Windows

Install Rbiips

  • Requirements: R (>= 3.0) with Rcpp and BH package

  • Download Rbiips

  • Install Rbiips package from R console:

install.packages('path/to/Rbiips_X.X.X.zip')

Install Matbiips

  • Requirements:

  • Download Matbiips for either Matlab or Octave

  • Extract Matbiips archive

  • Before using Matbiips, you need to add the directory to the Matlab/Octave search path by typing in Matlab/Octave console:

addpath('path/to/matbiips')

Mac OS X

Install Rbiips

  • Requirements: R (>= 3.0) with Rcpp package

  • Download Rbiips

  • Install Rbiips package from R console:

install.packages('path/to/Rbiips_X.X.X.tgz')

Install Matbiips

  • Requirements:

    • Matlab (>=R2011a)
    • Octave (>=3.6.4)

  • Download Matbiips for either Matlab or Octave

  • Extract Matbiips archive

  • Before using Matbiips, you need to add the directory to the search Matlab/Octave path by typing in Matlab/Octave console:

addpath('path/to/matbiips')

Linux

Install Rbiips from binary

  • Requirements: Debian/Ubuntu, R (>= 3.0) with Rcpp package

  • Download Rbiips

  • Install Rbiips package from R console:

install.packages('path/to/Rbiips_x.x.x_R_x86_64-pc-linux-gnu.tar.gz')

Install Rbiips from source

  • Requirements: biips, R (>= 3.0) with Rcpp package

  • Download Rbiips

  • Install Rbiips package from linux terminal:

If biips was installed as root in the standard paths:

R CMD INSTALL Rbiips_X.X.X.tar.gz

Else, if biips was installed in local paths:

env BIIPS_INCLUDE=path/to/biips/include/biips/ BIIPS_LIB=/path/to/biips/lib/ARCH R CMD INSTALL Rbiips_X.X.X.tar.gz

Install Matbiips

  • Requirements: Debian/Ubuntu, No previous biips installation is needed for Matbiips

    • Matlab (>=R2011a)
    • Octave (>=3.6.4)

  • Download Matbiips for either Matlab or Octave

  • Extract Matbiips archive

tar -xvzf matbiips_X.X.X.tar.gz
  • Start Matlab using the following command:
LD_PRELOAD=/usr/libARCH/libstdc++.so.6 matlab

where libARCH is a directory depending on your Linux distribution and architecture, e.g.:

  • on 64bit Debian/Ubuntu: libARCH=lib/x86_64-linux-gnu
  • on 64bit Fedora/openSUSE/Mandriva/CentOS: libARCH=lib64

Note: alternatively to using the LD_PRELOAD=... command, you can rename the path/to/MATLAB/R20XXx/sys/os/glnxa64/libstdc++.so.6 to e.g. libstdc++.so.6.bak. This usually requires administrator permissions.

  • Before using Matbiips, you need to add the directory to the search Matlab path by typing in Matlab console:
addpath('path/to/matbiips')

Install biips from binary

  • Requirements: Debian/Ubuntu, libboost-dev (>=1.49)

  • Download biips package

  • Root installation from terminal:

sudo dpkg -i biips_X.X.X_Linux.deb

…or double-click on the deb file in your file browser. This will install it as root in /usr/ directory.

  • Local installation from terminal:
dpkg-deb -x biips_X.X.X.deb  path/to/biips
  • Other Linux distributions:
    • OpenSuse: sudo rpm -i biips_x.x.x_Linux.rpm
    • Mandriva: sudo urpmi biips_x.x.x_Linux.rpm

Install biips from sources

  • Requirements:
    • git
    • cmake
    • gcc (>= 4.7)
    • boost (>=1.49.0)
    • R (>= 3.0) + Rcpp package
    • Matlab or Octave

  • Download biips sources

  • Extract source archive
tar -xvzf path matbiips_X.X.X.tar.gz path/to/sources
  • Configure
mkdir path/to/build
cd path/to/build
cmake -DCMAKE_INSTALL_PREFIX=/path/to/install -DCMAKE_BUILD_TYPE=Release path/to/sources
  • Compile
make -jN (where N = number of parallel jobs)
  • Install
make install
  • Test
make test

Note: If you lose control of your terminal during the tests, type

stty echo