[R-SIG-Mac] *** caught bus error *** address 0x114382544, cause 'non-existent physical address'

[Richard R. Liu]

I am experiencing a curious error running R64 (2009-11-18 r50482) on a  
MacBook Pro 17" Unibody early 2009 with 8GB RAM.  In the console  
excerpt below sentences.1000.clustered is a dataframe consisting of  
two vectors, sent and cluster.  sent is a vector of 1000 sentences  
chosen at random from over 3 million, and cluster is a vector of  
integers denoting to which of 5 clusters the sentence belongs.  For  
each cluster I want to display the sentences that belong to it as  
follows:


R version 2.10.0 Patched (2009-11-18 r50482)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[R.app GUI 1.30 (5521) x86_64-apple-darwin9.8.0]

[Workspace restored from /Users/richard/.RData]

 > library(filehash)
filehash: Simple key-value database (2.0-1 2008-12-19)
 > db <- dbInit("/Volumes/Work on RDR Test Documents/R Databases/ 
DB_TXT", type = "RDS")
 > dbLoad(db)
 >
 > sent.clust <- sentences.1000.clustered
 > i.clust.2 <- which(sent.clust$cluster == 2)
 > attributes(sent.clust)
$names
[1] "sent"    "cluster"

$row.names
    [1]    1    2    3    4    5    6    7    8    9   10   11   12    
13   14   15   16   17   18   19   20   21   22   23   24   25   26    
27   28   29
...
  [987]  987  988  989  990  991  992  993  994  995  996  997  998   
999 1000

$class
[1] "data.frame"

 > i.clust.2 <- which(sent.clust$cluster == 2)
 > nchar(sent.clust$sent[i.clust.2])
   [1]   232   419   787  1010  1926   357  2865   657   560   213   
2175  2363  1300   359   331   965   581   732   398   245  1650  
25893  1289   510
  [25]  1714   524   747  2378   465   651  2253   215   460   253   
2475   554  1130   529   261  1413   418  2168  1569  1538   301   
2506  1163  3036
  [49]  1445   199  1231   370  1307   371   379   232  1297   500    
409   481  2187   314   730  1634   971   860   362   506  1606    
394   145   480
  [73]  1582  1471  1269   308  1113   444   990   298  1644   445    
357  1204   322   638  2182   805  1545   368  1461  1347   649   399   
1094  1624
  [97] 14605  1637   269   503   502  2145  1398   481   122  2248
 > sent.clust$sent[i.clust.2]
   [1] "(patient continuing ...)  
______________________________________________________________________________________________________________________________________ 
  Investigator text for Adverse Events encoded using MedDRA version  
11.0. "
   [2]
  *** caught bus error ***
address 0x114382544, cause 'non-existent physical address'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

The point of

 > i.clust.2 <- which(sent.clust$cluster == 2)
 > nchar(sent.clust$sent[i.clust.2])

is to try to isolate the problem.  Indeed, the more compact sent.clust 
$sent[which(sent.clust$cluster == 2)] work when I start R in 32-bit  
mode.  In 64-bit mode, attempting to display the sentences in cluster  
5 also fails, whereas for clusters 1, 3, 4 it succeeds.  In 32-bit  
mode, I have experienced no such problem.

Does anybody have any ideas about what is wrong?

Regards,
Richard

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