I am trying to import a python module in R using the reticulate package. The module can be found here. I cloned the repository and ran python setup.py install which ran successfully. If I open a python shell, I'm able to import debot. However, when I try to import it in RStudio, I get the following error:
dbot=import("debot")
Error in py_module_import(module, convert = convert) :
ImportError: No module named debot
I am on macOS Sierra version 10.12.6 and installed python 3.6 through Anaconda. I have also tried giving the path to python as:
path_to_python <- "/anaconda/bin/python3.6"
use_python(path_to_python)
When I run python from a terminal, I get:
Python 3.6.1 |Anaconda 4.4.0 (x86_64)| (default, May 11 2017, 13:04:09)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Not sure if the path to python is correct.
Ok, did some more digging around and discovered that reticulate still refers to my older python path for python 2.7 which came as default with my Macbook. When I run py_config(), this is what I get:
python: /usr/bin/python
libpython: /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib
pythonhome: /System/Library/Frameworks/Python.framework/Versions/2.7:/System/Library/Frameworks/Python.framework/Versions/2.7
version: 2.7.10 (default, Feb 7 2017, 00:08:15) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
No matter what I try but I can't get reticulate to look at the correct path where the module has been installed using the use_python() function. I do believe this is an issue with reticulate. Any ideas what my next steps should be?
After reading this I finally figured out. I think before calling any other function from the reticulate package, it is imperative to specify the path to python to use. Hence the order I am following now is:
library(reticulate)
path_to_python <- "/anaconda/bin/python"
use_python(path_to_python)
Related
I have followed all the possible suggestion on stack overflow with no success.
When I run python --version the result :
Home-Macbook-Pro:~ pcmac$ python
WARNING: Python 2.7 is not recommended.
This version is included in macOS for compatibility with legacy software.
Future versions of macOS will not include Python 2.7.
Instead, it is recommended that you transition to using 'python3' from within Terminal.
Python 2.7.16 (default, Jun 5 2020, 22:59:21)
[GCC 4.2.1 Compatible Apple LLVM 11.0.3 (clang-1103.0.29.20) (-macos10.15-objc- on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit ()
How can I uninstall or force terminal to use Python version 3.8 please
Also the IDLE is running on old Python version 2.7.16
I had the same issue and this solution worked for me:
I am using macOS Catalina version 10.15.6 and used homebrew to install python 3.8.5.
All I did was type 'nano .zprofile' in terminal and then typing: alias python='python3' and saving it by hitting Ctrl+o and then Enter.
I am trying to make a Python script on my Mac (MacOS 10.14.6 Mojave) and I am getting trouble with installing a module (watchdog). I have the built-in Python 2 and I installed Python 3 with Homebrew.
If a type in the terminal python, I get:
Python 2.7.16 (default, Oct 16 2019, 00:34:56)
[GCC 4.2.1 Compatible Apple LLVM 10.0.1 (clang-1001.0.37.14)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
So Python 2 correctly uses GCC (the one provided by Apple? I am not sure) instead of Clang. Now, if I do python -m pip install watchdog it just works. But I want to install the module on Python 3, that for some reason uses Clang instead of GCC. In fact, if I type `python3', I get:
Python 3.8.0 (v3.8.0:fa919fdf25, Oct 14 2019, 10:23:27)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
I assume that as a consequence python3 -m pip install watchdog gives a compile error because Python 3 is not using GCC. The error message is very long and can be found here: https://pastebin.com/DEAKANQ9
In my $PATH I have /usr/local/bin (where gcc is installed) before /usr/bin, i.e.
echo $PATH
/Library/Frameworks/Python.framework/Versions/3.8/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin
I would say everything is set up correctly, but apparently that is not the case. How can I make Python 3 use GCC instead of Clang?
I have fixed the issue.
First, I have removed Python 3.8 which was installed using the pkg installer (by accident actually). Then, I have created an alias for Python 3 in the .bash_profile. Another mistake was that I created the file ~/.bashrc (as in Ubuntu) instead of editing the file ~/.bash_profile to modify the $PATH.
# ~/.bash_profile
#
# Python alias
alias python=/usr/local/bin/python3
# Setting PATH for Python 3.7.5 (Homebrew)
PATH="/usr/local/bin:${PATH}"
export PATH
# Set module path
PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.7/site-packages
# Set PATH priority to Homebrew installation folder
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
With this settings, I was able to install the module and make it work in my script!
I am using anaconda on mac-osx and have installed python-igraph. Currently not being able to import igraph.
Below is the error shown:
Python 2.7.12 |Anaconda 4.1.1 (x86_64)|
import igraph ----
ImportError: No module named igraph
It is present in this path - /Users/pc_name/anaconda/lib/python2.7/site-packages and I find only python_igraph-0.7.1.post6-py2.7.egg-info file.
I tried many things possible which are available on the other questions here at stack overflow. How can I solve this problem?
I used the following command and it worked for me in Python 3.7
pip install python-igraph
The detail about the package and its installation can be found
https://igraph.org/python/
You haven't mentioned how you installed python-igraph so it's hard to say anything. But I'm pretty sure that this package works nicely.
1)While in the python-igraph-master directory on my computer run the following:
conda install -c marufr python-igraph
2)In a new terminal window kick start python:
$python
Python 2.7.13 |Anaconda 4.3.1 (x86_64)| (default, Dec 20 2016, 23:05:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import igraph
>>>
I hope this helps
OSX. When I installed the Canopy IDE, Enthought Canopy Python 2.7.6 was set as the default Python for the bash shell:
$ python
Enthought Canopy Python 2.7.6 | 32-bit | (default, Sep 15 2014, 17:36:57)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
Currently, I am using another IDE (PyCharm) for a project where a Python module is needed. I tried to download the module directly from the bash shell using pip but it did not work:
pip install psycopg2 <---module
I believe it has something to do with Enthought Canopy Python running, so I attempted to restore the original python. However, I could not restore it. The instructions from this Enthought post (2011) did not work:
OS X - After EPD installation, restore system python to be default
They say to comment out the following lines from the ~/.bash_profile file, save the changes and restart the bash shell:
# PATH="/Library/Frameworks/Python.framework/Versions/Current/bin:${PATH}"
# export PATH
Didn't work.
Hi there I have downloaded the mac installer here, http://www.python.org/download/releases/3.1.2/ , & installed it. But when I run terminal & type python it says:
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
What I want to know is, is it safe to run Update Shell Profile.command in the Python 3.1 folder ? or should I run python 3.1.2 separately ? If I should run python 3.1.2 separately, how do I do so ? also how do I start IDLE ?
Is there another python executable, perhaps python31?
You can also install other python versions via MacPorts if you need (although you'll still have to choose the right executable).
This should also be relevant: Multiple versions of Python on OS X Leopard