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

Mon Nov 30 17:01:44 CET 2009

This problem disappeared in patched releases soon after I replied to  
Simon that I was unable to obtain the information that he required  
from the debugger.  After checking a few releases I quite monitoring  
the problem.  I assumed that it had been fixed with comment.  However,  
today, the patched release dated 2009-11-29 has the problem once  
again.  I have tried going back to the patched releases of 2009-11-27  
and 2009-11-22, the only ones for which I have kept installers here at  
work.  Both have the problem.  In neither can I obtain the debugging  
information that Simon requested when the problem initially arose.   
Can somebody tell me the current status of the problem, and when it  
might be fixed (again)?  It occurs at an extremely inconvenient time  
in my project.

Thanks,

Richard R. Liu
Dittingerstr. 33
CH-4053 Basel
Switzerland

Tel.:  +41 61 331 10 47
Mobil: +41 79 708 67 66
Email:  richard.liu at pueo-owl.ch

On Nov 18, 2009, at 21:07 , Simon Urbanek wrote:

> Richard,
>
> in order to track this down, please start R64, type
>
> Sys.getpid()
>
> and note down the number. Then in a separate window open Terminal  
> and type
>
> gdb
>
> Then on the gdb console (it will just say "(gdb)") type
>
> attach n
>
> where n is the number from above. It will do something for a while  
> and when it comes back in the console, type
>
> c
>
> Then do your work in R until you get a crash. Once you do, you will  
> see something happening in the gdb console. Then type
>
> bt
>
> and copy/paste everything that gdb printed since you typed "c" and  
> send it to me.
>
> Thanks,
> Simon
>
> -----
>
> Practical example -- in R:
>
> > Sys.getpid()
> [1] 19381
>
> in Terminal:
>
> ginaz:~$ gdb
> GNU gdb 6.3.50-20050815 (Apple version gdb-962) (Sat Jul 26 08:14:40  
> UTC 2008)
> [...]
> This GDB was configured as "i386-apple-darwin".
> (gdb) attach 19381
> Attaching to process 19381.
> Reading symbols for shared libraries . done
> [...]
> 0x9428a6fa in select$DARWIN_EXTSN ()
> (gdb) c
> Continuing.
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_PROTECTION_FAILURE at address: 0x00000003
> 0x00412d09 in SET_SYMVALUE (x=0x1007110, v=0x0) at ../../../../ 
> R-2.10-branch/src/main/memory.c:2809
> 2809	void (SET_SYMVALUE)(SEXP x, SEXP v) { CHECK_OLD_TO_NEW(x, v);  
> SYMVALUE(x) = v; }
> (gdb) bt
> #0  0x00412d09 in SET_SYMVALUE (x=0x1007110, v=0x0) at ../../../../ 
> R-2.10-branch/src/main/memory.c:2809
> #1  0x0041068e in Rf_ReplIteration (rho=0x1023c38, savestack=0,  
> browselevel=0, state=0xbfffe53c) at ../../../../R-2.10-branch/src/ 
> main/main.c:263
> #2  0x00410a40 in R_ReplConsole (rho=0x1023c38, savestack=0,  
> browselevel=0) at ../../../../R-2.10-branch/src/main/main.c:311
> #3  0x0041129b in run_Rmainloop () at ../../../../R-2.10-branch/src/ 
> main/main.c:964
> #4  0x00001ff0 in main (ac=1, av=0xbffff5c8) at ../../../../R-2.10- 
> branch/src/main/Rmain.c:33
> (gdb) q
> The program is running.  Quit anyway (and detach it)? (y or n) y
> Detaching from process 19381 thread 0x613.
>
>
> On Nov 18, 2009, at 14:39 , Richard R. Liu wrote:
>
>> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

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