I have been unable to get tensorflow to work in my R-studio. Every time I try to use install_tensorflow() R-studio throws the below error
Error in conda_python(envpath, conda = miniconda) :
no conda environment exists at path 'C:/Users/yaswanth/AppData/Local/r-miniconda/envs/r-reticulate'
Below are the steps I followed
-I have created an environment TensorFlowEnvironment in my anaconda.
-I have installed Tensorflow in this environment
-Launched R studio from this environment
-I ran the following two lines of code
install.packages("tensorflow")
library(tensorflow)
-But when I third line of code
install_tensorflow()
I get the error that no condo environment named as r-reticulate exist. Should I create a new environment named as r-reticulate? I am a tensorflow beginner so any help would be appreciated.
Try this: In Anaconda Navigator, in the Environments pane, create a new environment (click on create+ button) and name it "rminiconda". Include both Python and R (checkboxes in the popup window. Then in RStudio, tools/Options/Python, choose the new environment for Python.
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Summary
Installed R kernel in Anaconda environment
Works with Anaconda's browser Jupyter notebook, but not VS Code.
Details
I am trying to set up VS Code to recognize my R kernel for use with Jupyter Notebooks. The steps I have followed are as follows:
Create a new R environment (via the Anaconda interface... Rstudio works just fine).
Using the command line interface with the above environment activated, ensure Jupyter is installed: conda install jupyter
Install irkernel: conda install -c r r-irkernel
Run R from command line and initialize irkernel:
R
> IRkernel::installspec()
Open VS Code and create a new notebook. Select the R kernel that appears, and run a basic commannd in the first cell: file.path(getwd())
These follow the steps here, and in other Stackoverflow posts (here and here).
Unfortunately, I cannot get the kernel to work. The above code in item 5 results in the following error:
Failed to start the Kernel.
The kernel died. Error: ... View Jupyter log for further details.
There is a copy of the log available here (should be visible to everyone). The notebook is available here (but is literally just the one line of code mentioned above).
My hypothesis is that IRkernel::installspec() installs the kernel in a different location than the conda environment. The kernel is installed in C:\Users\aaron\AppData\Roaming\jupyter\kernels\ir, while in VS Code the kernel selected is in C:\Users\aaron\.conda\envs\rstudio\lib\R\bin\x64\R (the environment name is rstudio).
However, when I open Jupyter notebook via the Anaconda interface (not VS Code... i.e. the browser version), everything works just fine. The same code (file.path(getwd())) returns the appropriate 'C:/Users/aaron'.
I am sure I have done something silly wrong, and appreciate your help in advance!
I am try to install tensorflow within R and subsequently a package called "cellassign". I have installed tensorflow, reticulate, and keras with the following command and they all seem to be installed without any hiccups. I am also able to load the packages after installing.
devtools::install_github("rstudio/reticulate")
devtools::install_github("rstudio/tensorflow")
devtools::install_github("rstudio/keras")
However, I keep encountering the following issue when trying to use any command within tensorflow or keras package.
tensorflow::install_tensorflow()
Error: 'activate' is not a conda command.
Did you mean "source activate /home/users/ntu/ling0086/.conda/envs/r_env" ?
+ . /app/anaconda/3/bin/activate
+ conda activate '/home/users/ntu/ling0086/.conda/envs/r_env'
Also ran into another error if I tried using the following
> tensorflow::tf_config()
Python environments searched for 'tensorflow' package:
/home/users/ntu/ling0086/.conda/envs/r_env/bin/python3.10
/usr/bin/python
Python exception encountered:
ModuleNotFoundError: No module named 'six'
Any idea why this might be so? I am not familiar with linux-environment variables and I do not have sudo privilege. I was told that my "R" is loaded in a virtual environment and this might affect the path finding to the right packages. But I am unsure as to how I should rectify the above error. Any help would be deeply appreciated.
