1. Installation of the binary files
Maxime Lenormand, Boris Leroy and Pierre Denelle
Some functions (listed below) or at least part of them require binary files to run.
The function install_binaries
downloads and unzips the
bin folder needed to run these
functions. It also checks if the files have the permissions to be
executed as programs. It finally tests if the binary files are running
The function has two parameters.
binpath indicating the
path to the folder that will host the
bin folder containing
the binary files. By default, the binary files are installed in R’s
temporary directory (
binpath = "tempdir"). In this case the
bin folder will be automatically removed at the end of the
R session. Alternatively, the binary files can be installed in the
bioregion’s package folder (
binpath = "pkgfolder").
Any other folder can be chosen but in any case PLEASE MAKE SURE
to update the binpath argument in netclu_infomap,
The second parameter
infomap_version indicating the
Infomap version(s) to install. Only the Infomap version 2.1.0 and 2.6.0
are available for now.
The installation of the binary files is divided into six steps:
3. Check the permissions, try to change them automatically or propose an iterative process to change them manually
- The OpenMP versions of Infomap require
libomp-devon Ubuntu (
sudo apt-get install libomp-dev) and
libompon macOS (install Homebrew and run
brew install libomp).