[R] problem with nlme, environments, and packages

[Duncan Murdoch]

On 15/06/2015 8:32 PM, Greg Hather wrote:
> Hello R users,
> 
> I encountered a strange problem while writing a package that uses the
> nlme function.  First, I wrote some code that uses the nlme function,
> and it ran without errors.  However, when I tried to put the code into
> a package, the nlme function was unable to locate a function that was
> used in the formula.  Could it be that nlme is looking in the wrong
> environment?  I would appreciate any suggestions.  Below is a
> reproducible example with the problem.

I haven't tested this (I don't use the devtools stuff), but I'd say
there are two likely possibilities:

1.  nlme() isn't evaluating the formula properly.

2.  Your test isn't doing what you think it is doing, because you have a
second copy of main_function in your global environment.

Assuming you can rule out 2, could you put together a tarball of the
package that I could actually run?

Duncan Murdoch


> 
> ########### BEGIN EXAMPLE ##############
> 
> #' Fake package to show nlme error
> #' @export
> 
> main_function <- function(x){
>  library(nlme)
>  result <- nlme(height ~ SSasymp(age, Asym, R0, lrc) +
> nonlinear_function(age),
>                 data = Loblolly,
>                 fixed = Asym + R0 + lrc ~ 1,
>                 random = Asym ~ 1,
>                 start = c(Asym = 103, R0 = -8.5, lrc = -3.3))
>  result
> }
> 
> nonlinear_function <- function(x){
>  log(x)
> }
> 
> ########### END EXAMPLE ##############
> 
> The above code can be installed as a package and run with the commands
> 
> library(devtools)
> library(roxygen2)
> setwd("C:/test")  # or any prefered directory
> create("testPackage")
> setwd("./testPackage")
> document()
> setwd("..")
> install("testPackage")
> main_function()
> 
> The output is
> 
>> main_function()
> Error in eval(expr, envir, enclos) :
>  could not find function "nonlinear_function"
>>
>> sessionInfo()
> R version 3.1.3 (2015-03-09)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 8 x64 (build 9200)
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
> other attached packages:
> [1] nlme_3.1-120           testPackage_0.0.0.9000
> [3] roxygen2_4.1.1         devtools_1.8.0
> loaded via a namespace (and not attached):
> [1] curl_0.8        digest_0.6.8    git2r_0.10.1
> [4] grid_3.1.3      lattice_0.20-31 magrittr_1.5
> [7] memoise_0.2.1   Rcpp_0.11.6     rversions_1.0.1
> [10] stringi_0.4-1   stringr_1.0.0   tools_3.1.3
> [13] xml2_0.1.1
> 
> Note that if I simply paste main_function and nonlinear_function into
> the R console, then main_function() runs without errors.
> 
> Greg
> 
> 	[[alternative HTML version deleted]]
> 
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