Keras: Ubuntu/R-3.5.0: install_keras() fails with "Error: Error 1 occurred installing TensorFlow"

Created on 15 Jun 2018  ·  27Comments  ·  Source: rstudio/keras

On Ubuntu 14.04 and R-3.5.0 I'm trying to install keras like so:

library(keras)
install_keras()

But then I get:

Using existing virtualenv at  ~/.virtualenvs/r-tensorflow 
Upgrading pip ...
Traceback (most recent call last):
  File "~/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main
Error: Error 1 occurred installing TensorFlow

Any hints are very welcome?

picture leonjessen
👍2

All 27 comments

I would try removing the virtualenv before upgrading. So virtualenv_remove("r-tensorflow")

jjallaire picture jjallaire on 15 Jun 2018

Thanks for input - Unfortunately, this did not resolve the issue:

library(reticulate)
virtualenv_remove("r-tensorflow")
Remove virtualenv at ~/.virtualenvs/r-tensorflow? [Y/n]: Y
library(keras)
install_keras()
Creating virtualenv for TensorFlow at  ~/.virtualenvs/r-tensorflow 
Already using interpreter /usr/bin/python
New python executable in ~/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Downloading/unpacking pip
  Downloading pip-10.0.1-py2.py3-none-any.whl (1.3MB): 1.3MB downloaded
Installing collected packages: pip
Successfully installed pip
Cleaning up...
Upgrading wheel ...
Traceback (most recent call last):
  File "~/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main
Error: Error 1 occurred installing TensorFlow
leonjessen picture leonjessen on 15 Jun 2018

If you want to install for all server users you should do a regular sudo pip install of keras rather than trying to use the R base functions. Here are some docs on doing system-wide installs: https://tensorflow.rstudio.com/tensorflow/articles/installation_gpu.html#multiple-users

jjallaire picture jjallaire on 15 Jun 2018

Thanks for the link - I will look into it!

leonjessen picture leonjessen on 15 Jun 2018

Now I have tried working on the issue for a considerable amount of time, but alas, I am still stuck. The issue somehow seem to pertain to pip, the error I get is the following:

keras::install_keras(method = "virtualenv", tensorflow = "gpu")
Creating virtualenv for TensorFlow at  ~/.virtualenvs/r-tensorflow 
Already using interpreter /usr/bin/python
New python executable in /home/jessen/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Downloading/unpacking pip
  Downloading pip-10.0.1-py2.py3-none-any.whl (1.3MB): 1.3MB downloaded
Installing collected packages: pip
Successfully installed pip
Cleaning up...
Upgrading wheel ...
Traceback (most recent call last):
  File "/home/jessen/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main
Error: Error 1 occurred installing TensorFlow

If I then try to get the pip version installed with keras, I get the same error:

$ .virtualenvs/r-tensorflow/bin/pip -V
Traceback (most recent call last):
  File ".virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main

Any suggestions?

leonjessen picture leonjessen on 29 Jun 2018

This is an issue that some (very few as far as I can tell) Python systems get into after an upgrade to pip 10. Here are some additional details: https://github.com/pypa/pip/issues/5240. I'm hoping that thread has a way to get your system out of this state.

jjallaire picture jjallaire on 29 Jun 2018

Thanks for the link, I did come across it during the last couple of days. Unfortunately, so far I have yet to resolve the issue. I will make sure to come back to this thread, when I succeed.

leonjessen picture leonjessen on 29 Jun 2018

Slight progress - The virtual environment pip looks like so:

$ cat .virtualenvs/r-tensorflow/bin/pip
#!/home/jessen/.virtualenvs/r-tensorflow/bin/python

# -*- coding: utf-8 -*-
import re
import sys

from pip import main

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
    sys.exit(main())

and fails like so:

$ .virtualenvs/r-tensorflow/bin/pip -V
Traceback (most recent call last):
  File ".virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main

However, if I change the import call from from pip import main to from pip._internal import main, I get:

$ .virtualenvs/r-tensorflow/bin/pip -V
pip 10.0.1 from /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip (python 2.7)

But, when I issue the command keras::install_keras(method = "virtualenv", tensorflow = "gpu") from within R, it overwrites my correction with the faulty call to import.

