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I have installed the TeXLive distribution. From emacs running in cygwin mintty, the LaTeX binaries are visible from my PATH environment variable. I installed AucTeX using the built in Emacs package manager with the package from Elpa.

$ which latex
/cygdrive/c/texlive/2016/bin/win32/latex
$ which pdflatex
/cygdrive/c/texlive/2016/bin/win32/pdflatex
$ latex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/W32TeX) (preloaded format=latex)
 restricted \write18 enabled.
**

However, when I try C-c C-c from a LaTeX file, I get the following message:

TeX-command: ERROR: AUCTeX cannot find a working TeX distribution.
Make sure you have one and that TeX binaries are in PATH environment variable

Is there some AucTeX variable I could customize to point it in the right direction to the TeX distribution? I am pretty confident my PATH is set correctly.

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Turns out, I needed to delete the TeXLive distribution which I had installed manually using the TeXLive Windows installer and reinstall TeXLive with the Cygwin setup.exe. This will place everything in the correct places for emacs to be able to see them.

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