I know google colaboratory doesn't yet support an R kernel. What about rmagic? Can I use rpy2?
I tried :
!pip install rpy2==2.8.6
And got :
Collecting rpy2==2.8.6
Using cached https://files.pythonhosted.org/packages/32/54/d102eec14f9cabd0df60682a38bd45c36169a1ec8fb8a690bf436cb6d758/rpy2-2.8.6.tar.gz
Complete output from command python setup.py egg_info:
Error: Tried to guess R's HOME but no command 'R' in the PATH.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-3bSiiD/rpy2/
I'm guessing that it isn't working because R isn't installed on whatever cloud machine this notebook is running on, and that it probably isn't possible to install it. But I'm hoping I'm wrong and someone may know of a work around.
OK, I answered my own question. I thought for sure this would fail, but tried anyway:
!apt-get update
!apt-get install r-base
!pip install rpy2==2.8.6
And it worked!
Related
I am trying to install tensorflow-text through miniconda in Spyder. I have managed to install other modules in Spyder such as tensorflow itself, pandas, scikit-learn, etc. However, using the same command as all the other installations (with the specific package name replaced by tensorflow-text)
conda install spyder-kernels tensorflow-text -y
I continue to get the same error whenever I try to install tensorflow-text:
PackagesNotFoundError: The following packages are not available from current channels:
- tensorflow-text
followed by a suggestion to search for the package on anaconda.org. As such, I searched for the tensorflow-text package on the anaconda site and found one, albeit for linux, by rocketce. Attempting to run the commands listed under the tensorflow-text installation instructions on that webpage also yielded the same error.
At first, I tried to install tensorflow-text through pip and was able to successfully run the command
pip install -U tensorflow-text==2.10.0
which seemed to install tensorflow-text. But I could not figure out how to access it or if it was correctly installed. Specifically, I am looking to use tensorflow-text in the Spyder IDE. I was able to get tensorflow working in the IDE, but not the specific tensorflow-text.
I am using a Windows 10 system; I could not find anything on the anaconda site for Windows 10. I am rather inexperienced (if you could not already tell from the nature and description of the problem), so patience and clear explanations are appreciated. Thanks in advance!
For a deep-learning project, I was trying to import the 'models' library. But it's not installed on my colab notebook. So, I tried pip install models to install the library but it shows error which is as on the screenshot. I've also read somewhere that the library is renamed as 'pymodels'. I've also tried it but still not working.
I would be thankful for any help you can provide.
I am encoutering two kinds of issues while trying to install a package called Boltztrap2.
1) Trying to install Boltztrap2 using 'pip3'. However, when I punch in the command, the process goes smoothly for a while and then spits out an error :
BoltzTraP2/sphere/frontend.cpp:32:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
I did some troubleshooting and found out that it is just a path issue - I confirmed this by typing 'locate Python.h'. However, I don't get how to manually incorporate this change since the 'pip3' command that I use downloads the program and compiles it automatically. I don't seem to have access to change any scripts, or rather I do not know how to, since I'm kind of new to all this.
PS: I do not have sudo access.
2) Trying to install Boltztrap2 by manually compiling the python setup file: This seems to work fine until the system spits out an error saying:
Error:numpy is not installed.
PS: Again, I do not have sudo access.
I would be very glad if someone could help me install this package through either method. I just want to get the software to work. Thanks in advance for any assistance.
python3 -m pip install --upgrade pip
pip3 install numpy
Check if you can upgrade pip?
If that works then you can pip install numpy.
I'm trying to follow this guide to test this new algorithm: https://github.com/lalonderodney/SegCaps
I can't do it in my PC, so i'm using another server with Putty. Now I'm connected with the other server.
First of all I installed TensorFlow as indicates in the guide with :
pip install -r requirements.txt
After I wrote this code: ./main.py segcaps.png
in which segcaps.png is the image that i want to use
Finally I wrote python main.py --data_root_dir data
that is the only required parameter with the directory containing imgs and masks folders.
Now it gives me an error:
ModuleNotFoundError: No module named 'tensorflow.python.framework'
I searched it in the directory tensorflow/python/framework and it exists.
So, i don't know how to solve it. Ideas?
If you have multiple Python versions installed, then you'll (most likely) have multiple pip versions installed too. Make sure that the pip command you use installs the package(s) into the Python version you want it to. It may so happen that the package got installed into python2 but you wanted it in python3.
Since using pip did not install the packages in python3, pip3 is most likely to the PyPI for python3. Try
pip3 install -r requirements.txt
and that should work.
In case you have an EnvironmentError you can try this (bad idea):
pip3 install -r requirements.txt --user
This solves the problem most of the times on standalone machines. I'm not sure about the server; insufficient permissions might block this.
Why is the --user flag a bad idea? Read: What is the purpose “pip install --user …”?
You can use pip show tensorflow to see if it is installed or not.
As for ModuleNotFoundError try uninstalling keras and reinstalling an earlier version by pip install keras==2.1.6
I installed TensorFlow on my MacBook Pro 10.12.5 from source code by steps described here.
https://www.tensorflow.org/install/install_sources
TensorFlow itself works well but I cannot run TensorBoard.
It seems tensorboard is not installed properly.
When I try running tensorboard --logdir=... it says -bash: tensorboard: command not found. And locate tensorboard returns empty.
Do I need any additional step to install tensorboard?
You could call tensorboard as a python module like this:
python3 -m tensorboard.main --logdir=~/my/training/dir
or add this to your .profile
alias tensorboard='python3 -m tensorboard.main'
If no other methods work then try this one. It may help you.
1. check the location of Tensorflow
pip show tensorflow
It will show output something like this.
...
Name: tensorflow
Version: 1.4.0
Location: /home/abc/xy/.local/lib/python2.7/site-packages
...
2. Go to that location you get from the above output.
cd /home/abc/xy/.local/lib/python2.7/site-packages
There you can see a directory named tensorboard.
cd tensorboard
3. There must be a file named 'main.py'.
4. Execute the following command to launch the tensorboard.
python main.py --logdir=/path/to/log_file/
If you installed Tensorflow with Virtualenv, then first Check whether you have activated the tensorflow envirnoment or not
If you have activated the tensorflow session then your command prompt will look like this :
If not, Write the below command and try running tensorboard again.
source ~/tensorflow/bin/activate
Run this command:
python3 -m tensorboard.main --logdir=logdir
To run directory you can use,
Change =logdir to ="dir/TensorFlow"
(Directory path)
What version of Tensorflow are you running? Older versions don't include Tensorboard.
If you do have a newer version, I see you are using OSX, which apparently caused some problems for other people: https://github.com/tensorflow/tensorflow/issues/2115 Check this page to fix it!
As a MacPorts user, I'm used to running things from out of the path
/opt/local/bin. When you install a python package via MacPorts, that's
where the executables go --- even if they're just symbolic links to
files to a main python repository in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/
pip installs things into the latter directory, but apparently does NOT
add the symbolic link to /opt/local/bin
This has never been an issue (or even come up) for me before, because
I've only used pip to install (non-executable) packages which load
from within python. In conclusion, there is a
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/tensorboard
This is a pip / MacPorts-SOP mismatch / user error*, and nothing to do
with tensorboard in particular. Please close this issue. Thanks for
your help.
*my 'locate' database was in the process of updating but hadn't completed
Quickest solution -
echo "alias tensorboard='python3 -m tensorboard.main'" >> ~/.bash_profile
After adding this to your .bash_profile you can use
tensorboard --logdir=/path
If you are using pycharm in windows environment this may help:
python -m tensorboard.main --logdir=logs