I want to read a python file in R and I am using reticulate package for that.
I have certain packages in python file. Do I have to install them in R env again somehow, for the file to run? And how do I do that?
I am getting this error:
Error in py_run_file_impl(file, local, convert) :
ModuleNotFoundError: No module named 'descartes'
How do I fix this?
What worked for me was first installing the python customLibrary via the python command line interface.
Second, in my R project folder I specified the python function in a file customLibrary.py which specifies import as first line, such as:
import customLibrary as CL
def custoFunction(path):
A = CL.test(path)
return(A)
Third, I call the function from R via standard reticulate::source_python("customLibrary.py") implementation (You may need to check whether your directory-path is correct via R command getwd().)
It may be helpful to start with small steps to narrow down the issue:
just write a simple function, such as "addThree" that is essentially y = x + 3 etc.
try to execute it in python
try to execute if from R
If both works you can try to do the same thing with the custom library.
Related
I am new to Julia. I developed a few lines of code to get the results I needed from packages I was not able to find in Python or R. Now, I am trying to get this file to be easily accessible, and wrap the code in Python or R. Has anyone done this before? I have tried a few methods and have not found anything that has helped.
The most simple way to do this would be just a few lines of code that calls the .jl file, runs it (which the code is then added to a .txt file from julia), and then alerts you when the code is done.
Any help would be greatly appreciated. R is the preferable method and at this point Python would be appreciated as well.
Please find below instructions for Python, R and just an external process (which of course is an executable command that can be run from any other process). I recommend putting your code in a package and loading it in one of those languages rather than executing this as an external process.
Python
Use Python Anaconda (not in-built system Python) and install Julia
Run Julia and install PyCall
using Pkg
ENV["PYTHON"]="/path/to/your/python/executable"
pkg"add PyCall"
pkg"build PyCall"
Put your code into a Julia package
using Pkg
Pkg.generate("MyPackage")
In the folder src you will find MyPackage.jl, edit it to look like this:
module MyPackage
function main(x,y)
#do very complex staff or place it in your_other_file.jl
2x.+y
end
include("your_other_file.jl")
export main, and_whatever_other_functio_you_defined
end
Install pyjulia
python -m pip install julia
(On Linux systems you might want to use python3 instead of python command)
For this step note that while an external Python can be used with Julia. However, for a convenience it might be worth
to consider using a Python that got installed together with Julia as PyCall.
In that case for installation use a command such this one:
%HOMEPATH%\.julia\conda\3\python -m pip install julia
or on Linux
~/.julia/conda/3/python -m pip install julia
Note that if you have JULIA_DEPOT_PATH variable defined you can replace %HOMEPATH%\.julia or ~/.julia/ with its value.
Run the appropiate Python and tell it to configure the Python-Julia integration:
import julia
julia.install()
Now you are ready to call your Julia code:
>>> from julia import Pkg
>>> Pkg.activate(".\\MyPackage") #use the correct path
Activating environment at `MyPackage\Project.toml`
>>> from julia import MyPackage
>>> MyPackage.main([1,2],5)
[7,9]
Gnu R
Configure your system PATH variable to point to your Julia location. Hence when you type julia in the console it should start Julia
Run the script below to install R-Julia integration
install.packages("JuliaCall")
library(JuliaCall)
julia <- julia_setup()
Follow the above instructions for Python (step 3 only) and create the package named MyPackage
Run the code
library(JuliaCall)
julia_eval("using Pkg;Pkg.activate(\"C:/temp/rrr/MyPackage\")")
julia_library("MyPackage")
julia_eval("MyPackage.main(3,5)")
Bash (or just any language)
Build the package following instructions for Python (step 3 only)
Configure the system PATH variable
Being in the package directory run the command (note string(:.) is a Julian trick that I use to avoid apostrophe escaping in bash commands):
julia -e "using Pkg;Pkg.activate(string(:.));Pkg.instantiate();using MyPackage;MyPackage.main(3,4)"
This will install all dependencies for your package. In order to skip the installation remove Pkg.instantiate() from the above command.
