RGF (Regularized Greedy Forest)


The RGF package is a wrapper of the Regularized Greedy Forest (RGF) python package, which also includes a Multi-core implementation (FastRGF). More details on the functionality of the RGF package can be found in the blog-post and in the package Documentation.


UPDATE 26-07-2018: A Singularity image file is available in case that someone intends to run RGF on Ubuntu Linux (locally or in a cloud instance) with all package requirements pre-installed. This allows the user to utilize the RGF package without having to spend time on the installation process.


References:

Rie Johnson and Tong Zhang, Learning Nonlinear Functions Using Regularized Greedy Forest

RGF

FastRGF

python-package


System Requirements



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 RGF package installation (reticulate::py_discover_config() might be useful here).


Debian/Ubuntu/Fedora [ installed / tested on Python 2.7 ]


First install / upgrade the dependencies,


sudo pip install --upgrade pip setuptools

sudo pip install -U numpy

sudo pip install --upgrade scipy

sudo pip install -U scikit-learn


Then, download the rgf-python package and install it using the following commands,



git clone https://github.com/RGF-team/rgf.git

cd rgf/python-package

sudo python setup.py install


FastRGF will be installed successfully only if gcc >= 5.0.



Mac OS X [ installed / tested on Python >= 3.4 ]


Upgrade python to version 3 using,


brew upgrade python


Then install the dependencies for RGF and FastRGF


sudo pip3 install --upgrade setuptools

sudo pip3 install -U numpy

sudo pip3 install --upgrade scipy

sudo pip3 install -U scikit-learn


The FastRGF module requires a gcc >= 8.0. To install gcc-8 (or the most recent gcc) with brew follow the next steps,



# before running the following commands make sure that the most recent Apple command line tools for Xcode are installed

brew update

brew upgrade

brew info gcc

brew install gcc

brew cleanup


After the newest gcc version is installed the user should navigate to /usr/local/bin and if a gcc file exists (symbolic link) then the user should delete it. Then the user should run the following command,



sudo ln -s /usr/local/bin/gcc-8 /usr/local/bin/gcc


The user should then verify that the gcc has been updated using,



gcc -v

which gcc


After the new gcc is installed the user should continue with the installation of rgf_python,



git clone https://github.com/RGF-team/rgf.git

cd /rgf/RGF/build

export CXX=/usr/local/bin/g++-8 && export CC=/usr/local/bin/gcc-8

cmake /rgf/RGF /rgf/FastRGF

make

sudo make install

cd /rgf/python-package

sudo python3 setup.py install


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



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


and then,



reticulate::py_discover_config()


to validate that a user is in the python version where RGF or FastRGF are installed. Then,



install.packages(RGF)


library(RGF)


to load the R package. It is possible that the following warning in the R session appears if FastRGF is not installed,



UserWarning: Cannot find FastRGF executable files. FastRGF estimators will be unavailable for usage.
  warnings.warn("Cannot find FastRGF executable files. FastRGF estimators will be unavailable for usage.")
  



Windows OS [ installed / tested on Python >= 3.4 ]


NOTE : CURRENTLY THE PACKAGE ON WINDOWS CAN BE USED ONLY FROM THE COMMAND LINE (cmd)


First download of get-pip.py for windows


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 3 ),



C:\Python36;C:\Python36\Scripts


Install the Build Tools for Visual Studio


Open the Command prompt (console) and install the rgf_python dependencies,



pip3 install --upgrade setuptools

pip3 install -U numpy

pip3 install --upgrade scipy

pip3 install -U scikit-learn


Then download git for windows,



https://git-scm.com/download/win


and run the downloaded .exe file. Then do,



git clone https://github.com/RGF-team/rgf.git


FastRGF requires a gcc version > 5.0 . To find out the gcc version, open a command prompt (console) and type,



gcc --version


Installation / Upgrade of MinGW


Perform the following steps to upgrade the MinGW (so that simple RGF functions work – but not FastRGF)


