Materials for BioC-2016 workshop entitled "Introduction to Bayesian Inference using Stan with Applications to Cancer Genomics"
Most of the material for this package is contained within the vignettes.
To install this package, including vignettes:
devtools::install_github('jburos/biostan', build_vignettes=TRUE, dependencies=TRUE)
To list & review the vignettes, after having installed the package:
vignette(package = "biostan")
This package contains most dependencies in the
Requires section of the
DESCRIPTION file. The above-mentioned process should install it without any problems under most circumstances.
However, special consideration should be given to the installation of
clang++ C++ compiler
It is strongly recommended that you install & enable the clang++ C++ compiler on the system in addition to or instead of the more typical g++ compiler. The clang++ compiler will compile Stan models faster and with less memory, so that you can get by with an Amazon AMI that has less RAM.
To install it on Ubuntu, you can do
sudo apt-get install clang++
To configure R packages to use clang++, there needs to be a file whose path is
~/.R/Makevars that contains the following:
CXX=clang++ CXXFLAGS=-g -O3
although on Ubuntu the clang++ executable may actually be called something slightly different (ex:
In this case the
~/.R/Makevars should use the name of the executable (
CXX=clang++-3.4) instead of the above.
install packages from source
Finally, given that v2.10 is expected to be released to CRAN before the workshop (before 6/26), it is recommended for now to install the latest versions of both
rstanarm from github.
The following process should work:
- Install StanHeaders (version 2.10.0) from CRAN because it is hard to install from GitHub (due to its submodules)
- Make sure devtools is installed from CRAN
Install rstan from GitHub via
devtools::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan", build_vignettes = TRUE, dependencies = TRUE)
Install rstanarm from GitHub via
devtools::install_github("stan-dev/rstanarm", args = "--preclean", local = FALSE, build_vignettes = TRUE, dependencies = TRUE)
(Note the additional arg
--precleanprovided to the install of rstanarm).