[R] script works in Rstudio but not with Rscript

[Henrik Bengtsson]

Does it work with R -f script?  If so, then it's because Rscript does not
attaching methods package by default, but R does. Try loading methods at
the top of your script.

My $.02

Henrik
On Apr 8, 2015 07:41, "Milt Epstein" <mepstein at illinois.edu> wrote:

> Greetings.  I am new to R, but have quite a bit of experience
> programming with other languages (e.g., Perl, Java, Python, shell
> scripting).  I'm now working on a project where I need to use R.  A
> colleague wrote a number of small scripts that work fine in Rstudio,
> but a couple of them don't work when run using Rscript (which we're
> planning on doing).  The behavior is basically the same on a few
> different machines (two of them are Linux, one I think is a Mac).  To
> run the scripts using Rscript, we put one of the following lines at
> the top of the script:
>
> #!/usr/bin/Rscript
> #!/usr/bin/env Rscript
>
> or called the script using Rscript:
>
> Rscript scriptname
>
> In all cases, the behavior is the same.
>
> Here's one of the scripts:
>
> #!/usr/bin/env Rscript
>
> library(apcluster)
> options(stringsAsFactors = FALSE)
>
> args <- commandArgs(TRUE)
> num <- args[1]
>
> numClusters <- num
> mydata <- read.csv("input_data.csv")
> xData <- mydata[, 1]
> yData <- mydata[, 2]
>
> fit <- apclusterK(negDistMat(r=2), mydata, K = numClusters)
> #Leave the rest commented for now
> #output <- data.frame(xData, yData, c(as.data.frame(fit[1]),
> as.data.frame(fit[2]), as.data.frame(fit[3])))
> #write.csv <- write.table(output, file = "output_AP.csv", sep = ",",
> row.names = FALSE, col.names = FALSE)
>
> Here's a call to the script:
>
> $ ./affinity_propagation.R 3
>
> Attaching
>
> The following object is masked package::
>
>     heatmap
>
> Trying p = -15.41969
>    Number of clusters: 17
> Error in tmpk - K : non-numeric argument to binary operator
> Calls: apclusterK ... apclusterK -> .local -> apclusterK -> apclusterK ->
> .local
> Execution halted
>
> The line with the expression "tmpk - K" is from the code for the
> apclusterK() function (from the apcluster library).  The
> definition/value of tmpk is set using a call to the function length().
> I mention this because the failure we're getting with the other script
> also seems to involve an expression with call to length().  Here's the
> error from calling that script:
>
> $ ./spectral_clustering.R 3
> Loading required package: methods
> Error in length(tmpsig) * nc : non-numeric argument to binary operator
> Calls: specc -> specc -> .local -> matrix
> Execution halted
>
> The script is calling the specc() function in the kernlab library.
>
> Any ideas what's going on here, why it's not working and what we can
> do to get it to work?  Is there something that needs to be set or run
> in .Renviron or .Rprofile, say?
>
> Thanks.
>
> Milt Epstein
> Programmer in Computational Genomics
> Institute for Genomic Biology (IGB)
> University of Illinois at Urbana-Champaign (UIUC)
> mepstein at illinois.edu
>
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