I need to somehow avoid the automatic update of pip when installing keras, so that it is left untouched after my manual edit...

leonjessen picture leonjessen on 29 Jun 2018

My impression is that once you resolve the issue the automatic update should be okay. So you could simply comment out the automatic updates for one install and see if that makes the problem go away for good.

jjallaire picture jjallaire on 29 Jun 2018

I was thinking something along those lines and I can see I need to look at tensorflow::install_tensorflow(), I am however not sure how/where to comment out the lines:

else if (is_ubuntu()) {
  if (!have_pip) {
    install_commands <- c(install_commands, paste0("$ sudo apt-get install python", 
      pyver, "-pip"))
    pip <- paste0("/usr/bin/pip", pyver)
}

I tried copying the entire function to my_install and then comment out, but then it cannot find is_windows(), is_osx(), etc.

(On a side note... In Danish "pip" is synonym for crazy, which is not far from my current state-of-mind...)

leonjessen picture leonjessen on 29 Jun 2018

These are the lines to comment out: https://github.com/rstudio/tensorflow/blob/master/R/install.R#L427-L434

jjallaire picture jjallaire on 29 Jun 2018

@leonjessen Did you have any success. Having exactly the same problem.

ewenharrison picture ewenharrison on 6 Jul 2018

Ok, this works for me. 

# The attached file calls pip9.0.3, which doesn't have the pip10.0.1 issue that 
# many others have described 
source("install.R")
source("utils.R")

# I had a further issue with tensorflow 1.6 crashing R, which is not the case with v1.5.0.
install_tensorflow(version = "1.5.0")

# If wanting keras specifically, run:
install_tensorflow(version = "1.5.0", extra_packages = "keras")

# Check all is well.
library(tensorflow)
sess = tf$Session()
hello <- tf$constant('Hello, TensorFlow!')
sess$run(hello)

# Or
library(keras)
mnist <- dataset_mnist()
x_train <- mnist$train$x
y_train <- mnist$train$y
x_test <- mnist$test$x
y_test <- mnist$test$y

install_tensorflow.zip

ewenharrison picture ewenharrison on 7 Jul 2018
👍1

Been away for the WhyR conference and currently semi-offline, I’ll check up on this asap

leonjessen picture leonjessen on 7 Jul 2018

@ewenharrison Thank you! This has been driving me crazy for two days.

drotroff picture drotroff on 9 Jul 2018
👍1

I've just made a change to only update pip (and related tools) when pip is < v8.1 (the recommended minimum for installing TF). This should eliminate this issue entirely on newer systems (that code is really there for the built-in Python on Mac OS X, which has an ancient pip v7.

https://github.com/rstudio/tensorflow/commit/87af53829c42f45ab2d08dabf10e1ac7538a53e1

jjallaire picture jjallaire on 9 Jul 2018
👍1

Despite numerous attempts, I am still unable to get it to work. As it is clearly a pip issue and not R/Keras, I have opened an issue at pypa/pip.

leonjessen picture leonjessen on 14 Jul 2018

@leonjessen Does the output now show that you are calling pip 9.0.3? You should not get the "main" issue with this. You are definitely using the files I attached above?

ewenharrison picture ewenharrison on 14 Jul 2018

A pip maintainer here! 👋

You should be able to use python -m pip instead of pip -- the pip script might have been broken due to various reasons (outlined in a pip issue that's linked from the one @leonjessen opened).

pradyunsg picture pradyunsg on 20 Jul 2018

Cheers @ewenharrison, back from holidays, we're on the same page with your files, right up until:

> sess = tf$Session()
Error: Installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
/home/jessen/.virtualenvs/r-tensorflow/bin/python
/usr/bin/python2.7
/usr/bin/python3.4

You can install TensorFlow using the install_tensorflow() function.
leonjessen picture leonjessen on 3 Aug 2018

Can you provide the output during installation.