Not sure if this is of any help, but how I would normally run R entails:
module load anaconda/3
source activate r_env
R
I used to work in R 3.4.0 version. Hovewer, this version doesn't support such packages as keras and tensorflow.
I was adviced to upgrade my R version to the newest one.
I downloaded the most recent R version 4.0.2 from the official site, then ran the following code:
install.packages("keras")
library(keras)
install_keras()
And got the following error:
Error in install_keras() :
You should call install_keras() only in a fresh R session that has not yet initialized Keras and TensorFlow (this is to avoid DLL in use errors during installation)
After this, when I tried to quit R session by q() , I faced the following error:
Error: option error has NULL value
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error: option error has NULL value
I've never faced such an error before. When I used old R version, I typed q() and then had to choose between y and n. No errors appeared.
I'm asking you to help to to solve this problem.
You need to create a new environment and then you can install R 4.+ in Anaconda. Follow these steps.
conda create --name r4-base
After activating r4-base run these commands
conda activate r4-base
conda install -c conda-forge r-base
conda install -c conda-forge/label/gcc7 r-base
Finally, you will notice r-basa version 4 will be installed.
Thereafter, you can install any supported packages. But with this only, you won't have the ability to use it in the Jupyter notebook. You need to install install.packages('IRkernel') and Jupyter notebook as well if you want to use it. Otherwise you are good to go with R-Studio.
For Jupyter Installation and RKernel.
conda install jupyter
Then open the R console. Write in R console
install.packages('IRkernel')
IRkernel::installspec()
Congrats! You can use Notebook for Python and R.
Find the location of R.exe on your computer. In my computer, this executable is at
C:\Program Files\R\R-3.4.3\bin
Open another Anaconda Prompt as Administrator and change directories to wherever R.exe is on your computer with cd file path. On my computer, it’s cd C:\Program Files\R\R-3.4.3\bin, but it might be different for you.
Then run R from within Anaconda Prompt in Admin mode with R.exe
You’ll notice that you’re in an R session. From here, run the following three commands into the terminal.
install.packages("devtools")
devtools::install_github("IRkernel/IRkernel")
IRkernel::installspec()
In order, they (1) install the devtools package which gets you the install_github() function, (2) install the IR Kernel from GitHub, and (3) tell Jupyter where to find the IR Kernel.
Open Jupyter notebook and enjoy your new R kernel!
Get more information here
#Rheatey Bash works perfectly. but i was facing python.exe this program cant start because api-ms-win-core-path-l1-1-0.dll python system error. this is a problem running on windows 7 but i resolved this issue by installing the kernel following https://richpauloo.github.io/2018-05-16-Installing-the-R-kernel-in-Jupyter-Lab/ and it works fine
I am still in progress to get Jupyter-Notebook and R working together on Windows 10 machine. After solving the problem with install_github() I am now facing just another issue. I am still following the official installation guide, I am stuck at step 2:
Every time I get this error - I have tried this in R GUI and RStudio, the same:
> IRkernel::installspec()
Error in IRkernel::installspec() :
jupyter-client has to be installed but “jupyter kernelspec --version” exited with code 127.
In addition: Warning message:
In system2("jupyter", c("kernelspec", "--version"), FALSE, FALSE) :
'"jupyter"' not found
My attempts so far: It was suggested here and here, that this could be a problem with the PATH variable setting, so I have added Anaconda to the PATH enviroment. I also installed the jupyter-client via the Anaconda console. No change so far. Any ideas?
This answer is based on this by #Ryan, but since the question answered was actually about a Linux based system I put it here in a Windows question:
One way to overcome the problem - if adding PATH variables to the environment doesn't work - is the following:
If Anaconda is installed and the Jupyter-Notebook with it (should be the standard install), open up the Anaconda prompt, not the Windows command prompt or the Anaconda Navigator
Look up the executable of R (not Rgui or Rstudio), it should be somewhere like C:\Program Files\R\R-3.5.1\bin and copy the path
Paste the path into the Anaconda prompt and start R by typing R
Now execute IRkernel::installspec() once again, this time there shouldn't be an error
Now you can start an R kernel within Jupyter-Notebook
You should try to open R in the terminal, if you changed directory where R il located type:
R.exe
and then run:
IRkernel::installspec()
I was having this issue trying to run Jupyter Lab on my Ubuntu 18.04 LTS headless server running in an Azure VM.
