[R] Error RODBC: Random termination of R

Ulrich Leopold uleopold at science.uva.nl
Fri Feb 15 09:02:26 CET 2008 

Dear list,

I get random terminations of R-2.6.2 when using RODBC-1.2_3 and a remote
PostgreSQL-8.2.6 database, unixodbc-2.2.11-16,
odbc-postgresql-1:08.01.0200-2.1 on Ubuntu Linux 7.10.

The exact messages can be seen below. It seems that there is some memory
corruption going on. But it seems random to me and can neither be related to
addPK=T/F or fast=T/F. It happens for all possible combinations. Besides I do
not really understand what these messages mean.

Any idea to what it might be related exactly?

Thanks in advance,
Ulrich Leopold

Session details:

>sessionInfo()
R version 2.6.2 (2008-02-08)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RODBC_1.2-3

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

> library(RODBC)
> channel = odbcConnect("crtedb", uid = "uleopold")
> channel
RODB Connection 1
Details:
  case=tolower
  DSN=crtedb
  DATABASE=valid
  SERVER=10.3.1.91
  PORT=5432
  SSLMODE=prefer
  UID=uleopold
  PWD=******
  ReadOnly=Yes
  FakeOidIndex=No
  ShowOidColumn=No
  RowVersioning=No
  ShowSystemTables=No
  ConnSettings=
  Fetch=100
  Socket=8192
  UnknownSizes=0
  MaxVarcharSize=254
  MaxLongVarcharSize=8190
  Debug=0
  CommLog=0
  Optimizer=1
  Ksqo=1
  UseDeclareFetch=0
  TextAsLongVarchar=1
  UnknownsAsLongVarchar=0
  BoolsAsChar=1
  Parse=0
  CancelAsFreeStmt=0
  ExtraSysTablePrefixes=dd_

  LFConversion=0
  UpdatableCursors=0
  DisallowPremature=0
  TrueIsMinus1=0
  BI=0
  ByteaAsLongVarBinary=0
  UseServerSidePrepare=0
  LowerCaseIdentifier=0

