Rdbi.PgSQL segmentation faults
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Ido M. Tamir ▴ 320
@ido-m-tamir-1268
Last seen 10.2 years ago
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
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