This weekend, I decided it was time: I was going to update my Python environment and get Keras and Tensorflow installed so I could start doing tutorials (particularly for deep learning) using R. Although I used to be a systems administrator (about 20 years ago), I don’t do much installing or configuring so I guess that’s why I’ve put this task off for so long. And it wasn’t unwarranted: it took me the whole weekend to get the install working. Here are the steps I used to get things running on Windows 10, leveraging clues in about 15 different online resources — and yes (I found out the hard way), the order of operations is very important. I do not claim to have nailed the order of operations here, but definitely one that works.
Step 0: I had already installed the tensorflow and keras packages within R, and had been wondering why they wouldn’t work. “Of course!” I finally realized, a few weeks later. “I don’t have Python on this machine, and both of these packages depend on a Python install.” Turns out they also depend on the reticulate package, so install.packages(“reticulate”) if you have not already.
Step 1: Installed Anaconda3 to C:/Users/User/Anaconda3 (from https://www.anaconda.com/download/)
Step 2: Opened “Anaconda Prompt” from Windows Start Menu. First, to create an “environment” specifically for use with tensorflow and keras in R called “tf-keras” with a 64-bit version of Python 3.5 I typed:
conda create -n tf-keras python=3.5 anaconda
… and then after it was done, I did this:
Step 3: Install TensorFlow from Anaconda prompt. Using the instructions at https://storage.googleapis.com/tensorflow/windows/cpu/tensorflow-1.1.0-cp35-cp35m-win_amd64.whl I typed this:
pip install --ignore-installed --upgrade
I didn’t know whether this worked or not — it gave me an error saying that it “can not import html5lib”, so I did this next:
conda install -c conda-forge html5lib
I tried to run the pip command again, but there was an error so I consulted https://www.tensorflow.org/install/install_windows. It told me to do this:
pip install --ignore-installed --upgrade tensorflow
This failed, and told me that the pip command had an error. I searched the web for an alternative to that command, and found this, which worked!!
conda install -c conda-forge tensorflow
Step 4: From inside the Anaconda prompt, I opened python by typing “python”. Next, I did this, line by line:
import tensorflow as tf hello = tf.constant('Hello, TensorFlow!') sess = tf.Session() print(sess.run(hello))
It said “b’Hello, TensorFlow!'” which I believe means it works. (Ctrl-Z then Enter will then get you out of Python and back to the Anaconda prompt.) This means that my Python installation of TensorFlow was functional.
Step 5: Install Keras. I tried this:
pip install keras
…but I got the same error message that pip could not be installed or found or imported or something. So I tried this, which seemed to work:
conda install -c conda-forge keras
Step 6: Load them up from within R. First, I opened a 64-bit version of R v3.4.1 and did this:
It took a couple minutes but it seemed to work.
Step 7: Try a tutorial! I decided to go for https://www.analyticsvidhya.com/blog/2017/06/getting-started-with-deep-learning-using-keras-in-r/ which guides you through developing a classifier for the MNIST handwritten image database — a very popular data science resource. I loaded up my dataset and checked to make sure it loaded properly:
data <- data_mnist()
str(data) List of 2 $ train:List of 2 ..$ x: int [1:60000, 1:28, 1:28] 0 0 0 0 0 0 0 0 0 0 ... ..$ y: int [1:60000(1d)] 5 0 4 1 9 2 1 3 1 4 ... $ test :List of 2 ..$ x: int [1:10000, 1:28, 1:28] 0 0 0 0 0 0 0 0 0 0 ... ..$ y: int [1:10000(1d)] 7 2 1 0 4 1 4 9 5 9 ...
Step 8: Here is the code I used to prepare the data and create the neural network model. This didn’t take long to run at all.
trainx<-data$train$x trainy<-data$train$y testx<-data$test$x testy<-data$test$y train_x <- array(train_x, dim = c(dim(train_x), prod(dim(train_x)[-1]))) / 255 test_x <- array(test_x, dim = c(dim(test_x), prod(dim(test_x)[-1]))) / 255 train_y<-to_categorical(train_y,10) test_y<-to_categorical(test_y,10) model %>% layer_dense(units = 784, input_shape = 784) %>% layer_dropout(rate=0.4)%>% layer_activation(activation = 'relu') %>% layer_dense(units = 10) %>% layer_activation(activation = 'softmax') model %>% compile( loss = 'categorical_crossentropy', optimizer = 'adam', metrics = c('accuracy') )
Step 9: Train the network. THIS TOOK ABOUT 12 MINUTES on a powerful machine with 64GB high-performance RAM. It looks like it worked, but I don’t know how to find or evaluate the results yet.
model %>% fit(train_x, train_y, epochs = 100, batch_size = 128) loss_and_metrics <- model %>% evaluate(test_x, test_y, batch_size = 128)
Layer (type) Output Shape Param #
dense_1 (Dense) (None, 784) 615440
dropout_1 (Dropout) (None, 784) 0
activation_1 (Activation) (None, 784) 0
dense_2 (Dense) (None, 10) 7850
activation_2 (Activation) (None, 10) 0
Total params: 623,290
Trainable params: 623,290
Non-trainable params: 0
Step 10: Next, I wanted to try the tutorial at https://cran.r-project.org/web/packages/kerasR/vignettes/introduction.html. Turns out this uses the kerasR package, not the keras package:
X_train <- mnist$X_train Y_train <- mnist$Y_train X_test <- mnist$X_test Y_test <- mnist$Y_test > dim(X_train)  60000 28 28 X_train <- array(X_train, dim = c(dim(X_train), prod(dim(X_train)[-1]))) / 255 X_test <- array(X_test, dim = c(dim(X_test), prod(dim(X_test)[-1]))) / 255
To check and see what’s in any individual image, type:
At this point, the to_categorical function stopped working. I was supposed to do this but got an error:
Y_train <- to_categorical(mnist$Y_train, 10)
So I did this instead:
mm <- model.matrix(~ Y_train) Y_train <- to_categorical(mm[,2]) mod <- Sequential() # THIS IS THE EXCITING PART WHERE YOU USE KERAS!! :)
But then I tried this, and it was clear I was stuck again — it wouldn’t work:
mod$add(Dense(units = 512, input_shape = dim(X_train)))
Stack Overflow recommended grabbing a version of kerasR from GitHub, so that’s what I did next:
install.packages("devtools") library(devtools) devtools::install_github("statsmaths/kerasR") library(kerasR)
I got an error in R which told me to go to the Anaconda prompt (which I did), and type this:
conda install m2w64-toolchain
Then I went back into R and this worked fantastically:
mod <- Sequential()
mod$Add would still not work though, and this is where my patience expired for the evening. I’m pretty happy though — Python is up, keras and tensorflow are up on Python, all three (keras, tensorflow, and kerasR) are up in R, and some tutorials seem to be working.