First, I'm working on a Windows machine. I would like to specify a specific version of python to use in RStudio. I would like RStudio to use python 3 in the ArcGIS Pro folder in order to have arcpy available, along with the licensed extensions. I have reticulate installed and have tried the following methods to force RStudio to use the ArcGIS Pro version of python.
First I tried this:
library(reticulate)
use_python("C:/Program Files/ArcGIS/Pro/bin/Python/envs/arcgispro-py3/python.exe", required = TRUE)
The resulting error:
Error in path.expand(path) : invalid 'path' argument
Following some other tips, I tried setting the environment before loading the reticulate library.
Sys.setenv(RETICULATE_PYTHON = "c:/Program Files/ArcGIS/Pro/bin/Python/envs/arcgispro-py3/python.exe")
library(reticulate)
Then I retrieve information about the the version of Python currently being used by reticulate.
py_config
Error in path.expand(path) : invalid 'path' argument
I also tried creating and editing the .Renviron by using the usethis package
usethis::edit_r_environ()
Then entering the following
RETICULATE_PYTHON="C:/Program Files/ArcGIS/Pro/bin/Python/envs/arcgispro-py3/python.exe"
And saving it, restarting R..
library (reticulate)
py_config()
Error in path.expand(path) : invalid 'path' argument
And, to confirm, here is the location...
Any ideas on why I continue to receive invalid 'path' argument
I was having a similar issue. After trying a whole assortment of things, I finally installed an archived version of reticulate (reticulate_1.22) instead of using the most up-to-date version (reticulate_1.23) and now the issue is gone. It appears that this bug has been brought to the developers' attention (https://github.com/rstudio/reticulate/issues/1189).
Try using
use_python("C:/Program Files/ArcGIS/Pro/bin/Python/envs/arcgispro-py3")
Have you tried replacing Program Files with PROGRA~1 and have you maybe also checked for example a command like dir("path/to/your/env") although tbh your screenshot looks ok;
btw just in case - after editing your .Renviron file you need to restart your RStudio/R session for changes to take effect;
RStudio version 2022.02 has Python interpreter selection now available in Global Options
I ran into the same error with R version R-4.1.1, but when I switched back to the previous version R-4.0.5 everything worked as expected. It's a quick workaround but doesn't solve the underlying issue in the current version.
Related
I am new with programming, so it is maybe harder for me to understand but I have the following issue:
I have a script that imports "eurostag.dll", which according to its manual, should work until Python 3.6. (but the manual is not updated, so it may work also with later updates, I assume).\ The issue is that I have Python 3.8. and when running the script I receive the following message:
"Failed to load EUROSTAG library (Could not find module 'D:\Eurostag\eustag_esg.dll' (or one of its dependencies). Try using the full path with constructor syntax.)"
I have tried to move the .dll library where the script is, but nothing changed. I tried also changing the directory with os.chdir, but the same message appears (with the same 'D:\Eurostag\eustag_esg.dll', so the directory was not changed.
Does anybody know if there is any workaround for this?
Thank you!
I want to use a specific Python version: /Users/aviral.s/.pyenv/versions/3.5.2/bin/python. This version is not available for R.
I tried reading the documentation but following all the three steps(setting the env variable, using the API use_python() didn't help either.
With sudo, I run the following code:
library("reticulate")
py_config()
use_python("/Users/aviral.s/.pyenv/versions/3.5.2/bin/python")
py_config() # Unchanged.
I tried using any of the available ones in the py_config() which worked by setting the environment variable as in here
However, if I set the same env variable to my pyenv version, I get this error:
> library("reticulate")
> py_config()
Error in initialize_python(required_module, use_environment) :
Python shared library not found, Python bindings not loaded.
My env variable is correct:
echo $RETICULATE_PYTHON
/Users/aviral.s/.pyenv/versions/3.5.2/bin/python
I ran into the same problem a few days ago and i had to jump through all kinds of hoops to get where i wanted and i am not sure which one did it for me, but what definitely helped was using py_discover_config() instead of the regular py_config() command.
what might be another problem, is that apparently a python version with installed numpy will always be preferred by reticulate:
I am a big fan of Rstudio Cloud and would like to inter-grate R and Python by using the package Reticulate.
It looks like Rstudio Cloud is using python 2.7 (no problems with that). When I try to write Python Code in an R markdown document, nothing gets run.
---
title: "reticulate"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(reticulate)
py_config()
```
```{python}
import pandas
x = 4
```
Python code does not get run.
