I am trying to call R from within some python code using the rpy2 library. I need to use non-base packages, but keep on running into the following hiccup. Thanks for considering! Most of the code is copy-pasted from the manual.
import rpy2
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
# import rpy2's package module
import rpy2.robjects.packages as rpackages
base = importr('base')
# import R's utility package
utils = rpackages.importr('utils')
# select a mirror for R packages
utils.chooseCRANmirror(ind=1) # select the first mirror in the list
# R package names
packnames = ('pROC', 'bootLR')
# R vector of strings
from rpy2.robjects.vectors import StrVector
# Selectively install what needs to be install.
# We are fancy, just because we can.
names_to_install = [x for x in packnames if not rpackages.isinstalled(x)]
if len(names_to_install) > 0:
utils.install_packages(StrVector(names_to_install))
importr('bootLR')
Gives error
---------------------------------------------------------------------------
RRuntimeError Traceback (most recent call last)
<ipython-input-27-359b2847dddf> in <module>
1 utils.install_packages("bootLR")
----> 2 importr('bootLR')
~/opt/anaconda3/lib/python3.7/site-packages/rpy2/robjects/packages.py in importr(name, lib_loc, robject_translations, signature_translation, suppress_messages, on_conflict, symbol_r2python, symbol_check_after, data)
451 if _package_has_namespace(rname,
452 _system_file(package = rname)):
--> 453 env = _get_namespace(rname)
454 version = _get_namespace_version(rname)[0]
455 exported_names = set(_get_namespace_exports(rname))
RRuntimeError: Error in loadNamespace(name) : there is no package called ‘bootLR’```
My code
!pip install stldecompose
from stldecompose import decompose
Error Msg
ImportError Traceback (most recent call last)
in
2 # Install the library via PIP
3 get_ipython().system('pip install stldecompose')
----> 4 from stldecompose import decompose, forecast
~/opt/anaconda3/lib/python3.7/site-packages/stldecompose/init.py in
----> 1 from .stl import decompose, forecast
~/opt/anaconda3/lib/python3.7/site-packages/stldecompose/stl.py in
3 from pandas.core.nanops import nanmean as pd_nanmean
4 from statsmodels.tsa.seasonal import DecomposeResult
----> 5 from statsmodels.tsa.filters._utils import _maybe_get_pandas_wrapper_freq
6 import statsmodels.api as sm
7
ImportError: cannot import name '_maybe_get_pandas_wrapper_freq' from 'statsmodels.tsa.filters._utils' (/Users/georgeng/opt/anaconda3/lib/python3.7/site-packages/statsmodels/tsa/filters/_utils.py)
You have two pathway to go about this:
If you are running statsmodels==0.11.0, statsmodels.tsa.filters._utils function was removed from the library.
Alternatively you may use statsmodels.tsa.seasonal.STL, which gives similar functionality. See its documentation:
https://www.statsmodels.org/stable/generated/statsmodels.tsa.seasonal.STL.html#statsmodels.tsa.seasonal.STL
Downgrade to pip install statsmodels==0.10.2
I am using Jupyter notebook in anaconda and try to use the pvclust to perform hierarchical clustering on my data.
My codes:
from rpy2.robjects import r, pandas2ri
from rpy2.robjects.packages import importr
pandas2ri.activate()
base = importr("base")
pvclust = importr("pvclust")
But I got the error:
RRuntimeError Traceback (most recent call last)
<ipython-input-51-291b18105962> in <module>()
3 pandas2ri.activate()
4 base = importr("base")
----> 5 pvclust = importr("pvclust")
6 # data = robjects.DataFrame.from_csvfile(filepath + folders[0] + '\\vcfA_filled.csv')
7 # data
~\Anaconda3\lib\site-packages\rpy2-2.9.1-py3.6-win-amd64.egg\rpy2 \robjects\packages.py in importr(name, lib_loc, robject_translations, signature_translation, suppress_messages, on_conflict, symbol_r2python, symbol_check_after, data)
451 if _package_has_namespace(rname,
452 _system_file(package = rname)):
--> 453 env = _get_namespace(rname)
454 version = _get_namespace_version(rname)[0]
455 exported_names = set(_get_namespace_exports(rname))
RRuntimeError: Error in loadNamespace(name) : there is no package called 'pvclust'
It seems I need to install the pvclust first? But I am using jupyter notebook (python3.6) launched by anaconda and I am confused how to get a R package like this preinstalled and then import from rpy2?
