[英]RPY2: importr fails with .Renviron
Here's what should and does happen using rpy2.robjects.packages.importr
for base R-packages (eg stats
): 以下是使用
rpy2.robjects.packages.importr
进行基本R-packages(例如stats
)应该和确实发生的事情:
>>> from rpy2.robjects.packages import importr
>>> importr('stats')
<rpy2.robjects.packages.SignatureTranslatedPackage object at 0x7f3810>
but with an external package (eg ggplot2
) this is the result: 但是使用外部包(例如
ggplot2
),结果如下:
>>> importr('ggplot2')
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ggplot2'
Error in .Primitive("as.environment")("package:ggplot2") :
no item called "package:ggplot2" on the search list
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Library/Frameworks/Python.framework/Versions/7.0/lib/python2.7/site-packages/rpy2/robjects/packages.py", line 100, in importr
env = _as_env(rinterface.StrSexpVector(['package:'+name, ]))
rpy2.rinterface.RRuntimeError: Error in .Primitive("as.environment")("package:ggplot2") :
no item called "package:ggplot2" on the search list
A complication is that in my home directory I have the file .Renviron
define my user library location (where, for instance, ggplot2
libs are), and I have no problems with either of the R-commands library()
or require()
using R
and Rscript
. 一个复杂的问题是,在我的主目录中,我有文件
.Renviron
定义我的用户库位置(例如, ggplot2
libs所在的位置),我对R-commands library()
或require()
任何一个都没有问题R
和Rscript
。 The path looks something like this: 路径看起来像这样:
R_LIBS_USER="/path/to/my/packages"
So my question is why my user-library path excluded from the "search list" Rpy2
uses? 所以我的问题是为什么我的用户库路径被排除在
Rpy2
的“搜索列表” Rpy2
? Or, rather, how do I direct Rpy2
to look in the R_LIBS_USER
path as well? 或者,我如何指导
Rpy2
查看R_LIBS_USER
路径呢?
I assume the problem stems from the environment Rpy2
uses, but my ignorance is high in that regard. 我认为这个问题源于
Rpy2
使用的环境,但我的无知在这方面很高。
R: 2.13.0
Platform: x86_64-apple-darwin9.8.0/x86_64 (Mac, 10.6, 64-bit)
replicated with 复制了
Rpy2: 2.1.8, 2.2.1 (dev)
I use R, ggplot2, and python regularly, so any insight is very much welcome. 我经常使用R,ggplot2和python,因此非常欢迎任何见解。
By default, rpy2 is initializing in "vanilla" mode, and this ignores R_LIBS and friends. 默认情况下,rpy2正在“vanilla”模式下初始化,这会忽略R_LIBS和朋友。
>>> import rpy2.rinterface
>>> rpy2.rinterface.get_initoptions()
('rpy2', '--quiet', '--vanilla', '--no-save')
>>>
You can use 'rinterface.set_initoptions()' to change those. 您可以使用'rinterface.set_initoptions()'来更改它们。
For example: 例如:
import rpy2.rinterface as ri
ri.set_initoptions(('rpy2', '--verbose', '--no-save'))
ri.initr()
# from now on, just import the rest of rpy2 modules without thinking of the above.
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