Identical rmd files create different latex files when run on two computers - r-markdown

Question

When my colleague and I run the same Rmd file on our respective computers they produce different .tex files. This is a problem, because the tex-file my computer produces doesn't compile. Apparently there is some invisible local setting that is different between our computers but what could it be? I updated all the Rpackages I use but to no avail.
The Rmd file starts with
output:
bookdown::pdf_document2:
keep_tex: yes
toc: false
And both of us compile it by simply hitting the knit-button in Rstudio.
Noticeable differences in the tex-files are:
extra linebreaks in different places
a line that is commented out in the rmd-file (<!-- blabla -->) appears in my tex-file, not in his, but some other out-commented lines appear in neither (as they should)
at the end of lines in tables there is a \strut inserted in my tex-file but not in his
Section heads read \hypertaget{blabla} in his file but not mine
For none of these difference I can find any place in the Rmd-file where any choice w.r.t to this is made - apparently some local settings file I am not aware of is used in the process??
Please let me know if you need more information.
EDIT: we found a partial answer and full solution, but I am still interested in what the underlying mechanism is. It turned out that I was using an older version of Rstudio. (It took me long to find that out because the check for updates tool in Rstudio kept telling me that I was using the newest version, but that is a separate issue.) Using the same version of Rstudio we get the same result.

Answer 1

The translation from Rmd to tex has multiple steps:
All the code chunks are extracted and executed via knitr, resulting in a md file.
The md file is translated to tex via pandoc.
For most people pandoc comes bundled with RStudio. So when you updated that, you got a more recent pandoc version. You can test for the used pandoc version with rmarkdown::pandoc_version().