ewenharrison picture ewenharrison on 6 Aug 2018

Sure thing @ewenharrison:

```{r}

source("install_tensorflow/install.R")
source("install_tensorflow/utils.R")
install_tensorflow(version = "gpu", extra_packages = "keras")
Creating virtualenv for TensorFlow at ~/.virtualenvs/r-tensorflow
Already using interpreter /usr/bin/python
New python executable in /home/jessen/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Collecting pip==9.0.3
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
SNIMissingWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/ac/95/a05b56bb975efa78d3557efa36acaf9cf5d2fd0ee0062060493687432e03/pip-9.0.3-py2.py3-none-any.whl (1.4MB)
100% |████████████████████████████████| 1.4MB 11.6MB/s
Installing collected packages: pip
Successfully installed pip-10.0.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Upgrading wheel ...
Collecting wheel
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
SNIMissingWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/81/30/e935244ca6165187ae8be876b6316ae201b71485538ffac1d718843025a9/wheel-0.31.1-py2.py3-none-any.whl (41kB)
100% |████████████████████████████████| 51kB 1.7MB/s
Installing collected packages: wheel
Successfully installed wheel-0.31.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Upgrading setuptools ...
Collecting setuptools
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
SNIMissingWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/ff/f4/385715ccc461885f3cedf57a41ae3c12b5fec3f35cce4c8706b1a112a133/setuptools-40.0.0-py2.py3-none-any.whl (567kB)
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Installing collected packages: setuptools
Successfully installed setuptools-40.0.0
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Installing TensorFlow ...
Collecting tensorflow-gpu
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
SNIMissingWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/68/45/8ed49fb2decd4ce7849fc9755d9e066f414fb29c40e811bf4c12287de0af/tensorflow_gpu-1.9.0-cp27-cp27mu-manylinux1_x86_64.whl (229.6MB)
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/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/33/0c/1c5dfa85e05052aa5f50969d87c67a2128dc39a6f8ce459a503717e56bd0/h5py-2.8.0-cp27-cp27mu-manylinux1_x86_64.whl (2.7MB)
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/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/9e/a3/1d13970c3f36777c583f136c136f804d70f500168edc1edea6daa7200769/PyYAML-3.13.tar.gz (270kB)
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/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl (91kB)
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Collecting Pillow
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
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/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/34/7d/b1dedde8af99bd82f20ed7e9697aac0597de3049b1f786aa2aac3b9bd4da/Keras-2.2.2-py2.py3-none-any.whl (299kB)
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Collecting scipy
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
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Collecting mock>=2.0.0 (from tensorflow-gpu)
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl (56kB)
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Collecting grpcio>=1.8.6 (from tensorflow-gpu)
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InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/ea/96/234eaae211b6b34739018735be33e1616bc3e73c62d842c5189b80a4bd72/grpcio-1.14.0-cp27-cp27mu-manylinux1_x86_64.whl (9.2MB)
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Collecting numpy>=1.13.3 (from tensorflow-gpu)
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
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Building wheels for collected packages: pyyaml, termcolor, absl-py, gast
Running setup.py bdist_wheel for pyyaml ... done
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Installing collected packages: six, funcsigs, pbr, mock, futures, enum34, grpcio, termcolor, numpy, wheel, setuptools, protobuf, markdown, werkzeug, tensorboard, backports.weakref, absl-py, gast, astor, tensorflow-gpu, h5py, pyyaml, idna, urllib3, chardet, certifi, requests, Pillow, scipy, keras-applications, keras-preprocessing, keras
Successfully installed Pillow-5.2.0 absl-py-0.3.0 astor-0.7.1 backports.weakref-1.0.post1 certifi-2018.4.16 chardet-3.0.4 enum34-1.1.6 funcsigs-1.0.2 futures-3.2.0 gast-0.2.0 grpcio-1.14.0 h5py-2.8.0 idna-2.7 keras-2.2.2 keras-applications-1.0.4 keras-preprocessing-1.0.2 markdown-2.6.11 mock-2.0.0 numpy-1.15.0 pbr-4.2.0 protobuf-3.6.0 pyyaml-3.13 requests-2.19.1 scipy-1.1.0 setuptools-40.0.0 six-1.11.0 tensorboard-1.9.0 tensorflow-gpu-1.9.0 termcolor-1.1.0 urllib3-1.23 werkzeug-0.14.1 wheel-0.31.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Installation complete.

library(tensorflow)

Attaching package: ‘tensorflow’

The following object is masked _by_ ‘.GlobalEnv’:

install_tensorflow

sess = tf$Session()
Error: Installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
/home/jessen/.virtualenvs/r-tensorflow/bin/python
/usr/bin/python2.7
/usr/bin/python3.4

You can install TensorFlow using the install_tensorflow() function.
```

There is some sort of problem with which version installed python is being called, but I cannot seem to find a solution. Any input is much appreciated! 👍

leonjessen picture leonjessen on 6 Aug 2018

I'd try with the standard package before the GPU version.

