i trying install r package on python 3x in jupyter notebook.
i understand have pip install rpy2 , has been successful
this works fine when call built-in function in r such ccf or other easy issues.
# call function r import os os.environ['r_user'] = 'd:\anaconda3\lib\site-packages\rpy2' import rpy2.robjects robjects rpy2.robjects import pandas2ri pandas2ri.activate() however, if want install package such dirichletreg or vars, not easy there might more packages required downloaded.
i indeed followed link described in
r, python: install packages on rpy2
from rpy2.robjects.packages import importr utils = importr('utils') utils.install_packages('dirichletreg') but received following runtimeerror
--------------------------------------------------------------------------- rruntimeerror traceback (most recent call last) <ipython-input-16-32acf37e1ef9> in <module>() 1 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 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 found difficulty earlier?
jupyter notebook users (windows)
1) seems have been gone through r library not in same directory in python library
2) seems packages need installed in r first
to solve requires 2 major steps 1 in r , other in python jupyter notebook
step1: go r (rstudio)
code:
install.packages('dirichletreg', dep = true) this show
package ‘httpuv’ unpacked , md5 sums checked package ‘xtable’ unpacked , md5 sums checked package ‘sourcetools’ unpacked , md5 sums checked package ‘htmlwidgets’ unpacked , md5 sums checked package ‘shiny’ unpacked , md5 sums checked package ‘misctools’ unpacked , md5 sums checked package ‘rgl’ unpacked , md5 sums checked package ‘maxlik’ unpacked , md5 sums checked package ‘dirichletreg’ unpacked , md5 sums checked then load package in r
> loadnamespace('dirichletreg') it give output as:
<environment: namespace:dirichletreg> double check directory coding in r:
r.home() check output as
"c:/progra~1/r/r-33~1.3" trick!!!
this not place r downloading packages to. can see downloading coding in r:
.libpaths() say outcome xyz (copy this)
step 2: go jupyter notebook
check current r directory (i assume have rpy2 installed)
import rpy2 import os os.environ['r_user'] = 'd:\anaconda3\lib\site-packages\rpy2' rpy2.robjects.packages import importr base = importr('base') print(base.r_home()) the output be
"c:/program files/r/r-3.3.3" hence not match r library directory packages in xyz
hence import or install new package required to
dirichletreg = importr("dirichletreg", lib_loc = "xyz") this usaually work work me others
mi = importr("mi", lib_loc = "xyz") ggplot2 = importr("ggplot2", lib_loc = "xyz") but did not work dirichletreg gave me error
rruntimeerror: error in loadnamespace(name) : there no package called 'ggplot2' 
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