[BioC] Rdbi.PgSQL segmentation faults

Wed Aug 24 16:26:05 CEST 2005

Hi, 
since trying to load my data with Rdbi.PgSQL
I am getting segmentation faults as soon as I try to access my 
returned dataframes.

getAll <- function(){
    key <- read.sampleKey()
    con <- dbConnect(PgSQL(),host = "localhost", dbname = "test")
    result <- dbSendQuery( con, paste("SELECT * FROM all" ))
    val <- dbGetResult( result )
    dbClearResult(result)
    dbDisconnect(con)
    return(val)
}

as soon as I call this function and then print(val) or source the file again
I get someting like the error dumps below or Segmentation faults.

Thank you very much for answers, tips (switch to mysql?) etc...
ido

System:
fedora core 4: 
postgresql-8.0.3-1
postgresql-libs-8.0.3-1
postgresql-server-8.0.3-1
postgresql-tcl-8.0.3-1
postgresql-contrib-8.0.3-1
postgresql-jdbc-8.0.3-1
postgresql-pl-8.0.3-1
postgresql-python-8.0.3-1
postgresql-docs-8.0.3-1
postgresql-devel-8.0.3-1
postgresql-odbc-08.00.0100-1
postgresql-test-8.0.3-1

R: Version 2.1.1 
Rdbi            "Rdbi"            "/usr/lib/R/library" "1.1.2"   NA
RdbiPgSQL       "RdbiPgSQL"       "/usr/lib/R/library" "1.1.4"   NA

*** glibc detected *** /usr/lib/R/bin/exec/R: double free or corruption 
(!prev): 0x097c43e0 ***
======= Backtrace: =========
/lib/libc.so.6[0x174424]
/lib/libc.so.6(__libc_free+0x77)[0x17495f]
/usr/lib/libpq.so.4(PQclear+0x47)[0xa63c90]
/usr/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25)
[0xb24d21]
/usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x149)[0x33fbf0]
/usr/lib/R/lib/libR.so[0x33fd45]
/usr/lib/R/lib/libR.so[0x341c5e]
/usr/lib/R/lib/libR.so(Rf_cons+0x115)[0x3424be]
/usr/lib/R/lib/libR.so(Rf_allocList+0x41)[0x342548]
/usr/lib/R/lib/libR.so(Rf_matchArgs+0x43a)[0x33eda1]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x7a)[0x325219]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so[0x34aed5]
/usr/lib/R/lib/libR.so(Rf_usemethod+0x44e)[0x34b5b8]
/usr/lib/R/lib/libR.so(do_usemethod+0x21d)[0x34bc1a]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so[0x323a77]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(do_for+0x224)[0x3247b8]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so(Rf_eval+0x411)[0x322267]
/usr/lib/R/lib/libR.so[0x34abd5]
/usr/lib/R/lib/libR.so(do_usemethod+0x195)[0x34bb92]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so(Rf_eval+0x411)[0x322267]
/usr/lib/R/lib/libR.so[0x34abd5]
/usr/lib/R/lib/libR.so(do_usemethod+0x195)[0x34bb92]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(do_if+0x8d)[0x324b1b]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(do_if+0x8d)[0x324b1b]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so[0x34aed5]
/usr/lib/R/lib/libR.so(Rf_usemethod+0x44e)[0x34b5b8]
/usr/lib/R/lib/libR.so(do_usemethod+0x21d)[0x34bc1a]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x325468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x322365]
/usr/lib/R/lib/libR.so(do_set+0xce)[0x323fdf]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x322464]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x3241ce]
======= Memory map: ========
00111000-00235000 r-xp 00000000 03:06 65279      /lib/libc-2.3.5.so
00235000-00237000 r-xp 00124000 03:06 65279      /lib/libc-2.3.5.so
00237000-00239000 rwxp 00126000 03:06 65279      /lib/libc-2.3.5.so
00239000-0023b000 rwxp 00239000 00:00 0
0023b000-0025d000 r-xp 00000000 03:06 65317      /lib/libm-2.3.5.so
0025d000-0025e000 r-xp 00021000 03:06 65317      /lib/libm-2.3.5.so
0025e000-0025f000 rwxp 00022000 03:06 65317      /lib/libm-2.3.5.so
0025f000-00261000 r-xp 00000000 03:06 65337      /lib/libdl-2.3.5.so
00261000-00262000 r-xp 00001000 03:06 65337      /lib/libdl-2.3.5.so
00262000-00263000 rwxp 00002000 03:06 65337      /lib/libdl-2.3.5.so
00263000-00272000 r-xp 00000000 03:06 65989      /lib/libresolv-2.3.5.so
00272000-00273000 r-xp 0000e000 03:06 65989      /lib/libresolv-2.3.5.so
00273000-00274000 rwxp 0000f000 03:06 65989      /lib/libresolv-2.3.5.so
00274000-00276000 rwxp 00274000 00:00 0
00277000-00291000 r-xp 00000000 03:06 65277      /lib/ld-2.3.5.so
00291000-00292000 r-xp 00019000 03:06 65277      /lib/ld-2.3.5.so
00292000-00293000 rAborted

##############################################################################or:

