Installing Radford Neal's pqR on Mac OS 10.8. More information on pqR can be found at: http://radfordneal.wordpress.com/ and https://github.com/radfordneal/pqR

INSTALLpqR.md

Installing pqR on Mac OS X (10.8)

** THIS DOESN'T WORK ANY MORE ** Recent updates to XCode seem to have stopped this from working. I am attempting to get this working again. Updates will be posted here.

Use the right version of gcc

The version of gcc that ships with Mac OS X doesn't have openMP enabled, which means you can't use "helper threads", which make pqR super-fast. So, we first need to install that and get OS X to use it...

Get homebrew so you can install a newer version of gcc, then:

brew tap homebrew/versions
brew install gcc48
brew install gfortran

now make gcc 4.8 the version of gcc that will be used by default:

export CC=/usr/local/bin/gcc-4.8

(maybe put this in your .bash_profile so it's always that version)

Actually install pqR

Then get pqR

git clone [email protected]:radfordneal/pqR.git

run ./configure and hopefully get this output at the end:

R is now configured for x86_64-apple-darwin12.5.0

  Source directory:          .
  Installation directory:    /Library/Frameworks

  C compiler:                /usr/local/bin/gcc-4.8 -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:       gcc -g -O2 -fobjc-exceptions

  Interfaces supported:      X11, aqua, tcltk
  External libraries:        readline, ICU, lzma
  Additional capabilities:   PNG, JPEG, TIFF, NLS
  Options enabled:           helper threads, framework, shared BLAS, R profiling, Java

  Byte compile packages:     yes
  Recommended packages:      yes

The helper threads option is the thing that will improve performance a lot, so make that that is enabled (this should just happen if you use the right gcc.

Now, run make and wait... (took about 10 mins on my 2013 MacBook Air).

Tests and documentation

Having run make check I get:

running tests of Internet and socket functions
  expect some differences
running code in 'internet.R' ...make[3]: *** [internet.Rout] Error 1
make[2]: [test-Internet] Error 2 (ignored)

But I don't think this is problematic (i.e. I was still able to run code...)

Making the documentation:

make info
make pdf

Using pqR

Rather than running make install, I left the folder as it was but then added an alias to my .bash_profile:

alias pqR='/Users/dill/sources/pqR/bin/R --quiet --no-save --no-restore --no-environ --helpers=2'

by default this will run pqR with 2 helper threads (and not save or load any workspace).

Problems?

Doesn't look like you can install Rcpp (from CRAN), so certain packages like lme4 and gamm4 will not install (from CRAN). Need to investigate this further.

I wonder if installing Rcpp from source will work?

... oh I see...its the fact that pqR is based on on R2.15