1. Installation of the binary files

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" ,
                 download_only =  FALSE,
                 infomap_version = c("2.1.0", 
                                     "2.6.0",
                                     "2.7.1",
                                     "2.8.0"))

##

## 1. Download bin.zip

##

## The folder has been successfully downloaded to /tmp/Rtmpj6VsSZ.

##

## 2. Unzip folder

##

## The folder has been successfully unzipped in /tmp/Rtmpj6VsSZ.

##

## 3. Check permissions

##

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.1.0/infomap_omp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.1.0/infomap_noomp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.6.0/infomap_omp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.6.0/infomap_noomp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.7.1/infomap_omp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.7.1/infomap_noomp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.8.0/infomap_omp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.8.0/infomap_noomp_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/LOUVAIN/convert_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/LOUVAIN/louvain_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/OSLOM/oslom_dir_lin as program: denied.

## Permission to execute /tmp/Rtmpj6VsSZ/bin/OSLOM/oslom_undir_lin as program: denied.

##

## Try to change permissions automatically

##

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.1.0/infomap_omp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.1.0/infomap_noomp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.6.0/infomap_omp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.6.0/infomap_noomp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.7.1/infomap_omp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.7.1/infomap_noomp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.8.0/infomap_omp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/INFOMAP/2.8.0/infomap_noomp_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/LOUVAIN/convert_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/LOUVAIN/louvain_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/OSLOM/oslom_dir_lin can now be executed as progam

## Automatic change of permission succeed, /tmp/Rtmpj6VsSZ/bin/OSLOM/oslom_undir_lin can now be executed as progam

##

## 4. Test Infomap

##

## Congratulation, you successfully install the 2.1.0 OpenMP version of Infomap!

## Congratulation, you successfully install the 2.6.0 OpenMP version of Infomap!

## Congratulation, you successfully install the 2.7.1 OpenMP version of Infomap!

## Congratulation, you successfully install the 2.8.0 OpenMP version of Infomap!

##

## 5. Test Louvain

##

## Congratulation, you successfully install the version 0.3 of Louvain!

##

## 6. Test OSLOM

##

## Congratulation, you successfully install the version 2.5 of OSLOM!

The function has three 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.

Note that in this case, and only in this case, download_only can be set to TRUE (only the first step will be executed), but you must ensure that the files have the necessary permissions to be executed as programs otherwise.

The third parameter infomap_version indicating the Infomap version(s) to install. Only the Infomap version 2.1.0, 2.6.0, 2.7.1 and 2.8.0 are available for now.

The installation of the binary files is divided into six steps:

Download bin.zip
Unzip bin.zip in the binpath
Check the permissions, try to change them automatically or propose an iterative process to change them manually
Test that Infomap is running properly
Test that Louvain is running properly
Test that OSLOM is running properly

The function is designed to help you change the permissions during the third step. Subsequently, the binary files of Infomap, Louvain, and OSLOM are tested, and a file check.txt is added to each folder bin/INFOMAP/X.X.X, bin/LOUVAIN and bin/OSLOM to inform the package that netclu_infomap, netclu_louvain and netclu_oslom can be used without any issues.

However, it may happen (particularly on macOS) that the function fails to automatically or manually assist you in changing the permissions. In this case, set the argument download_only to TRUE to download bin.zip into a folder myfolder of your choice (different from tempdir and pkgfolder) so that you can manually change the permissions yourself. Note that you will be on your own; the package will not be able to test the binary files before running netclu_infomap, netclu_louvain or netclu_oslom (i.e., no check.txt will be added to the folders…). To bypass the automatic check while using these functions, use the argument check_install = FALSE, but without any guarantee of success.

install_binaries(binpath = "myfolder" ,
                 download_only =  TRUE,
                 infomap_version = c("2.1.0", 
                                     "2.6.0",
                                     "2.7.1",
                                     "2.8.0"))

comat <- matrix(sample(1000, 50), 5, 10)
rownames(comat) <- paste0("Site", 1:5)
colnames(comat) <- paste0("Species", 1:10)

net <- similarity(comat, metric = "Simpson")
com <- netclu_infomap(net,
                      binpath = "myfolder",
                      check_install = TRUE)

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).

Maxime Lenormand, Boris Leroy and Pierre Denelle

2024-12-16

Run install_binaries()

Known issues