*** glibc detected *** /usr/lib/R/bin/exec/R: free(): invalid pointer: 
0x00900001 ***
======= Backtrace: =========
/lib/libc.so.6[0x2f8424]
/lib/libc.so.6(__libc_free+0x77)[0x2f895f]
/usr/lib/libpq.so.4(PQclear+0x29)[0x437c72]
/usr/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25)
[0x559d21]
/usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x149)[0x795bf0]
/usr/lib/R/lib/libR.so[0x795d45]
/usr/lib/R/lib/libR.so[0x797c5e]
/usr/lib/R/lib/libR.so(Rf_cons+0x115)[0x7984be]
/usr/lib/R/lib/libR.so(Rf_duplicate+0x23b)[0x76124b]
/usr/lib/R/lib/libR.so(do_subset2_dflt+0x38d)[0x8152db]
/usr/lib/R/lib/libR.so(do_subset2+0x7e)[0x815744]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(Rf_DispatchOrEval+0x5f)[0x77942d]
/usr/lib/R/lib/libR.so(do_subset2+0x55)[0x81571b]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(do_set+0xce)[0x779fdf]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x77a1ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(do_if+0x47)[0x77aad5]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x77a1ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(do_for+0x224)[0x77a7b8]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(do_begin+0x37)[0x77a1ce]
/usr/lib/R/lib/libR.so(Rf_eval+0x60e)[0x778464]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2c9)[0x77b468]
/usr/lib/R/lib/libR.so(Rf_eval+0x50f)[0x778365]
/usr/lib/R/lib/libR.so(Rf_ReplIteration+0x143)[0x79303c]
/usr/lib/R/lib/libR.so[0x793277]
/usr/lib/R/lib/libR.so(run_Rmainloop+0x60)[0x79355b]
/usr/lib/R/lib/libR.so(Rf_mainloop+0x1c)[0x794290]
/usr/lib/R/bin/exec/R(main+0x23)[0x804860b]
/lib/libc.so.6(__libc_start_main+0xc6)[0x2a9de6]
/usr/lib/R/bin/exec/R[0x8048565]
======= Memory map: ========
00111000-00112000 r-xp 00000000 03:06 1952785    /usr/lib/gconv/ISO8859-1.so
00112000-00114000 rwxp 00000000 03:06 1952785    /usr/lib/gconv/ISO8859-1.so
00114000-00149000 r-xp 00000000 03:06 
3782777    /usr/lib/R/library/stats/libs/stats.so
00149000-0014b000 rwxp 00034000 03:06 
3782777    /usr/lib/R/library/stats/libs/stats.so
0014b000-00161000 r-xp 00000000 03:06 3783664    /usr/lib/R/modules/R_X11.so
00161000-00162000 rwxp 00016000 03:06 3783664    /usr/lib/R/modules/R_X11.so
00162000-0016e000 rwxp 00162000 00:00 0 
0016e000-0023e000 r-xp 00000000 03:06 1887739    /usr/X11R6/lib/libX11.so.6.2
0023e000-00242000 rwxp 000cf000 03:06 1887739    /usr/X11R6/lib/libX11.so.6.2
00242000-00260000 r-xp 00000000 03:06 2777346    /usr/lib/libjpeg.so.62.0.0
00260000-00261000 rwxp 0001d000 03:06 2777346    /usr/lib/libjpeg.so.62.0.0
00261000-00263000 r-xp 00000000 03:06 
97835      /usr/lib/R/library/Biobase/libs/Biobase.so
00263000-00264000 rwxp 00001000 03:06 
97835      /usr/lib/R/library/Biobase/libs/Biobase.so
00264000-00266000 r-xp 00000000 03:06 
1341       /usr/lib/R/library/vsn/libs/vsn.so
00266000-00267000 rwxp 00001000 03:06 
1341       /usr/lib/R/library/vsn/libs/vsn.so
00267000-00269000 r-xp 00000000 03:06 65992      /lib/libcom_err.so.2.1
00269000-0026a000 rwxp 00001000 03:06 65992      /lib/libcom_err.so.2.1
00277000-00291000 r-xp 00000000 03:06 65277      /lib/ld-2.3.5.so
00291000-00292000 r-xp 00019000 03:06 65277      /lib/ld-2.3.5.so
00292000-00293000 rwxp 0001a000 03:06 65277      /lib/ld-2.3.5.so
00295000-003b9000 r-xp 00000000 03:06 65279      /lib/libc-2.3.5.so
003b9000-003bb000 r-xp 00124000 03:06 65279      /lib/libc-2.3.5.so
003bb000-003bd000 rwxp 00126000 03:06 65279      /lib/libc-2.3.5.so
003bd000-003bf000 rwxp 003bd000 00:00 0 
003c1000-003e3000 r-xp 00000000 03:06 65317      /lib/libm-2.3.5.so
003e3000-003e4000 r-xp 00021000 03:06 65317      /lib/libm-2.3.5.so
003e4000-003e5000 rwxp 00022000 03:06 65317      /lib/libm-2.3.5.so
003e7000-003e9000 r-xp 00000000 03:06 65337      /lib/libdl-2.3.5.so
003e9000-003ea000 r-xp 00001000 03:06 65337      /lib/libdl-2.3.5.so
003ea000-003eb000 rwxp 00002000 03:06 65337      /lib/libdl-2.3.5.so
00402000-00429000 r-xp 00000000 03:06 2777656    /usr/lib/libreadline.so.5.0
00429000-0042d000 rwxp 00027000 03:06 2777656    /usr