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).