NmslibR

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nmslibR (Non Metric Space Library in R)

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The nmslibR package is a wrapper of the Non-Metric Space Library (NMSLIB) python package. More details on the functionality of the nmslibR package can be found in the blog-post and in the package Documentation.

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Reference:

https://github.com/nmslib/nmslib

https://github.com/nmslib/nmslib/blob/master/manual/latex/manual.pdf

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System Requirements

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• Python (>= 2.7)

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All modules should be installed in the default python configuration (the configuration that the R-session displays as default), otherwise errors will occur during the nmslibR package installation (reticulate::py_discover_config() might be useful here).

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The installation notes for Linux, Macintosh, Windows are based on Python 3.

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Debian/Ubuntu

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Installation of the system requirements,

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sudo apt-get install python3-pip

sudo pip3 install --upgrade setuptools

sudo pip3 install -U numpy

sudo pip3 install --upgrade scipy

sudo apt-get install libboost-all-dev libgsl0-dev libeigen3-dev

sudo apt-get install cmake

pip3 install --upgrade pybind11

sudo pip3 install nmslib

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Fedora

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Installation of the system requirements,

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dnf install python3-pip

sudo pip3 install --upgrade setuptools

sudo pip3 install -U numpy

sudo pip3 install --upgrade scipy

yum install python3-devel

yum install boost-devel

yum install gsl-devel

yum install eigen3-devel

pip3 install --upgrade pybind11

sudo pip3 install nmslib

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Macintosh OSX

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Upgrade python to version 3 using,

brew upgrade python

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Install the requirements,

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sudo pip3 install --upgrade pip setuptools wheel

sudo pip3 install -U numpy

sudo pip3 install --upgrade scipy

brew install boost

brew install eigen

brew install gsl

brew install cmake

brew link --overwrite cmake

pip3 install --upgrade pybind11

sudo pip3 install nmslib

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After a successful installation of the requirements the user should open an R session and give the following reticulate command to change to the relevant (brew-python) directory (otherwise the nmslibR package won't work properly),

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reticulate::use_python('/usr/local/bin/python3')

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and then,

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reticulate::py_discover_config()

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to validate that a user is in the python version where nmslibR is installed.

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Windows OS (the instructions were tested with the version 1.0.0 of the R package, thus use with caution)

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First download of get-pip.py for windows

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Update the Environment variables ( Control Panel >> System and Security >> System >> Advanced system settings >> Environment variables >> System variables >> Path >> Edit ) by adding ( for instance in case of python 2.7 ),

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C:\Python36;C:\Python36\Scripts

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Install the Build Tools for Visual Studio

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Open the Command prompt (console) and install / upgrade the system requirements,

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pip3 install --upgrade pip setuptools wheel

pip3 install -U numpy

pip3 install --upgrade scipy

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Installation of cmake

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First download cmake for Windows, win64-x64 Installer. Once the file is downloaded run the .exe file and during installation make sure to add CMake to the system PATH for all users.

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Then install the nmslib library,

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pip3 install --upgrade pybind11

pip3 install nmslib

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Installation of the nmslibR package

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To install the package from CRAN use,

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install.packages('nmslibR')

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and to download the latest version from Github use the install_github function of the remotes package, <br><br>

remotes::install_github(repo = 'mlampros/nmslibR')

<br> Use the following link to report bugs/issues, <br><br>

https://github.com/mlampros/nmslibR/issues

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Citation:

If you use the code of this repository in your paper or research please cite both nmslibR and the original articles / software https://CRAN.R-project.org/package=nmslibR/citation.html:

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@Manual{,
  title = {{nmslibR}: Non Metric Space (Approximate) Library in R},
  author = {Lampros Mouselimis},
  year = {2021},
  note = {R package version 1.0.7},
  url = {https://CRAN.R-project.org/package=nmslibR},
}

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