[R] script works in Rstudio but not with Rscript

Milt Epstein mepstein at illinois.edu
Wed Apr 8 16:41:12 CEST 2015

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/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

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


The following object is masked package::


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?


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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