I got very similar behaviour with RODBC and the ODBC postgresql driver in
unixODBC, with postgresql 7.3.1. The segfault was in the driver.
Getting the latest driver fixed it, so my guess is that something has
changed recently in the postgresql interface: I tried to find out what but
the code had been changed in many minor ways.
On Thu, 6 Feb 2003, Rafael A. Irizarry wrote:
> one more bit of information about this problem. If I start R as the
> user "postgres" i dont have the segmentation fault.
>
> ---------- Forwarded message ----------
> Date: Wed, 5 Feb 2003 19:19:39 -0500 (EST)
> From: Rafael A. Irizarry <ririzarr at jhsph.edu>
> Reply-To: rafa at jhu.edu
> To: "R-Help (E-mail)" <r-help at r-project.org>
> Subject: rdbi segmentation fault
>
> hi! i am experiencing the same behaviour explained here:
>
> http://finzi.psych.upenn.edu/R/Rhelp02/archive/2482.html
> (i copied the message below)
>
> has anybody found a solution?
>
> here is the code that gives me a segmentation fault
> library(Rdbi)
> library(Rdbi.PgSQL)
>
> conn <- dbConnect(PgSQL(), dbname = "PGA")
> tmp <- "create table test ( expid int, name varchar(128));"
> result <- dbSendQuery(conn,tmp)
> dbClearResult(result)
>
> the last line can be substituted by
> dbDisconnect(conn)
> and you get a segmentation fault too.
>
> The database PGA does exist and the dbSendQuery does create a table (i
> checked via psql)
>
> i followed the instructions given by tim (see url or msg below) and im
> sending (what think is) the backtrace:
> Program received signal SIGSEGV, Segmentation fault.
> Rf_getAttrib (vec=0x8b50cd0, name=0x81d19b8) at attrib.c:93
> 93 if (TAG(s) == name) {
> (gdb) backtrace
> #0 Rf_getAttrib (vec=0x8b50cd0, name=0x81d19b8) at attrib.c:93
> #1 0x080c0a8f in Rf_usemethod (generic=0xbffff0c0 "print",
obj=0x8b50cd0,
> call=0x880c5a0, args=0x81d1b08, rho=0x89dd900, callrho=0x81e6f68,
> defrho=0x81e6f14, ans=0xbffff0bc) at objects.c:271
> #2 0x080c1058 in do_usemethod (call=0x880c5a0, op=0x81e4f80,
> args=0x880c5bc,
> env=0x89dd900) at objects.c:409
> #3 0x0809cd29 in Rf_eval (e=0x880c5a0, rho=0x89dd900) at eval.c:404
> #4 0x0809d26d in Rf_applyClosure (call=0x89de354, op=0x880c4c0,
> arglist=0x89dd874, rho=0x81e6f68, suppliedenv=0x81d1b08) at eval.c:595
> #5 0x0809cf1d in Rf_eval (e=0x89de354, rho=0x81e6f68) at eval.c:439
> #6 0x080f013c in Rf_PrintValueEnv (s=0x8b50cd0, env=0x81e6f68) at
> print.c:662
> #7 0x080b5597 in Rf_ReplIteration (rho=0x81e6f68, savestack=0,
> browselevel=0,
> state=0xbffff550) at main.c:236
> #8 0x080b56ad in R_ReplConsole (rho=0x81e6f68, savestack=0,
> browselevel=0)
> at main.c:280
> #9 0x080b5d4b in run_Rmainloop () at main.c:579
> #10 0x0811570e in main (ac=1, av=0xbffffa34) at system.c:99
> #11 0x42017499 in __libc_start_main () from /lib/i686/libc.so.6
>
>
> thanks,
> rafael
>
> MESSGAGE from archive:
>
> I've not seen this behavior. Try "R -d gdb" and then type
"run" at the
> gdb prompt. Run your R session until the seg fault and send me the
> backtrace. Thanks.
>
> Tim
>
> On Thu, 2002-04-25 at 18:05, Andrew Schuh wrote:
> > I can use the Rdbi package to connect to a PostGreSQL server fine but
> > when I use the dbDisconnect(), I get a segmentation error and it
throws
> > me out of R. I'm using RH7.2, R1.4.1, Rdbi 0.1-2, and Rdbi.PgSQL
0.1-2.
> >
> > Anyone else seen anything like this and have an possible answer?
> >
> > Andrew Schuh
> >
> >
> >
>
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--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595