P.S. Is there any Python package that can perform hierarchical clustering with p-value? All I need is to use some function that can bootstrap my data and cluster the data with p-values.
Thanks a lot.
Please let me know the procedure, what settings needed to call R packages from Python.
I use Spyder (python 2.7)
I am trying to call apriori package from Python.it fails in arules.
Any help would be appreciated.
I already tried the following
import rpy2
from rpy2 import *
import rpy2.interactive as r
arules = r.packages.importr("arules")
from rpy2.robjects.vectors import ListVector
od = OrderedDict()
od["supp"] = 0.0005
od["conf"] = 0.7
od["target"] = 'rules'
result = ListVector(od)
dataset = 'c:/Apriori/testcase.txt'
my_rules = arules.apriori(dataset, parameter=result)
print('my_rules',my_rules)
I'm using Rpy2 on windows 7 64 and having trouble loading a package:
in R:
using(mi)
in python:
from rpy2.robjects.packages import importr
mi=importr('mi')
---------------------------------------------------------------------------
RRuntimeError Traceback (most recent call last)
<ipython-input-30-2d393a6df544> in <module>()
----> 1 mi=importr('mi')
C:\Anaconda\lib\site-packages\rpy2\robjects\packages.pyc in importr(name, lib_loc, robject_translations, signature_translation, suppress_messages, on_conflict, data)
397 if _package_has_namespace(rname,
398 _system_file(package = rname)):
--> 399 env = _get_namespace(rname)
400 version = _get_namespace_version(rname)[0]
401 exported_names = set(_get_namespace_exports(rname))
RRuntimeError: Error in loadNamespace(name) : there is no package called 'm
Any suggestions?
I had a similar problem:
rpy2.rinterface.RRuntimeError: Error in loadNamespace(name) : there is no package called speedglm
I noticed that the issue is that rpy2 does not know the location of all R libraries. In my case, typing (in R)
.libPaths()
gave me
[1] "/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4"
[2] "/usr/lib64/R/library"
[3] "/usr/share/R/library"
While, typing (in Python 3)
import rpy2.rinterface
rpy2.rinterface.set_initoptions((b'rpy2', b'--no-save', b'--no-restore', b'--quiet'))
from rpy2.robjects.packages import importr
base = importr('base')
print(base._libPaths())
gave me only
[1] "/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4"
I couldn't find a way to append the other two paths to base._libpath(). If you find a way to do it, please let me know. I used another workaround:
import rpy2
import rpy2.robjects as RObjects
from rpy2.robjects.packages import importr
utils = importr("utils")
d = {'print.me': 'print_dot_me', 'print_me': 'print_uscore_me'}
try:
thatpackage = importr('speedglm', robject_translations = d, lib_loc = "/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4")
except:
try:
thatpackage = importr('speedglm', robject_translations = d, lib_loc = "/usr/lib64/R/library")
except:
thatpackage = importr('speedglm', robject_translations = d, lib_loc = "/usr/share/R/library")
This works. I hope other people who have the same problem find this useful.
For me, in importr, the argument lib_loc inside it worked, putting the first path that appears in the output of .libPaths() in R, like:
importr('name package', lib_loc="/home/nbarjest/R/x86_64-redhat-linux-gnu-library/3.4"),
where the path is the path in the output example of the #Nbarjest answer.
In python: Check the version of R being used by rpy2
import rpy2.robjects as robjects
robjects.r['version']
Check your rpy2 library location
base = importr('base')
print(base._libPaths())
In R: Check your R library location for this version of r
.libPaths()
copy the library installed in your version of r to the folder used by rpy2.
I also have this problem,and i copy the package i need to base._libPaths() ,here , and it works.
import rpy2.robjects as objects
from rpy2.robjects.packages import importer
base = importr('base')
base._libPaths()[0]
I had a similar problem. I had to uninstall R and reinstall it with admin rights, then reinstall the R package while running R with admin rights, so it would install to the standard library location (not a personal library). Then add R to the PATH variable, and reinstall rpy2.
This is was cross-posted, and answered, on the issue tracker for rpy2: https://bitbucket.org/rpy2/rpy2/issue/265/windows-error-in-loadnamespace