Re: [Rd] [R] Segfault in pure R code

From: Göran Broström <goran.brostrom_at_gmail.com>
Date: Wed 13 Dec 2006 - 23:08:48 GMT

On 12/13/06, Peter Dalgaard <p.dalgaard@biostat.ku.dk> wrote:
> Göran Broström wrote:
> > I tried once more under the debugger, and
> >
> > ++++++++++++++++++++++++++++++++++++++++++
> > gb@kasparov:~/R/BEMANNING/Doc$ R -d gdb
> > GNU gdb 6.5-debian
> > Copyright (C) 2006 Free Software Foundation, Inc.
> > GDB is free software, covered by the GNU General Public License, and you are
> > welcome to change it and/or distribute copies of it under certain conditions.
> > Type "show copying" to see the conditions.
> > There is absolutely no warranty for GDB. Type "show warranty" for details.
> > This GDB was configured as "i486-linux-gnu"...Using host libthread_db
> > library "/lib/tls/i686/cmov/libthread_db.so.1".
> >
> > (gdb) run
> > Starting program: /usr/local/lib/R/bin/exec/R
> > Failed to read a valid object file image from memory.
> >
> > R version 2.4.0 Patched (2006-10-29 r39744)
> > Copyright (C) 2006 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.
> >
> > [Previously saved workspace restored]
> >
> >
> >> library(xtable)
> >> ?xtable)
> >>
> > Error: syntax error in "?xtable)"
> >
> >> ?xtable
> >> help.start()
> >>
> > Making links in per-session dir ...
> > If '/usr/bin/firefox' is already running, it is *not* restarted, and
> > you must switch to its window.
> > Otherwise, be patient ...
> >
> >> library(bemanning)
> >> load("bemanning07-32.rda")
> >> courses("Ingrid")
> >>
> >
> > Program received signal SIGSEGV, Segmentation fault.
> > 0x080f5026 in R_gc_internal (size_needed=17588127) at memory.c:1313

> > 1313 PROCESS_NODES();
> > (gdb)
> > ++++++++++++++++++++++++++++++++++++++++++++
> >
> > How do I continue?
> >

>

> Ouch. Call the marines...
>

> The error comes from the garbage collector, which means that something
> got corrupted in internal data structures some time previously.
>

> The most important thing is to preserve the bug. Rebuild anything and
> the symptom disappears, but the bug will still be there. So keep the R
> binary, the script, and the .RData file around.

OK, I'll do that. However, I have no time this week to look into the things you suggest below, but I'll try to get at it next week.

Göran

>

> Some ideas:
>

> Is it reproducible on other machines?
>

> Do you have valgrind installed? Notes for using it are on
> http://developer.r-project.org/valgrind-internal.html
>

> Turning on gctorture() may trigger the bug at an earlier state.
>

> The last resort is to painstakingly backtrace to the point of the
> damage using watchpoints and whatever, but I'd rather not go there
> right away.
>

