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