The answer from #przemyslaw-szufel is correct but maybe a bit overcomplicated. You don't necessarily need to wrap your code in a module or define a custom environment (yes it is good practice, but a step at the time...)
First create a file juliaScripts.jl with content:
function getAnElement(array,n)
return array[n]
end
To run functions defined in a .jl file in R
Then in R you just do:
> install.packages("JuliaCall")
> library(JuliaCall)
> julia_setup() # on every new R session !
> julia_source("juliaScript.jl")
> out <- julia_call("getAnElement",c(10,20,30),2)
> out
[1] 20
Note that the R vector has been automatically converted to a Julia Array.
To run functions defined in a .jl file in Python
In Python, it is even easier:
$ python3 -m pip install --user julia
>>> import julia
>>> julia.install() # only once, not every session
>>> jl=julia.Julia(compiled_modules=False)
>>> from julia import Main
>>> Main.include("juliaScript.jl")
>>> Main.getAnElement([1,2,3],2)
20
Also in Python arrays (native python lists as well Numpy arrays and other commonly used data structures) are automatically converted between Python and Julia.
Not to make advertising, but more details on interfacing R <-> Julia or Python <-> Julia are on my Apress(2019) book "Julia Quick Syntax reference" in Chapter 7 "Interfacing Julia with other languages" (I shouldn't say it, but you can easily find the pdf online in well-known sites...)
Using the JuliaConnectoR package:
library(JuliaConnectoR)
fun <- juliaCall("include", "/path/to/file.jl") # you may need to provide the full path
For more info on JuliaConnectoR, see the link above as well as this paper, which additionally compares it to alternative packages suck as JuliaCall and XRJulia.
I'm working on a web application using Dash, and I would like to use arules and aruleViz from R within a python script to get a graph of association rules obtained by using an Aprioi algorithm.
I found the rpy2 package and I installed it using conda conda install rpy2 ,then I try to import some packages like base tools by:
from rpy2.robjects.packages import importr`
arules = importr("tools",)`
That was fine(the package was imported)
And when I use: arules = importr("arules",) or arules = importr("arulesViz",)
I got receive the following error:
RRuntimeError: Error in loadNamespace(name) : there is no package called ‘arulesViz’
I saw an option in the importrpackage (lib_loc=None). I'm not sure how can I change it.
If there is any way to solve this, or if you know of a package in python that will help me plot a graph with vertices (I know how to so that with matplot.lib library using scatter but i'm not happy with it) I would greatly appreciate the help!
Thank you!
R packages must be installed before rpy2 can hope to find them. rpy2's importr() relies on R's own package loading system.
If you are certain to have installed that package earlier, you might have installed it in different directory, in a previous R process, and your current R process does not know about that directory. The optional named argument lib_loc accepts the path to that directory (see the doc).
(Note that there is also a utility function to check if an R package is installed without loading it)
Working with R in Python using rpy2 on windows 7.
I need to open some rasters as RasterLayer using the function raster() from the raster package. I manage to install the package, but not to use its function.
I install the packages that I need (rgdal, sp, raster, lidR, io) using
utils.install_packages(StrVector(names_to_install))
names_to_install is a list of the packages that are still not installed. This works fine.
I know how to try the "basic" functions, like sum, and it works:
import rpy2.robjects as robjects
function_sum = robjects.r['sum']
But the same doesn't seem to work with the raster function from the raster package:
function_raster = robjects.r['raster']
since I get the error:
LookupError: 'raster' not found
I also tried the following:
raster_package = importr('raster')
with the intention to be able to run the next and load my raster file:
raster_package.raster(my_raster_file)
but the first line (import('raster')) causes the crash of python and I get the error:
Process finished with exit code -1073741819 (0xC0000005)
This doesn't happen with other loaded packages like rgdal, but with the raster package and with the lidR package I get the error.
I looked up this error, seems to be access violation, but I don't know what I can do about it and why it only happens with certain packages.
I expect to be able to call the raster function from the package raster.
