Upgrade Your msys2 Installation
Without pacman ErrorsEDIT 9/11/2014: A new installer/zip of msys2 was released on 9/10/2014 and at least for now, the following procedure is not really necessary for new installs. Base files are all up to date upon a fresh install. The procedure below describes upgrading an old installation or a new install where the current repo packages are newer than the ones in the installer or installation zipfile.
I recently became obsessed with achieving a clean upgrade and reinstallation of all packages on a fresh install of msys2. I finally figured out a sequence of pkg upgrades that has no pacman execution errors.
I used 64bit msys2 available here: http://sourceforge.net/projects/msys2/