Preview and Skim are not opening Latex compiled pdf file
My machine has MacOS 10.12.5 and MacTeX-2016 and it works fine, both with Preview and Skim. I used the command-line in Terminal. Here are what latexmk --version and pdflatex --version report on my system, respectively.

Latexmk, John Collins, 22 April 2016. Version 4.45

pdfTeX 3.14159265-2.6-1.40.17 (TeX Live 2016)
kpathsea version 6.2.2
Copyright 2016 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.21; using libpng 1.6.21
Compiled with zlib 1.2.8; using zlib 1.2.8
Compiled with xpdf version 3.04


I know this does not really qualify as an answer but I don't have enough reputation to comment on your question!