> -p
> > Göran
> >
> > On 12/12/06, Göran Broström <goran.brostrom@gmail.com> wrote:
> >
> >> On 12/12/06, Peter Dalgaard <p.dalgaard@biostat.ku.dk> wrote:
> >>
> >>> Göran Broström wrote:
> >>>
> >>>> I just caught a segfault:
> >>>>
> >>>>
> >>>>
> >>>>> courses("Ingrid")
> >>>>>
> >>>>>
> >>>> *** caught segfault ***
> >>>> address 0x99b279c, cause 'memory not mapped'
> >>>>
> >>>> Traceback:
> >>>> 1: structure(y, class = oldClass(x), row.names = attr(x, "row.names"))
> >>>> 2: `[.data.frame`(gudata, -(1:5))
> >>>> 3: gudata[-(1:5)]
> >>>> 4: names(gudata[-(1:5)])
> >>>> 5: inherits(x, "factor")
> >>>> 6: is.factor(table)
> >>>> 7: match(x, table, nomatch = 0)
> >>>> 8: who %in% names(gudata[-(1:5)])
> >>>> 9: courses("Ingrid")
> >>>>
> >>>> when running a function 'courses' in an R package without compiled
> >>>> code. Is this "possible"? I have got many segfaults when testing my
> >>>> own packages, but it has always been caused by stupidities in C or
> >>>> Fortran code, never with pure R code.
> >>>>
> >>>> So, before I start debugging, I'd like to know if a segfault in pure R
> >>>> code indicates a bug in R itself, or if it can be in my function?
> >>>>
> >>>>
> >>>>
> >>> By definition, reproducible segfaults in R code are bugs in R, unless
> >>> caused by abuse of .C calls or similar. (Irreproducible ones are often
> >>> hardware faults.)
> >>>
> >>> However, at least presently, you are the only one with a handle on the
> >>> bug. So either you get to do the debugging or you have to provide
> >>> something that others can reproduce.
> >>>
> >>> Astarting point could be to run R under the debugger (R -d gdb) and
> >>> generate a C backtrace, then look at the variables involved.
> >>>
> >> Thanks, Peter,
> >>
> >> the error is reproducible. The full session is
> >>
> >> +++++++++++++++++++++++++++++++++++++++++
> >> gb@kasparov:~/R/BEMANNING/Doc$ R
> >>
> >> R version 2.4.0 Patched (2006-10-29 r39744)
> >> Copyright (C) 2006 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.
> >>
> >> [Previously saved workspace restored]
> >>
> >>
> >>> library(xtable)
> >>> ?xtable)
> >>>
> >> Error: syntax error in "?xtable)"
> >>
> >>> ?xtable
> >>> help.start()
> >>>
> >> Making links in per-session dir ...
> >> If '/usr/bin/firefox' is already running, it is *not* restarted, and
> >> you must switch to its window.
> >> Otherwise, be patient ...
> >>
> >>> library(bemanning)
> >>> load("bemanning07-32.rda")
> >>> courses("Ingrid")
> >>>
> >> *** caught segfault ***
> >> address 0x99b279c, cause 'memory not mapped'
> >>
> >> Traceback:
> >> 1: structure(y, class = oldClass(x), row.names = attr(x, "row.names"))
> >> 2: `[.data.frame`(gudata, -(1:5))
> >> 3: gudata[-(1:5)]
> >> 4: names(gudata[-(1:5)])
> >> 5: inherits(x, "factor")
> >> 6: is.factor(table)
> >> 7: match(x, table, nomatch = 0)
> >> 8: who %in% names(gudata[-(1:5)])
> >> 9: courses("Ingrid")
> >>
> >> Possible actions:
> >> 1: abort (with core dump)
> >> 2: normal R exit
> >> 3: exit R without saving workspace
> >> 4: exit R saving workspace
> >> Selection:
> >> +++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> Notes:
> >>
> >> 1. Tried to remove one line at a time, but then no error.
> >> 2. R -d gdb: No errors
> >> 3. Starting with 'R --vanilla': No errors.
> >>
> >> i.e., it seems as if my previously saved workspace '.RData' is part of
> >> the error.
> >> Could it be corrupt and cause a segfault in a bug free R?
> >>
> >> I'll try to build a newer version of R and check (but not tonight).
> >>
> >> Göran
> >>
> >>
> >>> (Further discussion should probably go on r-devel instead of r-help).
> >>>
> >>> -p
> >>>
> >>>
> >>>> I have used 'courses' many times before without problems.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Göran
> >>>> ++++++++++++++++++++++++++++++++++++++
> >>>>
> >>>>
> >>>>> sessionInfo()
> >>>>>
> >>>>>
> >>>> R version 2.4.0 Patched (2006-10-29 r39744)
> >>>> i686-pc-linux-gnu
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >> --
> >> Göran Broström
> >>
> >>
> >
> >
> >
>
>
>


-- 
Göran Broström

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