On 6 August 2018 at 08:43, Leon Eyrich Jessen notifications@github.com
wrote:

Sure thing @ewenharrison https://github.com/ewenharrison:

source("install_tensorflow/install.R")
source("install_tensorflow/utils.R")
install_tensorflow(version = "gpu", extra_packages = "keras")
Creating virtualenv for TensorFlow at ~/.virtualenvs/r-tensorflow
Already using interpreter /usr/bin/python
New python executable in /home/jessen/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Collecting pip==9.0.3
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
SNIMissingWarning
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InsecurePlatformWarning
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Installing collected packages: pip
Successfully installed pip-10.0.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Upgrading wheel ...
Collecting wheel
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
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Installing collected packages: wheel
Successfully installed wheel-0.31.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Upgrading setuptools ...
Collecting setuptools
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
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/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/2d/99/b2c4e9d5a30f6471e410a146232b4118e697fa3ffc06d6a65efde84debd0/futures-3.2.0-py2-none-any.whl
Collecting markdown>=2.6.8 (from tensorboard<1.10.0,>=1.9.0->tensorflow-gpu)
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/6d/7d/488b90f470b96531a3f5788cf12a93332f543dbab13c423a5e7ce96a0493/Markdown-2.6.11-py2.py3-none-any.whl (78kB)
100% |████████████████████████████████| 81kB 6.0MB/s
Collecting werkzeug>=0.11.10 (from tensorboard<1.10.0,>=1.9.0->tensorflow-gpu)
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecurePlatformWarning
Downloading https://files.pythonhosted.org/packages/20/c4/12e3e56473e52375aa29c4764e70d1b8f3efa6682bef8d0aae04fe335243/Werkzeug-0.14.1-py2.py3-none-any.whl (322kB)
100% |████████████████████████████████| 327kB 2.7MB/s
Building wheels for collected packages: pyyaml, termcolor, absl-py, gast
Running setup.py bdist_wheel for pyyaml ... done
Stored in directory: /home/jessen/.cache/pip/wheels/ad/da/0c/74eb680767247273e2cf2723482cb9c924fe70af57c334513f
Running setup.py bdist_wheel for termcolor ... done
Stored in directory: /home/jessen/.cache/pip/wheels/7c/06/54/bc84598ba1daf8f970247f550b175aaaee85f68b4b0c5ab2c6
Running setup.py bdist_wheel for absl-py ... done
Stored in directory: /home/jessen/.cache/pip/wheels/4c/16/ef/e36a23f2432e9220f8845f94e2c3abd39e7d9d1cd458d3159d
Running setup.py bdist_wheel for gast ... done
Stored in directory: /home/jessen/.cache/pip/wheels/9a/1f/0e/3cde98113222b853e98fc0a8e9924480a3e25f1b4008cedb4f
Successfully built pyyaml termcolor absl-py gast
Installing collected packages: six, funcsigs, pbr, mock, futures, enum34, grpcio, termcolor, numpy, wheel, setuptools, protobuf, markdown, werkzeug, tensorboard, backports.weakref, absl-py, gast, astor, tensorflow-gpu, h5py, pyyaml, idna, urllib3, chardet, certifi, requests, Pillow, scipy, keras-applications, keras-preprocessing, keras
Successfully installed Pillow-5.2.0 absl-py-0.3.0 astor-0.7.1 backports.weakref-1.0.post1 certifi-2018.4.16 chardet-3.0.4 enum34-1.1.6 funcsigs-1.0.2 futures-3.2.0 gast-0.2.0 grpcio-1.14.0 h5py-2.8.0 idna-2.7 keras-2.2.2 keras-applications-1.0.4 keras-preprocessing-1.0.2 markdown-2.6.11 mock-2.0.0 numpy-1.15.0 pbr-4.2.0 protobuf-3.6.0 pyyaml-3.13 requests-2.19.1 scipy-1.1.0 setuptools-40.0.0 six-1.11.0 tensorboard-1.9.0 tensorflow-gpu-1.9.0 termcolor-1.1.0 urllib3-1.23 werkzeug-0.14.1 wheel-0.31.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Installation complete.

