Error in install_keras() in R since Ubuntu update - r

Question

I used the book "Deep Learning with R" since one month now, and it enables me to make my first neural networks.
I am using Ubuntu. Until 2 days ago, everything was OK and worked fine. But two days ago I updated my Ubuntu to Ubuntu 18.02. Since then, my R code is not working anymore.
I have re-done what is recommended in the book (and what has worked one month ago):
$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install python-pip python-dev
$ sudo apt-get install build-essential cmake git unzip pkg-config libopenblas-dev liblapack-dev
I had no error.
then in R:
install.packages("keras")
library(keras)
install_keras()
This last command is supposed to install the core Keras library along with its dependencies in a Python virtual environment using TensorFlow.
But I obtained the following error that I really do not understand:
> install_keras()
Using existing virtualenv at ~/.virtualenvs/r-tensorflow
Upgrading pip ...
Traceback (most recent call last):
File "/home/baragatt/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
from pip._internal import main
File "/home/baragatt/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_internal/__init__.py", line 5, in <module>
import logging
File "/usr/lib/python2.7/logging/__init__.py", line 26, in <module>
import sys, os, time, cStringIO, traceback, warnings, weakref, collections
File "/usr/lib/python2.7/weakref.py", line 14, in <module>
from _weakref import (
ImportError: cannot import name _remove_dead_weakref
Erreur : Error 1 occurred installing TensorFlow
I have re-installed R, python, tensorflow, but I always have the same error. I do not understand this error. Maybe this is a problem with the virtualenv?
Can someone help me please? It is so frustrating, because two days ago my code was running, and now impossible to work...
I am working with Ubuntu 18.02, at the installed versions are python 2.7.15~rc1-1, R-3.4.4 and tensorflow-1.10.0.

Answer 1

Thanks a lot for this post. I do not really understand what the commands in this post are supposed to fix. But I have done the following:
cd /home/baragatt/.virtualenvs/r-tensorflow/
Then, as proposed in the post:
virtualenv . --system-site-packages
I obtained the following messages:
Running virtualenv with interpreter /usr/bin/python2
New python executable in /home/baragatt/.virtualenvs/r-tensorflow/bin/python2
Not overwriting existing python script /home/baragatt/.virtualenvs/r-tensorflow/bin/python (you must use /home/baragatt/.virtualenvs/r-tensorflow/bin/python2)
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/virtualenv.py", line 2375, in <module>
main()
File "/usr/lib/python3/dist-packages/virtualenv.py", line 724, in main
symlink=options.symlink)
File "/usr/lib/python3/dist-packages/virtualenv.py", line 946, in create_environment
site_packages=site_packages, clear=clear, symlink=symlink))
File "/usr/lib/python3/dist-packages/virtualenv.py", line 1417, in install_python
os.symlink(py_executable_base, full_pth)
OSError: [Errno 17] File exists
I also tried:
virtualenv -p /usr/bin/python2.7 .
And I obtained:
Running virtualenv with interpreter /usr/bin/python2.7
New python executable in /home/baragatt/.virtualenvs/r-tensorflow/bin/python2.7
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/virtualenv.py", line 2375, in <module>
main()
File "/usr/lib/python3/dist-packages/virtualenv.py", line 724, in main
symlink=options.symlink)
File "/usr/lib/python3/dist-packages/virtualenv.py", line 946, in create_environment
site_packages=site_packages, clear=clear, symlink=symlink))
File "/usr/lib/python3/dist-packages/virtualenv.py", line 1278, in install_python
shutil.copyfile(executable, py_executable)
File "/usr/lib/python2.7/shutil.py", line 97, in copyfile
with open(dst, 'wb') as fdst:
IOError: [Errno 40] Too many levels of symbolic links: '/home/baragatt/.virtualenvs/r-tensorflow/bin/python2.7'

Answer 2

I finally find a solution, by looking at different forums.
I thought that the problem should be because of the virtualenvironment that should be created when doing the following command in R.
install_keras()
Hence, I deleted the virtual environment(s) by deleting the directory in which these environements are located (I imagine).
cd ~/.virtualenvs
rm -r r-tensorflow/
Then I have tried the following commands in R
install.packages("keras")
library(keras)
install_keras()
And it works! Honestly, I still do not understand what was the problem that occured after my Ubuntu update.