Normally MinGW is installed in the C:\ directory. So, first delete the folder C:\MinGW (if it already exists), and then remove the environment variable from (Control Panel >> System and Security >> System >> Advanced system settings >> Environment variables >> System variables >> Path >> Edit) which usually is C:\MinGW\bin. Then download the most recent version of MinGW, and especially the mingw-get-setup.exe which is an automated GUI installer assistant. After the new version is installed successfully, update the environment variable by adding C:\MinGW\bin in (Control Panel >> System and Security >> System >> Advanced system settings >> Environment variables >> System variables >> Path >> Edit). Then open a new command prompt (console) and type,



gcc --version


to find out if the new version of MinGW is installed properly.


A word of caution, If Rtools is already installed then make sure that it does not point to an older version of gcc. Just observe the Path field of the environment variables (accessible as explained previously).


Perform the following steps only in case that a FastRGF installation is desired and gcc version is < 5.0


FastRGF works only with MinGW-w64 because only this version provides POSIX threads. It can be downloaded from the project’s official SourceForge page. After a successful download and installation the user should also update the environment variables field in (Control Panel >> System and Security >> System >> Advanced system settings >> Environment variables >> System variables >> Path >> Edit) by adding the following path (assuming the software is installed in C:\Program Files (x86) folder),



C:\Program Files (x86)\mingw-w64\i686-7.2.0-posix-dwarf-rt_v5-rev1\mingw32\bin


Installation of cmake


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.


Before the installation of rgf I might have to remove Rtools environment variables, such as C:\Rtools\bin (accessible as explained previously), otherwise errors might occur.


Installation of RGF, FastRGF and rgf_python [ assuming the installation takes place in the c:/ directory ]


Open a console with administrator privileges (right click on cmd and run as administrator), then



# download the most recent version of rgf-python from the GitHub repository 
#--------------------------------------------------------------------------

git clone http://github.com/RGF-team/rgf.git



# then navigate to 
#-----------------

cd /rgf/RGF/

mkdir bin

cd c:/


# then download the latest "rgf.exe" from https://github.com/RGF-team/rgf/releases and place the "rgf.exe" inside the previously created "bin" folder ( /rgf/RGF/bin )



# installation of RGF
#--------------------

cd /rgf/RGF/build

mingw32-make

cd c:/



# installation of FastRGF
#------------------------

cd /rgf/FastRGF/

mkdir build

cd build


# BEFORE PROCEEDING WITH cmake MAKE SURE THAT THE "Rtools" folder IS NOT IN THE SAME DIRECTORY (IF THAT IS THE CASE THEN REMOVE IT TEMPORARILY, i.e. copy-paste the "Rtools" folder somewhere else)


cmake .. -G "MinGW Makefiles"

mingw32-make

mingw32-make install

cd c:/


# IF APPLICABLE, PASTE THE "Rtools" FOLDER IN THE INITIAL LOCATION / DIRECTORY


# installation of rgf-python
#---------------------------

cd rgf/python-package

python setup.py install


Then open a command prompt (console) and type,



python 


to launch Python and then type



import rgf

exit()


to observe if rgf is installed properly. Then continue with the installation of the RGF package,



install.packages(RGF)


On windows the user can take advantage of the RGF package currently only from within the command prompt (console). First, find the full path of the installation location of R (possible if someone right-clicks in the R short-cut (probably on Desktop) and navigates to properties >> shortcut >> target). In case, for instance, that R is located in C:\Program Files\R\R-3.4.0\bin\x64\R, then, by opening a command prompt (console) and giving,



cd C:\Program Files\R\R-3.4.0\bin\x64\

R

library(RGF)


one can proceed with the usage of the RGF package.


Installation of the RGF package


To install the package from CRAN use,



install.packages('RGF')


and to download the latest version from GitHub use the install_github function of the devtools package,


devtools::install_github(repo = 'RGF-team/rgf', subdir = 'R-package')


Use the following link to report bugs/issues,

https://github.com/RGF-team/rgf/issues