I tried to Knit HTML the following Rmd file:
---
title: \"Untitled\"
author: \"Florian Privé\"
date: \"12 septembre 2016\"
output: html_document
I experienced this error today on windows 10, and the outputs you included are as good as identical to those of mine.
Neither J_F's workaround or adding "c:\Rtools\bin" to paths through advanced system settings solved it.
What solved it for me was to uninstall Rtools and reinstall it, checking the option to change the paths during installation. I put the paths: "c:\Rtools\bin", "C:\Rtools\mingw_32\bin", "C:\Program Files\R\R-3.3.1\bin\i386" and "C:\Program Files\R\R-3.3.1\bin\x64" in there.
I wonder why adding "c:\Rtools\bin" to paths through advanced system settings didnt change the output of Sys.getenv()['PATH']