I've been using QGIS 2.6 (Brighton) happily for awhile but suddenly it became extremely slow during certain operations, after being reasonably fast in past use. I'm merging NAIP JP2 files to virtual raster, reprojecting the raster to another vrt, then clipping that raster and using gdal_retile to cut it into tiles. All files are on an external USB hard drive.
It takes more than 24 hours for the Mac (2.9ghz Core i5, 8gb ram, Yosemite 10.10.1) to cut a single tile. Meanwhile, duplicating the exact same steps, a quad core i5 Windows machine outputs a tile every 29 minutes. I certainly didn't expect the Mac to be faster - the Windows machine is speedier, but it is slower by a factor of 10 or more.
What is very strange is that I used to be able to cut a single tile using a vector shape as a mask layer in about an hour. Now, that also takes over a day. I've tried deleting and re-installing QGIS and the KyngChaos frameworks but the problem persists.
Any suggestions about what may be causing this?