[R] Ignoring loadNamespace errors when loading a file

[Martin Morgan]

On 08/21/2011 11:52 PM, Allan Engelhardt wrote:
> On a Unix machine I ran caret::rfe using the multicore package, and I
> saved the resulting object using save(lm2, file = "lm2.RData").
> [Reproducible example below.]
>
> When I try to load("lm2.RData") on my Windows laptop, I get
>
> Error in loadNamespace(name) : there is no package called 'multicore'
>
> I completely understand the error and I would like to ignore it and
> still load the saved object data.
>
> I imagine that I can make myself an empty multicore package for Windows
> and load the data file successfully, but is there another way?
>
> (I am not going to use any multicore functionality; I just want to
> inspect some of the data stored in the object and the reference in
> question is just an unfortunately stored link from the original call.)
>
> (I did search for this question in the archives, but could only find it
> discussed in connection with starting R with a .RData file where the
> consensus seems to be to start R in vanilla mode and install the missing
> package. This situation is different and installing a Unix-only package
> on Windows is obviously a non-starter, except as I proposed above.)
>
> Obligatory reproducible example: On the Unix machine do
>
> library("multicore")
> a <- list(data = 1:10, fun = mclapply)
> save(a, file = "a.RData")
>
> and then try to load the "a.RData" file on Windows. The question is if I
> can recover the data (1:10) on that platform.

Is this a more realistic reproducible example (from ?rfe, modified to 
use computeFunction=mclapply)?

   data(BloodBrain)

   x <- scale(bbbDescr[,-nearZeroVar(bbbDescr)])
   x <- x[, -findCorrelation(cor(x), .8)]
   x <- as.data.frame(x)

   set.seed(1)
   lmProfile <- rfe(x, logBBB,
                    sizes = c(2:25, 30, 35, 40, 45, 50, 55, 60, 65),
                    rfeControl = rfeControl(functions = lmFuncs,
                      number = 5,
                      computeFunction=mclapply))

Maybe provide a computeFunction that only indirectly references mclapply

   computeFunction=function(...) {
       if (require(multicore)) mclapply(...)
       else lapply(...)
   }

or editing the result object to remove references to mclapply

   lmProfile$control$computeFunction <- NULL

Martin


>
> Allan
>
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] compiler stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] caret_4.98 cluster_1.14.0 reshape_0.8.4 plyr_1.6
> [5] lattice_0.19-31 boot_1.3-2 ctv_0.7-3
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1 tools_2.13.1
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


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