I haven't tried on another machine, but if it works on yours, it means that mine has a problem. I fully reinstalled R and remove all libraries, reinstalled DESeq2, still the same... I suspect something more vicious, maybe related to GCC compiler or C++ libraries. I'll have a look at it next week, here everything is closing with Irma coming. I'll let you know when I find a solution, if I find one (hope so :).

Sorry, I didn't have the opportunity to work on it. Everything shut down here because of Irma.

I worked on a machine with Ubuntu 14.4. I tried to reinstall all packages and R, but nothing changed. I have the feeling that it's related to GCC as it says when I install DESeq2 that openMP is not working while I have gcc-4.8 and gcc-4.9 (default) installed on my computer, both enabling the use of openMP. I tried to find a way to tell R which gcc to use, but it's really not clear how it works and I couldn't find a way to do it properly. I have a virtualbox with Windows 10 so I installed R on it and I'm now able to run lfcShrink normally. It's great in the sense that I'm not stuck and I can analyze the data I have, but it's frustrating not to be able to understand why it's not working with Ubuntu. Do you have any idea?

I'd recommend using vst() for variance stabilization and then making PCA plots or heatmaps. Not sure why you are experiencing more than a minute with lfcShrink:

> system.time({ vsd <- vst(dds, blind=FALSE) })
   user  system elapsed
  2.942   0.116   3.108

> system.time({
+ res <- results(dds, contrast=c("condition","US.RbKO","US.Wt"))
+ res <- lfcShrink(dds, contrast=c("condition","US.RbKO","US.Wt"), res=res)
+ })
   user  system elapsed
 51.153   1.309  53.800

I'm using DESeq2 v1.17 which is similar to the current release v1.16.