Erin, at first glance I would say that this is an R error. When Rpy2
detects an error it will pass it through errors as library errors like
this. At first glance it appears that your r code is not loading the
requisite packages as it cannot find them. That I suspect is what is
causing your coordinates error.
I would first run R and confirm that you can load the requisite libraries
in it before depending upon them in rpy2. In general I find that rpy2 is
a bad interface for debugging R code and you need to run it in R first to
get the problems out.
Best,
Collin.
On Sun, 17 Nov 2013, Erin Hodgess wrote:
> Hello again!
>
> I'm using python, rpy2, and R for a project. It's actually pretty
> interesting. Anyhow, I pass in an R file to the python program. However,
> I am getting the following errors, which seem more like R errors(?):
>
> Loading required package: gstat
> Loading required package: automap
> Error in coordinates(x.df) <- ~x + y :
> could not find function "coordinates<-"
> In addition: Warning messages:
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, :
> there is no package called ?gstat?
> 2: In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, :
> there is no package called ?automap?
> Traceback (most recent call last):
> File "reg4.py", line 38, in <module>
> spat1.spat1(file1=file1,file2=file2)
> File
"/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py",
> line 86, in __call__
> return super(SignatureTranslatedFunction, self).__call__(*args,
> **kwargs)
> File
"/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py",
> line 35, in __call__
> res = super(Function, self).__call__(*new_args, **new_kwargs)
> rpy2.rinterface.RRuntimeError: Error in coordinates(x.df) <- ~x + y :
> could not find function "coordinates<-"
>
> I've checked and gstat and automap are both there. Here is the actual
R
> code:
> spat1 <- function(file1,file2) {
> require(gstat)
> require(automap)
> x.df <- read.table(file=file1,header=TRUE)
> coordinates(x.df) <- ~x+y
> zz <- scan(file=file2,what="character")
> proj4string(x.df) <- zz
> png(file="map1.png")
> u <- autoKrige(x.df at data[,1]~1,x.df)
> plot(u)
> return(u)
> }
>
>
> I know that there are a few people who have used both rpy2, python and R,
> so I thought I'd launch this out.
>
> Thanks in advance for any help.
>
> Sincerely,
> Erin
>
>
> --
> Erin Hodgess
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: erinm.hodgess at gmail.com
>
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>
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