[R] Mysterious seg fault.

[Duncan Murdoch]

On 12/08/2018 6:32 PM, Rolf Turner wrote:
> 
> On 12/08/18 17:42, Eric Berger wrote:
> 
>> Hi Rolf,
>> When faced with such a situation I take the following approach which
>> often helps.
>> Use the same setup that caused the seg fault (you need a reproducible
>> problem.)
>> Start your R session using valgrind. e.g. in linux I do:
>>
>> $ valgrind R
>>
>> Assuming that a seg fault still occurs then valgrind should provide info
>> as to where.
>>
>> HTH
> 
> Well, it probably *would* help if I weren't such a thicko.
> 
> The story so far:  I have managed to install valgrind (downloaded a
> tarball and installed from source).  Seemed to go OK, but:
> 
> * when I type "valgrind" I get "command not found"
> * however valgrind is in /usr/local/bin (I did "configure" with
>     prefix="/usr/local" so this is as it should be)
> * /usr/local/bin/valgrind is executable
> * /usr/local/bin is in my path
> 
> So how in god's name can the command not be found?  And why do these
> things always happen to *me*???
> 
> I can work around this problem by giving the full path name, however.
> 
> So I did:
> 
> /usr/local/bin/valgrind R

I believe on your system R is a script, so you can't run valgrind this 
way.  It's just debugging bash, not R.  You need to use

R -d valgrind

(though with your weird path problems, you might need a fully qualified 
/usr/local/bin/valgrind there).

You run gdb the same way:

R -d gdb

and then give the command "r" to gdb to start R.  It will give a report 
when you get the segfault.  I don't know which report will be more 
informative.

Duncan Murdoch

> 
> and got a lot of (mysterious to me) output:
> 
>> /usr/local/bin/valgrind R
>> ==18051== Memcheck, a memory error detector
>> ==18051== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
>> ==18051== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
>> ==18051== Command: /usr/local/bin/R
>> ==18051==
>> ==18051== Invalid free() / delete / delete[] / realloc()
>> ==18051==    at 0x4C2ECF0: free (vg_replace_malloc.c:530)
>> ==18051==    by 0x45E280: ??? (in /bin/bash)
>> ==18051==    by 0x45E42F: run_unwind_frame (in /bin/bash)
>> ==18051==    by 0x47B714: parse_and_execute (in /bin/bash)
>> ==18051==    by 0x47B102: ??? (in /bin/bash)
>> ==18051==    by 0x47B35C: source_file (in /bin/bash)
>> ==18051==    by 0x4849C7: source_builtin (in /bin/bash)
>> ==18051==    by 0x43378D: ??? (in /bin/bash)
>> ==18051==    by 0x43592C: ??? (in /bin/bash)
>> ==18051==    by 0x4369C7: execute_command_internal (in /bin/bash)
>> ==18051==    by 0x43851D: execute_command (in /bin/bash)
>> ==18051==    by 0x42139D: reader_loop (in /bin/bash)
>> ==18051==  Address 0x4241008 is in the brk data segment 0x4228000-0x4246fff
>> ==18051==
>> ==18051== Invalid free() / delete / delete[] / realloc()
>> ==18051==    at 0x4C2ECF0: free (vg_replace_malloc.c:530)
>> ==18051==    by 0x45E280: ??? (in /bin/bash)
>> ==18051==    by 0x45E42F: run_unwind_frame (in /bin/bash)
>> ==18051==    by 0x4849D3: source_builtin (in /bin/bash)
>> ==18051==    by 0x43378D: ??? (in /bin/bash)
>> ==18051==    by 0x43592C: ??? (in /bin/bash)
>> ==18051==    by 0x4369C7: execute_command_internal (in /bin/bash)
>> ==18051==    by 0x43851D: execute_command (in /bin/bash)
>> ==18051==    by 0x42139D: reader_loop (in /bin/bash)
>> ==18051==    by 0x41FDB0: main (in /bin/bash)
>> ==18051==  Address 0x4240708 is in the brk data segment 0x4228000-0x4246fff
>> ==18051==
>>
> 
> Not at all clear to me what to make of this.  Does it indicate problems
> or memory leaks in my installation of R?  Anyhow, things then proceed in
> an expected manner:
> 
>> R version 3.5.1 (2018-07-02) -- "Feather Spray"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> 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.
>>
>> Loading required package: misc
>> [Previously saved workspace restored]
> 
> I then loaded the problematic package and issued the problematic command:
> 
>>> library(hmm.discnp)
>> hmm.discnp 2.0-9
>>
>>       This package has changed SUBSTANTIALLY from its
>>       previous release.  Read the documentation
>>       carefully.  Note in particular that the meaning of
>>       the argument "nsim" of the function rhmm() has
>>       changed, and a new argument "ylengths" now plays
>>       essentially the role previously played by
>>       "nsim".
>>
>>> xxx <- get.hgl(p3,2,yyy)
>>
>>   *** caught segfault ***
>> address (nil), cause 'unknown'
>> Segmentation fault (core dumped)
> 
> Nothing informative.  Is there something else I should be doing?
> 
> Sorry for being a nuisance, but I am at a loss.
> 
> cheers,
> 
> Rolf
>