Edit
I tried it on a computer with windows 10 and the error doesn't show anymore when running
raster_package = importr('raster')
Still would be nice to know what is the problem with Windows 7 and if there is any solution.
rpy2 does not currently have Windows support. This is not a final situation, most of what is likely needed is contributions to finalize this: https://github.com/rpy2/rpy2/blob/master/rpy2/rinterface_lib/embedded_mswin.py
Iam new bee to the jmeter
My code is working in the Python 2.7 with importing additional packages Dateutil, parser .
Problme : But when I am trying to run same code in the J Meter-JSR-223 PreProcessors , an error saying No module named dateutil in.
So , I have tried another approach to use Jython .
Installed the Jython ( downloaded the dateutil) and provide the packages reference under
import sys
sys.path.append('C:/Jython27/Lib/site-packages')
sys.path.append('C:/Jython27/Lib/site-packages/python_dateutil-2.4.2-py2.7/dateutil')
sys.path.append('C:/Jython27/Lib/site-packages/python_dateutil-2.4.2-py2.7/dateutil')
Now packages error is gone but string syntax error is present .
java.sql.Date' object has no attribute .
I believe dateutil package can be picked up from CPython as it doesn't require any extra wrappers for Java.
Install dateutil normally using pip like:
pip install python-dateutil
Add site-packages folder of Python (not Jython) installation to sys.path like:
sys.path.append("C:\Python27\Lib\site-packages")
That's it, now you should be able to use dateutil module functions from the JSR223 Test Elements:
Be aware that invoking Python scripts via Jython interpreter is not the best idea from performance perspective and if you're about to invoke your Python code only limited number of times and/or with a single thread - it might be better to go for the OS Process Sampler.
If you plan to use the Python code to create the main load - consider using Locust tool instead of JMeter. If you don't want to change JMeter a good approach would be rewriting your Python code in Groovy - it will be way better from the performance perspective.
hi please find follwing
import sys
sys.path.append('C:/Python27/Lib/site-packages')
sys.path.append('C:/Python27/Lib/site-packages/python_dateutil-2.4.2-py2.7/dateutil')
from dateutil.parser import *
sourceDateTimeOfEvent = ""
dateTimeOfEvent = ""
a=parse('2016-07-01 13:00:00')
sourceDateTimeOfEvent = a.isoformat()+"+05:30Z"
dateTimeOfEvent = a.isoformat()+ "Z"
vars.put("sourceDateTimeOfEvent", sourceDateTimeOfEvent)
vars.put("dateTimeOfEvent", dateTimeOfEvent)
This sourceDateTimeOfEvent and dateTimeOfEvent considered as two variables and passed it to the json file
For context: My goal is to create a graphic interface so that the user can run a program that I have been developing in R. The interface is done using the Tkinter module from python (version 3.3). Right now I am trying to make it work in Windows.
I believe I have successfully called the R interpreter using python to run my R file (run.R). In this file I call the R package 'seqinr'. However when I call the R interpreter from python I obtain this:
I run this:
os.system('C:/"Program Files"/R/R-3.6.1/bin/Rscript run.R')
and I obtain this:
Error in library(seqinr) : there is no package called 'seqinr'
Calls: source -> withVisible -> eval -> eval -> library
Execution halted
However, when I run the 'C:/"Program Files"/R/R-3.6.1/bin/Rscript run.R' command in the Command Prompt, it works perfectly and I have no problems.
I also checked where my package is installed and it's in the default directory that R uses to install all the packages. I also do not have any other R versions installed in my machine.
I have no clue what is happening now, so I would appreciate any help.
Thank you!
Although probably not satisfactory, I'd recommend changing your "run.R" file to include the following lines:
if (!("seqinr" %in% installed.packages())) {
install.packages('seqinr', repos = "https://cloud.r-project.org")
}
library(seqinr)
This will install the package if it isn't available to wherever R is looking for packages when being called from Python. Additionally, you could include print(rownames(installed.packages())) in your "run.R" file to see what packages are currently available to your R installation at run time when calling from Python. Inclusion of the line print(.libPaths()) will tell you where R is looking for installed packages at run time as well.