[R-SIG-Mac] Difference between Terminal output and GUI output.

[Joseph Kunkel]

Dear R-sig-Mac,

Sorry, this was sent via another email(non-SIG-member instance) and I am resending this in order to get consideration perhaps more quickly.

I have a problem with output from the R.app GUI which is at odds in part with the Terminal console output which I prefer.  The GUI does debug requests interspersed with the desired output.

My system is:

 Model Name:   MacBook Pro
 Model Identifier:     MacBookPro10,1
 Processor Name:       Intel Core i7
 Processor Speed:      2.7 GHz
 Number of Processors: 1
 Total Number of Cores:        4
 L2 Cache (per Core):  256 KB
 L3 Cache:     6 MB
 Memory:       16 GB
System Software Overview:
System Version:        OS X 10.9.4 (13E28)
Kernel Version:        Darwin 13.3.0

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)

R.app GUI 1.65 (6784 Snow Leopard build), S.

An R-script accesses an array XX which has ...

> attributes(XX)
$dim
[1] 12  3  8

The R-script that gives me the problem:
# GetCL.R
for (i in 1:4) { out<- round(((sum((XX[3,,i]-XX[10,,i])^2))^0.5 + (sum((XX[2,,i]-XX[10,,i])^2))^0.5)/2,3)
                   cat(out,'\n')
                   }

The correct output obtained in Terminal mode is:

> source("GetCL.R")
35.791
35.811
44.625
43.316

In the GUI I get:

> source("GetCL.R")
debug at GetCL.R#3: out <- round(((sum((XX[3, , i] - XX[10, , i])^2))^0.5 + (sum((XX[2,
   , i] - XX[10, , i])^2))^0.5)/2, 3)
Browse[2]>
debug at GetCL.R#4: cat(out, "\n")
Browse[2]>
35.791
debug at GetCL.R#3: out <- round(((sum((XX[3, , i] - XX[10, , i])^2))^0.5 + (sum((XX[2,
   , i] - XX[10, , i])^2))^0.5)/2, 3)
Browse[2]>
debug at GetCL.R#4: cat(out, "\n")
Browse[2]>
35.811
debug at GetCL.R#3: out <- round(((sum((XX[3, , i] - XX[10, , i])^2))^0.5 + (sum((XX[2,
   , i] - XX[10, , i])^2))^0.5)/2, 3)
Browse[2]>
debug at GetCL.R#4: cat(out, "\n")
Browse[2]>
44.625
debug at GetCL.R#3: out <- round(((sum((XX[3, , i] - XX[10, , i])^2))^0.5 + (sum((XX[2,
   , i] - XX[10, , i])^2))^0.5)/2, 3)
Browse[2]>
debug at GetCL.R#4: cat(out, "\n")
Browse[2]>
43.316

Of course this output gets more tedious if I try to process the entire array by running for i in 1:larger-n.
Is there any way to get rid of these debug and browse messages messages in GUI mode?
I have never experienced this debug output in my ca. 12+ years of using R intensely.

I just recently upgraded to R version 3.1.1 (2014-07-10) and renewed all my libraries.

-·.  .· ·.  .><((((º>·.  .· ·.  .><((((º>·.  .· ·.  .><((((º> .··.· >=-       =º}}}}}><
Joseph G. Kunkel, Emeritus Professor
Biology Department
UMass Amherst 
Amherst MA 01003
joe at bio.umass.edu