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)
Related
I was wondering if you have used the library "trimesh" in python. It looks quite useful, but right now im having some trouble with the method "Trimesh.spli()" on the last line of the code attached. the code was working fine up to that line, which is suppose to return a list of trimesh objects.
However, when I try to run this code, I get the error ImportError: no graph engines available!
Do you know how can I set up a graph engine? or if there is any turnaround this issue?
Thanks for your support,
Regards
import numpy as np
import trimesh
# Load the stl files into the script
mesh = trimesh.load('Path_to_STL_file')
mesh2 = trimesh.load('Path_to_raw_material_in_STL')
# Confirm both files are closed
assert mesh.is_watertight
assert mesh2.is_watertight
#Boolean operation
mesh3 = trimesh.Trimesh.difference(mesh2,mesh)
list_mesh = trimesh.Trimesh.split(mesh3)
I found the issue. The library does not install all dependancies unless you ask for it. Usually, it only requires numpy.
One option to install most of the dependancies is:
pip install trimesh[easy]
or, if that doesn't solve it, you could use:
pip install trimesh[all]
You need to also install either scipy or networkx to satisfy the graph engine dependency. There's a comment in the source code that networkx is 5-10 times slower than scipy so it's probably best to install scipy. If you're using pip then it's
pip install scipy
or if you're using conda:
conda install scipy
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
I have installed spacepy using the following command (MacOS Mojave):
pip install git+https://github.com/spacepy/spacepy.git
But I keep getting this error while trying to from spacepy import pycdf:
Exception: Cannot load CDF C library; checked . Try 'os.environ["CDF_LIB"] = library_directory' before import.
I have tried following the directions from their website, but it seems like those directions are a bit outdated.
You can do something like:
import os
os.environ["CDF_LIB"] = "~/CDF/lib" # Give the path of the cdf library
# e.g. in this case the library is in your home directory.
Before doing:
from spacepy import pycdf
Source of the error can be found on this SpacePy website.
The cdf library is available here.
Basically, you need to set up the CDF_LIB (if pycdf has a trouble finding it) before importing the module. You can read the documentation here.
I need this library "plot_utils" for analysis and plotting but I can't find it in the web. this library is related to Brian2 (a library in python) for spiking neural network.
I installed brian2 through anaconda. when I want to import plot_utils and using in my code I receive error :
ModuleNotFoundError: No module named 'plot_utils'
Could you please help me?
You need to give more info about where did you stumble upon that name, eg some copied code etc.
With the only reference you've given (ie. brian2) this seems related.
https://brian2.readthedocs.io/en/stable/examples/frompapers.Stimberg_et_al_2018.plot_utils.html
Maybe just copy that code into a file named 'plot_utils.py' and keep it at the path your code is searching for it.
First, you need to install the module in your work environment using "pip install plot_utils" then you can import the library using "import plot_utils".
This link will help you: https://libraries.io/pypi/plot-utils[this is the official documentation from plot_utils]
It's my first time using R in jupyter. I've installed everything like jupyter, python, R and lRkernel. I can use just typing or calculation in jupyter but whenever I want to use a graph library like plot or ggplot2 it shows
Error in loadNamespace(name): there is no package called 'Cairo'
Traceback: plot without title
Someone please guide me about how to handle this issue.
I had the precise same issue and fixed it by installing Cairo package:
install.packages("Cairo")`
library(Cairo)
Thanks to my collegue Bartek for providing this solution