To resolve the issued, I had to navigate to /usr/bin and open R from there. It turns out that despite my path, calling R from the terminal opened the anaconda3 version in /home/<you>/anaconda3/bin/R.
Run IRkernel::installspec() from /usr/bin/R in as sudo and it should add the kernel.
If jupyter.exe is installed under c:\python36\sripts, run
"setwd("c:/python36/scripts")" on R GUI, run "IRkernel::installspec()"
Simply create a new virtual environment for R. Either using the CLI or the anaconda Navigator (best recommended, If and if you're using Anaconda).
I had Tensorflow installed with Anaconda. Now I want use it in R and I need to reinstall Tensorflow, because the note here
NOTE: You should NOT install TensorFlow with Anaconda as there are
issues with the way Anaconda builds the python shared library that
prevent dynamic linking from R.
I already tried to uninstall from Anaconda and install with pip but its came to the same place in anaconda directory. Tesorflow is working from terminal but in R shows Error: Command failed (1)
Anybody can help me to how I can solve the problem? Should I uninstall anaconda and install Tensorflow using pip?
You have several options on what to do. Probably the cleanest one is to install a system-wide python (if not installed yet) and then create a virtual environment. This basically takes your system python binaries and moves them to its own compartment where everythign is isolated from the rest, incl. anaconda. Once you are inside an activated virtual environment you can install all the necessary Python appendages for TensorFlow. Once that is done, make sure you set up a correct environmental PATH for TensorFlow from where R can reach it:
Sys.setenv(TENSORFLOW_PYTHON="/path/to/virtualenv/python/binary")
devtools::install_github("rstudio/tensorflow")
Example of the path to where you installed the virtual environment project would be, I think, something like ~/minion/medvedi/venv_medvedi/bin/python.
This is no longer an issue, the documentation was updated too.
See here:
https://github.com/rstudio/tensorflow/commit/4e1e11d6ba2fe7efe1a03356f96172dbf8db365e
With the help of Keras, we can install the TensorFlow package in R.
install_keras()
library(keras)
devtools::install_github("rstudio/keras")
install_tensorflow(package_url = "https://pypi.python.org/packages/b8/d6/af3d52dd52150ec4a6ceb7788bfeb2f62ecb6aa2d1172211c4db39b349a2/tensorflow-1.3.0rc0-cp27-cp27mu-manylinux1_x86_64.whl#md5=1cf77a2360ae2e38dd3578618eacc03b")
library(tensorflow)
Keras is a high-level neural network API for deep learning from TensorFlow Google.
my suggestion is to install anaconda and create an environment called "r-reticulate".
you can do it using anaconda navigator or
reticulate::conda_create(envname = "r-reticulate")
then to check that env detected by reticulate, use reticulate::conda_python().it must return directory of python.exe for your env.
after that you can install tensorflow by install_tensorflow(). [not working in my case]
so I install the tesnorflow from CMD.
follow these steps:
open the cmd :]
activate the r-reticulate env using conda activate r-reticulate (you may need your directory to conda directory if you did not add conda to your PATH)
use : conda install -c anaconda tensorflow
now in R, you can use TensorFlow.
for installing Keras, you can use pip install Keras. [i tried install_keras() function after the installation of tensorflow, but it ruined my TensorFlow installation also]
Eventually I found the best and fast method to do it in R:
devtools::install_github("rstudio/keras")
library(keras)
install_keras(method = "conda")
install_keras(tensorflow = "gpu")
tensorflow::install_tensorflow()