MiKTeX released a major new version this week, with some breaking
changes that may be important for Windows users and sysadmins.
The MiKTeX versioning has changed to a date-based scheme. The previous
version was called 2.9, the distribution is now called miktex-20.6.
The default installation path has changed from "C:/Program
Files/MiKTeX 2.9/" to "C:/Program Files/MiKTeX/". Hence this may
require updating scripts that set the PATH to pdflatex and others. I
have updated the r-base build script, so people that use this to build
R locally need to make sure MikTeX is available at the new path.
Finally, the 20.6 release contains a bad bug that causes pdftex to not
work at all, including failing to build R manuals:
https://github.com/MiKTeX/miktex/issues/568 . It seems to have been
fixed and a new pdftex is rolled out via the miktex package manager,
so make sure to update the miktex packages after installing
miktex-20.6 (or wait for the 20.7 release).