Unable to install R package in python (Jupyter notebook)?

Question

I am trying to install R package on python 3x in the jupyter notebook.

I understand that I have to pip install rpy2 and it has been successful

This works fine when I call a built-in function in R such as ccf or other easy issues.

# Call function from R
import os
os.environ['R_USER'] = 'D:\Anaconda3\Lib\site-packages\rpy2'
import rpy2.robjects as robjects
from rpy2.robjects import pandas2ri
pandas2ri.activate()

However, if I want to install a package such as DirichletReg or vars, it is not that easy especially that there might be more packages that are required to be downloaded.

I indeed followed the link as described in

R, Python: install packages on rpy2

from rpy2.robjects.packages import importr
utils = importr('utils')
utils.install_packages('DirichletReg')

but received the following RuntimeError

---------------------------------------------------------------------------
RRuntimeError                             Traceback (most recent call last)
<ipython-input-16-32acf37e1ef9> in <module>()
      1 from rpy2.robjects.packages import importr
      2 utils = importr('utils')
----> 3 utils.install_packages('DirichletReg')

D:\Anaconda3\lib\site-packages\rpy2\robjects\functions.py in __call__(self, *args, **kwargs)
    176                 v = kwargs.pop(k)
    177                 kwargs[r_k] = v
--> 178         return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
    179 
    180 pattern_link = re.compile(r'\\link\{(.+?)\}')

D:\Anaconda3\lib\site-packages\rpy2\robjects\functions.py in __call__(self, *args, **kwargs)
    104         for k, v in kwargs.items():
    105             new_kwargs[k] = conversion.py2ri(v)
--> 106         res = super(Function, self).__call__(*new_args, **new_kwargs)
    107         res = conversion.ri2ro(res)
    108         return res

RRuntimeError: Error in (function (pkgs, lib, repos = getOption("repos"), contriburl = contrib.url(repos,  : 
py2/R/win-library/3.3'\Anaconda3\Lib\site-packages

did anyone found this difficulty earlier?

Answer 1

Jupyter Notebook Users (Windows)

1) It seems that what I have been gone through was that the R library was not in the same directory as in the python library

2) It seems that some packages need to be installed in R first

To solve this requires 2 Major steps one in R and the other in Python Jupyter notebook

Step1: Go to R (Rstudio)

Code:

install.packages('DirichletReg', dep = TRUE)

This will show you that

package ‘httpuv’ successfully unpacked and MD5 sums checked
package ‘xtable’ successfully unpacked and MD5 sums checked
package ‘sourcetools’ successfully unpacked and MD5 sums checked
package ‘htmlwidgets’ successfully unpacked and MD5 sums checked
package ‘shiny’ successfully unpacked and MD5 sums checked
package ‘miscTools’ successfully unpacked and MD5 sums checked
package ‘rgl’ successfully unpacked and MD5 sums checked
package ‘maxLik’ successfully unpacked and MD5 sums checked
package ‘DirichletReg’ successfully unpacked and MD5 sums checked

Then load the package in R as

> loadNamespace('DirichletReg')

It will give an output as:

<environment: namespace:DirichletReg>

double check the directory by coding in R:

R.home()

Check the output as

"C:/PROGRA~1/R/R-33~1.3"

Trick!!!

This is not the place where R is downloading the packages to. You can see where it is downloading to by coding in R:

.libPaths()

Say the outcome is XYZ (copy this)

Step 2: Go to Jupyter notebook

Check the current R directory (I assume you have rpy2 already installed)

import rpy2
import os
os.environ['R_USER'] = 'D:\Anaconda3\Lib\site-packages\rpy2'
from rpy2.robjects.packages import importr
base = importr('base')
print(base.R_home())

the output will be

"C:/Program Files/R/R-3.3.3"

Hence does not match with the R library directory where packages are in XYZ

hence to import or install the new package all required is to

DirichletReg = importr("DirichletReg", lib_loc = "XYZ")

This will usaually work like it work with me for all others

mi = importr("mi", lib_loc = "XYZ")
ggplot2 = importr("ggplot2", lib_loc = "XYZ")

But it did not work for DirichletReg it gave me the error

RRuntimeError: Error in loadNamespace(name) : there is no package called 'ggplot2'