I have been trying to keep my environment non-redundant and clean so I made an R environment and wiped out all other existing Rs on my computer.
That environment is called r-conda and it is in:
/Users/jespinoz/anaconda/envs/r-conda/bin/R
I realized I didn't have rpy2 installed and to install it through conda it wanted to install the a new version of R and all of the r-essentials which I don't want since I already have a perfectly working R environment.
I realized I could install rpy2 for the Python associated within the R conda environment:
source activate r-conda
pip install rpy2
source deactivate
But not all of the paths are lined up
How can I make rpy2 recognize all of my R associated files and paths in my r-conda environment?
It's not finding the files correctly when I am trying to import packges:
os.environ['R_HOME'] = "/Users/jespinoz/anaconda/envs/r-conda/bin/R"
from rpy2.robjects.packages import importr
importr("dynamicTreeCut")
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-29-8b0a88dfe12d> in <module>()
1 # os.environ['R_HOME'] = '/Users/jespinoz/anaconda/envs/r-conda/bin/'
2 os.environ['R_HOME'] = "/Users/jespinoz/anaconda/envs/r-conda/bin/R"
----> 3 from rpy2.robjects.packages import importr
4 importr("dynamicTreeCut")
/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/robjects/__init__.py in <module>()
14 import itertools
15 from datetime import datetime
---> 16 import rpy2.rinterface as rinterface
17 import rpy2.rlike.container as rlc
18
/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/__init__.py in <module>()
90 del(os)
91
---> 92 from rpy2.rinterface._rinterface import (baseenv,
93 emptyenv,
94 endr,
ImportError: dlopen(/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so, 2): Library not loaded: @rpath/R/lib/libR.dylib
Referenced from: /Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so
Reason: image not found
Fixed that error by adding this to my ~/.bash_profile but generated a similar new error:
I gave this a try, and the error changed:
export LD_LIBRARY_PATH="/Users/jespinoz/anaconda/envs/r-conda/lib/R/lib/:$LD_LIBRARY_PATH"
>>> from rpy2.robjects.packages import importr
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/robjects/__init__.py", line 16, in <module>
import rpy2.rinterface as rinterface
File "/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/__init__.py", line 92, in <module>
from rpy2.rinterface._rinterface import (baseenv,
ImportError: dlopen(/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so, 2): Library not loaded: libicuuc.54.dylib
Referenced from: /Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so
Reason: image not found
So I tried this, then got the same error:
export LD_LIBRARY_PATH="/Users/jespinoz/anaconda/envs/r-conda/lib/R/lib/:/Users/jespinoz/anaconda/pkgs/icu-54.1-0/lib/:$LD_LIBRARY_PATH"
If I use conda install rpy2 it wants to install a Python=3.5.2 even though my default version of my main conda environment is Python=3.6. @asmeurer gave a suggestion to specify Python=3.6 when installing rpy2 in my r-conda environment but now it's looking like a package conflicting error:
(r-conda) jespinozlt-osx:~ jespinoz$ conda install rpy2 python=3.6
Fetching package metadata .............
Solving package specifications: .
UnsatisfiableError: The following specifications were found to be in conflict:
- python 3.6*
- r-permute
- rpy2
Use "conda info <package>" to see the dependencies for each package
