INSTALL.md

In rdrr1990/kerasformula: A High-Level R Interface for Neural Nets

Installing kerasformula

This document provides install instructions to handle recent version changes in both the relevant R and Python libraries.

Choose either Python3 (recommended) or Python2.7 or Python2.7 in a Virtual Environment (most complicated). The version requirements are very strict on both R and the Python side. Though particular combinations of older libraries still work, in general, upgrading everything is recommended. (Conda environments likely still need to update the packages mentioned below, especially tensorflow and keras.)

Python3 Instructions

These instructions were confirmed using Python 3.7.3 (on Mac OSX Sierra 10.12.6). Enter the following shell command:

brew install python3

The following instructions are lightly adapted from here; if the above command doesn't work, see details there for background requirements.

pip3 install tensorflow
pip3 install keras

Now open R.

 install.packages("keras")
devtools::install_github("rdrr1990/kerasformula")

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

You can confirm the install worked as follows.

library(kerasformula)
out <- kms(mpg~., mtcars, verbose=0)

Troubleshooting Python3 Installation

If the above kms command throws an error, check the path for python3. In R:

system("which python3")

Then use that path with the reticulate::use_python command shown above.

If that's not the issue, upgrade Python to be at least 3.7.3.

The version requirements on both the R and the Python side are very strict. Without current versions at least certain data objects in R will be mishandled by Python, throwing an error, even before the model is estimated in Tensorflow. These instructions have been tested on both R 3.5.0 and R 3.6.0. Here is the session info for the latter:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin16.7.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /Users/mohanty/Dropbox/R-3.6.0/lib/libRblas.dylib
LAPACK: /Users/mohanty/Dropbox/R-3.6.0/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.12    kerasformula_1.7.0 Matrix_1.2-17      dplyr_0.8.0.1     
[5] keras_2.2.4.1     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        whisker_0.3-2     magrittr_1.5      tidyselect_0.2.5 
 [5] munsell_0.5.0     colorspace_1.4-1  lattice_0.20-38   R6_2.4.0         
 [9] rlang_0.3.4       plyr_1.8.4        grid_3.6.0        gtable_0.3.0     
[13] tfruns_1.4        lazyeval_0.2.2    assertthat_0.2.1  tibble_2.1.1     
[17] crayon_1.3.4      tensorflow_1.13.1 purrr_0.3.2       ggplot2_3.1.1    
[21] base64enc_0.1-3   zeallot_0.1.0     glue_1.3.1        compiler_3.6.0   
[25] pillar_1.3.1      generics_0.0.2    scales_1.0.0      jsonlite_1.6     
[29] pkgconfig_2.0.2  

Python2.7

In terminal, check to see if your version of pip is new enough to install packages.

pip install utils np_utils

If that command throws an error about internet protocol security ( details on Stack ), upgrade pip as follows:

curl https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py

Next, install the following libraries

pip install utils np_utils
pip install --upgrade setuptools
pip install --upgrade tensorflow
pip install --upgrade keras

Python2.7 in a Virtual Environment

Here are instructions for Python 2.7.10 in a virtual environment. (These instrucitons will accomplish what keras::install_keras aims to by default. However, due to some of the issues discussed below, these are recommended instead of that configuration function.) These is the most complicated route, in part because the Python 2 that ships with many Macs contains a no longer functioning version of pip. Upgrading Python with brew is recommended.

brew upgrade python

Enter the followings shell commands to create a hidden folder where the R library(keras) and library(kerasformula) will look for the Python copy of keras. Do not use the R function keras::install_keras(), which creates a virtual environment with an outdated version of pip that cannot complete the installation.

virtualenv .virtualenvs/r-tensorflow        
source .virtualenvs/r-tensorflow/bin/activate

Next, you likely need to upgrade pip since older versions of pip that come bundled with Python2 are deemed insecure, preventing installation ( details on Stack ).

curl https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py

Next install the following packages...

pip install --upgrade setuptools utils np_utils
pip install tensorflow
pip install keras

Check the path to Python, which you'll need in a moment.

which python

Now, open R.

install.packages("keras")
devtools::install_github("rdrr1990/kerasformula")

Let R know about the version of Python you want:

reticulate::use_python("/usr/bin/python")

You can confirm the install worked as follows.

library(kerasformula)
out <- kms(mpg~., mtcars, verbose=0)

 install.packages("keras")
devtools::install_github("rdrr1990/kerasformula")

You can confirm the install worked as follows.

library(kerasformula)
out <- kms(mpg~., mtcars, verbose=0)

Troubleshooting Python 2.7 virtual environment install

If the above kms command throws an error, check whether keras installed correctly.

keras::is_keras_available()

If that returns TRUE but the kerasformula example above does not work, it is likely because either Python is outdated or some of the dependencies are.

The version requirements on both the R and the Python side are very strict. Without current versions at least certain data objects in R will be mishandled by Python, throwing an error, even before the model is estimated in Tensorflow. These instructions have been tested on both R 3.5.0 and R 3.6.0. Here is the session info for the latter:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin16.7.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /Users/mohanty/Dropbox/R-3.6.0/lib/libRblas.dylib
LAPACK: /Users/mohanty/Dropbox/R-3.6.0/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] kerasformula_1.7.0 Matrix_1.2-17      dplyr_0.8.0.1      keras_2.2.4.1     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        whisker_0.3-2     magrittr_1.5      tidyselect_0.2.5 
 [5] munsell_0.5.0     colorspace_1.4-1  lattice_0.20-38   R6_2.4.0         
 [9] rlang_0.3.4       plyr_1.8.4        grid_3.6.0        gtable_0.3.0     
[13] tfruns_1.4        lazyeval_0.2.2    assertthat_0.2.1  tibble_2.1.1     
[17] crayon_1.3.4      tensorflow_1.13.1 purrr_0.3.2       ggplot2_3.1.1    
[21] base64enc_0.1-3   zeallot_0.1.0     glue_1.3.1        compiler_3.6.0   
[25] pillar_1.3.1      generics_0.0.2    scales_1.0.0      reticulate_1.12  
[29] jsonlite_1.6      pkgconfig_2.0.2  

rdrr1990/kerasformula documentation built on June 6, 2019, 8:02 a.m.