Installation instructions

Dependencies

PEER depends on a small number of freely downloadable pieces of software:

• CMake 2.8 or later
• R 2.10 or later (optional: needed for building the R package)
• Python 2.5 or later (optional: needed for building the Python package)
• scipy
• numpy
• SWIG 2.0 or later

Building PEER

PEER is built using the CMake build system. To build and install PEER from source, first pull it from our git source code repository:

git clone [email protected]:PMBio/peer.git

Then create a target directory for the build:

cd peer mkdir build

Then go to the build directory and call CMake

cd build

cmake ./..

Finally, compile and install PEER

make

make install

Installing the PEER R package from a pre-built package

We have prepared prebuilt PEER R packages for some common platforms:

• 64-bit Intel, Mac OS X
• 64-bit Intel, Linux

To install the PEER R package using one of the above binary packages, simply download the package for the correct platform, for instance peer_osx_64_1.0.tgz, then run R CMD INSTALL peer_osx_64_1.0.tgz.

Building the R package

To build the R package, you need to pass an additional argument to CMake: -DBUILD_R_PACKAGE=1. The full sequence of build commands needed is then as follows:

mkdir build

cd build

cmake ./..

cmake -DBUILD_R_PACKAGE=1 ./..

make

make install

NOTE! You need SWIG 2.0 or later to build the R package. Building will fail with earlier SWIG versions. At the time of writing SWIG 1.x is still the one made available by default on many Linux distributions, so be sure to check the version.

Building peer on OS X

By default, peer is not built as an universal binary on OS X. This can be easily changed by adding the following configuration parameter to CMake: -DBUILD_UNIVERSAL=1. This will cause peer to be built as an Intel 32/64 bit binary. For more control over the included architectures, edit the file CMakeLists.txt in the root directory of the project.

Troubleshooting and further details

• Installing peer binaries. If make is called with the install flag, the standard behaviour is to install a peer binary and the peer C++ library to the system-wide targets. Use cmake ./.. -DCMAKE_INSTALL_PREFIX=~/my_software/peer or equivalent to specify your own build target.
• Python module. The python module is not affected by CMAKE_INSTALL_PREFIX. Instead, cmake tries to build the python module and installs it using the python version which is in the path when using the command python. You can specify your own python binary by editing CMakeLists.txt. The python interface requires a recent numpy version.
• R module. TODO: Matias