library(tensorflow)

Attaching package: ‘tensorflow’

The following object is masked _by_ ‘.GlobalEnv’:

install_tensorflow

sess = tf$Session()
Error: Installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
/home/jessen/.virtualenvs/r-tensorflow/bin/python
/usr/bin/python2.7
/usr/bin/python3.4

You can install TensorFlow using the install_tensorflow() function.

There is some sort of problem with which version installed python is being
called, but I cannot seem to find a solution. Any input is much
appreciated! 👍

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--
Ewen M Harrison MB ChB MSc PhD FRCS (Gen Surg)
Senior Lecturer in General Surgery | Consultant Transplant and
Hepatobiliary Surgeon
ChM General Surgery http://www.chm.rcsed.ac.uk Programme Director|
GlobalSurg http://globalsurg.org Research Collaborative Lead
Surgical Informatics | Centre for Medical Informatics | Usher
Institute | University
of Edinburgh
http://www.ed.ac.uk/schools-departments/surgery/staff/surgical-profiles/ewen-harrison
Mobile: +44 (0) 797 442 0495 | [email protected] | Twitter:
@ewenharrison | Web: DataSurg http://datasurg.net | SurgicalInformatics
http://surgicalinformatics.org

ewenharrison picture ewenharrison on 6 Aug 2018

I understand, but It has to be the GPU version... It's a petty letting a perfectly nice nvidia tesla card sitting idle - I need to put it to work 👍

leonjessen picture leonjessen on 6 Aug 2018

To debug your installation install the CPU version.
Then start on the necessary systems required for the GPU system.
https://tensorflow.rstudio.com/tools/local_gpu.html

On 6 August 2018 at 08:59, Leon Eyrich Jessen notifications@github.com
wrote:

I understand, but It has to be the GPU version... It's a petty letting a
perfectly nice nvidia tesla card sitting idle - I need to put it to work
👍

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You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/rstudio/keras/issues/434#issuecomment-410621639, or mute
the thread
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.

--
Ewen M Harrison MB ChB MSc PhD FRCS (Gen Surg)
Senior Lecturer in General Surgery | Consultant Transplant and
Hepatobiliary Surgeon
ChM General Surgery http://www.chm.rcsed.ac.uk Programme Director|
GlobalSurg http://globalsurg.org Research Collaborative Lead
Surgical Informatics | Centre for Medical Informatics | Usher
Institute | University
of Edinburgh
http://www.ed.ac.uk/schools-departments/surgery/staff/surgical-profiles/ewen-harrison
Mobile: +44 (0) 797 442 0495 | [email protected] | Twitter:
@ewenharrison | Web: DataSurg http://datasurg.net | SurgicalInformatics
http://surgicalinformatics.org

ewenharrison picture ewenharrison on 6 Aug 2018

Hi Leon,

were you able to solve this, so we could close the issue?

If not, I can understand this

I understand, but It has to be the GPU version... It's a petty letting a perfectly nice nvidia tesla card sitting idle

very well, so I'm just asking, very pragmatically, does it have to be virtualenv? So far, I've never had any problems using conda...

skeydan picture skeydan on 15 Sep 2018

No need to re-open, just wanted to give my final verdict: I had to give up! I spend hours and hours looking online and tried all proposed solutions and nothing worked. Once your system is caught in an inconsistent state with pip, then you are in deep deep trouble. On my Ubuntu 14.04 I was able to get tensorflow up and running after installing miniconda3 and then in R-3.5.1 issue install_keras(method = "conda", tensorflow = "gpu"). However, I have decided to do, what would have been more time efficient, had I done so initially; clean install Ubuntu 18.04 LTS and then redo the whole Cuda/Keras/Tensorflow/R setup. You live you learn... Thanks for input during the process, much appreciated!

leonjessen picture leonjessen on 28 Nov 2018
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