我一直在努力让我的环境保持非冗余和清洁,因此我创建了一个R
环境并清除了计算机上所有其他现有R
。
该环境称为r-conda
,它位于:
/Users/jespinoz/anaconda/envs/r-conda/bin/R
我意识到我没有安装rpy2
并通过conda安装它想要安装新版本的R
和所有r-essentials
我想要的因为我已经拥有一个完美的R环境,所以我想要。
我意识到我可以为rpy2
环境中关联的Python
安装R conda
:
source activate r-conda
pip install rpy2
source deactivate
但并非所有路径都排成一行
如何让rpy2
识别我R
环境中的所有r-conda
相关文件和路径?
我在尝试导入数据包时没有正确找到文件:
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
通过将此添加到我的~/.bash_profile
修复了该错误,但生成了类似的新错误:
我试了一下,错误改变了:
export LD_LIBRARY_PATH="/Users/jespinoz/anaconda/envs/r-conda/lib/R/lib/:$LD_LIBRARY_PATH"
>>> from rpy2.robjects.packages import importr
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/robjects/__init__.py", line 16, in <module>
import rpy2.rinterface as rinterface
File "/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/__init__.py", line 92, in <module>
from rpy2.rinterface._rinterface import (baseenv,
ImportError: dlopen(/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so, 2): Library not loaded: libicuuc.54.dylib
Referenced from: /Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so
Reason: image not found
所以我尝试了这个,然后得到了同样的错误:
export LD_LIBRARY_PATH="/Users/jespinoz/anaconda/envs/r-conda/lib/R/lib/:/Users/jespinoz/anaconda/pkgs/icu-54.1-0/lib/:$LD_LIBRARY_PATH"
如果我使用conda install rpy2
,即使我的主要conda环境的默认版本为Python=3.5.2
,也要安装Python=3.6
。 @asmeurer在我的Python=3.6
环境中安装rpy2
时提出了指定r-conda
的建议,但现在它看起来像是一个包冲突的错误:
(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
答案 0 :(得分:3)
你应该conda install rpy2
而不是pip安装它。此外,保持环境激活。您应该将python
和要使用的任何Python软件包安装到同一个R环境中,以便一切都在一个环境中完成。