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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 properly.

Run install_binaries()

The function install_binaries should be run prior to using netclu_infomap, the Cpp version of netclu_louvain and netclu_oslom as follows.

install_binaries(binpath = "tempdir" , infomap_version = c("2.1.0", "2.6.0"))

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, netclu_louvain and netclu_oslom accordingly.

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:

1. Download

2. Unzip in the binpath

3. Check the permissions, try to change them automatically or propose an iterative process to change them manually

4->6. Test that Infomap, Louvain and OSLOM are running properly

Known issues

  • The OpenMP versions of Infomap require libomp-dev on Ubuntu (sudo apt-get install libomp-dev) and libomp on macOS (install Homebrew and run brew install libomp).