I am also finding that if I want to install python packages in an R script using reticulate. I have to create a virtual environment. What is the reason behind that?
library(reticulate)
virtualenv_create("r-reticulate")
virtualenv_install("r-reticulate", "scipy")
virtualenv_install("r-reticulate", "pandas")
If I use conda_install, I get an error message.
conda_create("r-reticulate")
Error: Unable to find conda binary. Is Anaconda installed?
conda_install("r-reticulate", "scipy")
Error: Unable to find conda binary. Is Anaconda installed?
The goal is to have python working in Rstudio cloud on R markdown. I can not install packages and execute code.
I just succeeded in getting Conda installed in Rstudio cloud after receiving the same error message as you1, so thought I'd share how I got this working.
I created two scripts:
to install miniconda (i think that's the step you're missing, and why Conda didn't work for you) and then restartSession for this to be accessible
to seperately store the commands for setting up Conda, with the running of this script passed as a command to the call to restartSession (because otherwise the commands are triggered before R has restarted, and they fail; sys.sleep() didn't seem to work, but this method did)
setup.R
setwd("/cloud/project") # to ensure students get required resources
install.packages("rstudioapi") # to restart R session w/ installations
install.packages("reticulate") # for python
reticulate::install_miniconda("miniconda") # for python
# Restart again to make sure all system things are loaded
# and then create a new Conda environment
rstudioapi::restartSession(command="source('nested_reticulate_setup.R')")
nested_reticulate_setup.R
reticulate::conda_create("r-reticulate")
reticulate::conda_install("r-reticulate", "scipy")
Sys.setenv(RETICULATE_PYTHON="/cloud/project/miniconda/envs/r-reticulate/bin/python")
reticulate::use_condaenv("r-reticulate")
osmnx <- reticulate::import("scipy")
Then if you make a call to scipy, eg scicpy$`__version__` , I believe it should work for you without that error you observed.
I couldn't find a solution to this issue elsewhere, so thought it worth responding to this old post in case it helps somebody some day. I am sure there are other ways of approaching this.
1 Perhaps for a different reason; i'll explain later in the post...
One thing I can't get over - when I use numpy in Visual Studio and I want to declare an array of zeroes, I write:
x = numpy.zeros(n)
and it is correct for the interpreter. BUT THE AUTOCOMPLETION GIVES ME:
X = numpy.zeros_like ...
How can I change it to get actually helpful autocompletion? In C++ I get everything allright, so I guess it's an internal problem in Python case.
Edit: As I see the problem is that numpy.zeros is defined in numeric.py as:
zeros = multiarray.zeros. Apparently this is not enough for IntelliSense (or VisualAssist for this matter), which requires def function to actually see the structure.
You need to install the python 3.5 and download the corresponding wheel for numpy. Then using the command: pip install xxxx(numpy wheel version that you download) to install it. For more the detail information about the installation staff, you can have a look at this.
Then open or create a python application project in VS and set the python 3.5 as the default environment, then I can found the intellisense for numpy.zeros also works fine in .py file like the following screenshot: (python 3.5)
If set the python 2.7 as the default environment, the intellisense just like your description as below:
I am trying to import the brew installed version of python by emulating the Global Libraries structure existing for the (mostly) working mac os built-in 2.7.2. However IJ is unable to infer the types or to create the library properly.
Update this is a large existing project. Creating a new project just to get a different version of python is not an option.
Here are the steps:
Try to create new Global Library: Fail : no python .
OK, so I use Copy to clone the built-in SDK:
Now - let us try to emulate the paths included in the original built-in but with the brew base dir: here is a starting point:
And here is one of the exact entries from the builtin library:
So let us clikc on the + to add it:
So .. IJ is unable to handle it properly. I also tried a half dozen others - all with same shrug result from IJ.
So then what is the correct process?
Update Here is the project SDK dialog (thanks to scribbles).
And trying to add: **but the "OK" button is not enabled! So then IJ is not able to load it..
New Project -> Select SDK.
See this video if you still have any questions.
EDIT: Is this more along the lines of what you're looking for (link)?
This is old, but but I ran into the same problem with the current Python 2 install from homebrew in High Sierra. Instead of choosing a directory like it needed in the previous setup, I just setup the Python SDK pointing to the python executable link in /usr/local/opt/python/libexec/bin (which is the directory I added to my path for Python 2. It seems to be working just fine now.
Hopefully this will help someone.