> sqlDrop(channel, "clx_test")
character(0)
> sqlSave(channel, clx_test, varTypes=varspec, addPK=TRUE, fast=TRUE) >
odbcClose(channel)
*** glibc detected *** /usr/lib/R/bin/exec/R: corrupted double-linked list:
0x082dd498 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0xb7b8c3f9]
/lib/tls/i686/cmov/libc.so.6[0xb7b8db6e]
/lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7b91800]
/usr/lib/R/lib/libR.so(R_chk_free+0x21)[0xb7d687c1]
/usr/local/lib/R/site-library/RODBC/libs/RODBC.so[0xb742db8d]
/usr/local/lib/R/site-library/RODBC/libs/RODBC.so(RODBCClose+0x2a)[0xb742dd5a]
/usr/lib/R/lib/libR.so[0xb7d13ea2]
/usr/lib/R/lib/libR.so(Rf_eval+0x707)[0xb7d406a7]
/usr/lib/R/lib/libR.so[0xb7d43037]
/usr/lib/R/lib/libR.so(Rf_eval+0x444)[0xb7d403e4]
/usr/lib/R/lib/libR.so[0xb7d41967]
/usr/lib/R/lib/libR.so(Rf_eval+0x444)[0xb7d403e4]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x2a7)[0xb7d439b7]
/usr/lib/R/lib/libR.so(Rf_eval+0x2e2)[0xb7d40282]
/usr/lib/R/lib/libR.so(Rf_ReplIteration+0x19b)[0xb7d6632b]
/usr/lib/R/lib/libR.so(run_Rmainloop+0x107)[0xb7d666f7]
/usr/lib/R/lib/libR.so(Rf_mainloop+0x1c)[0xb7d6674c]
/usr/lib/R/bin/exec/R(main+0x46)[0x8048776]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb7b3a050]
/usr/lib/R/bin/exec/R[0x8048691]
======= Memory map: ========
08048000-08049000 r-xp 00000000 08:03 422045     /usr/lib/R/bin/exec/R
08049000-0804a000 rw-p 00000000 08:03 422045     /usr/lib/R/bin/exec/R
0804a000-09941000 rw-p 0804a000 00:00 0          [heap]
a7700000-a7721000 rw-p a7700000 00:00 0
a7721000-a7800000 ---p a7721000 00:00 0
a78ef000-a793e000 r-xp 00000000 08:03 259109     /usr/lib/libgcrypt.so.11.2.3
a793e000-a7940000 rw-p 0004e000 08:03 259109     /usr/lib/libgcrypt.so.11.2.3
a7940000-a7943000 r-xp 00000000 08:03 259082    
/usr/lib/libgpg-error.so.0.3.0 a7943000-a7944000 rw-p 00002000 08:03 259082   
 /usr/lib/libgpg-error.so.0.3.0 a7944000-a7953000 r-xp 00000000 08:03 266851  
  /usr/lib/libtasn1.so.3.0.9 a7953000-a7954000 rw-p 0000e000 08:03 266851    
/usr/lib/libtasn1.so.3.0.9 a7954000-a79be000 r-xp 00000000 08:03 730108    
/usr/lib/libgnutls.so.13.3.0 a79be000-a79c4000 rw-p 0006a000 08:03 730108    
/usr/lib/libgnutls.so.13.3.0 a79c4000-a79da000 r-xp 00000000 08:03 732700    
/usr/lib/libsasl2.so.2.0.22 a79da000-a79db000 rw-p 00015000 08:03 732700    
/usr/lib/libsasl2.so.2.0.22 a79db000-a79e6000 r-xp 00000000 08:03 732704    
/usr/lib/liblber.so.2.0.130 a79e6000-a79e7000 rw-p 0000b000 08:03 732704    
/usr/lib/liblber.so.2.0.130 a79e7000-a79f6000 r-xp 00000000 08:03 712558
/lib/tls/i686/cmov/libresolv-2.6.1.so
a79f6000-a79f8000 rw-p 0000f000 08:03 712558
/lib/tls/i686/cmov/libresolv-2.6.1.so
a79f8000-a79fa000 rw-p a79f8000 00:00 0
a79fa000-a7a01000 r-xp 00000000 08:03 259121    
/usr/lib/libkrb5support.so.0.1 a7a01000-a7a02000 rw-p 00006000 08:03 259121   
 /usr/lib/libkrb5support.so.0.1 a7a02000-a7a26000 r-xp 00000000 08:03 259108  
  /usr/lib/libk5crypto.so.3.1 a7a26000-a7a27000 rw-p 00024000 08:03 259108    
/usr/lib/libk5crypto.so.3.1 a7a27000-a7a5b000 r-xp 00000000 08:03 732705    
/usr/lib/libldap_r.so.2.0.130 a7a5b000-a7a5c000 rw-p 00034000 08:03 732705    
/usr/lib/libldap_r.so.2.0.130 a7a5c000-a7a61000 r-xp 00000000 08:03 712529
/lib/tls/i686/cmov/libcrypt-2.6.1.so
a7a61000-a7a63000 rw-p 00004000 08:03 712529
/lib/tls/i686/cmov/libcrypt-2.6.1.so
a7a63000-a7a8a000 rw-p a7a63000 00:00 0
a7a8a000-a7ab2000 r-xp 00000000 08:03 259107    
/usr/lib/libgssapi_krb5.so.2.2 a7ab2000-a7ab3000 rw-p 00027000 08:03 259107   
 /usr/lib/libgssapi_krb5.so.2.2 a7ab3000-a7b39000 r-xp 00000000 08:03 259120  
  /usr/lib/libkrb5.so.3.3 a7b39000-a7b3b000 rw-p 00086000 08:03 259120    
/usr/lib/libkrb5.so.3.3 a7b3b000-a7c66000 r-xp 00000000 08:03 825999
/usr/lib/i686/cmov/libcrypto.so.0.9.8
a7c66000-a7c7b000 rw-p 0012a000 08:03 825999
/usr/lib/i686/cmov/libcrypto.so.0.9.8
a7c7b000-a7c7e000 rw-p a7c7b000 00:00 0
a7c7e000-a7cbb000 r-xp 00000000 08:03 826000
/usr/lib/i686/cmov/libssl.so.0.9.8
a7cbb000-a7cbf000 rw-p 0003c000 08:03 826000
/usr/lib/i686/cmov/libssl.so.0.9.8
a7cbf000-a7cdd000 r-xp 00000000 08:03 259480     /usr/lib/libpq.so.5.1
a7cdd000-a7cde000 rw-p 0001e000 08:03 259480     /usr/lib/libpq.so.5.1
a7cde000-a7ce9000 r-xp 00000000 08:03 267880     /usr/lib/libAborted (core
dumped)






_______________________________________________

Ulrich Leopold MSc.

Dep. Phys. Geography and Soil Science
Inst. for Biodiversity and Ecosystem Dynamics
Faculty of Science
University of Amsterdam
Nieuwe Achtergracht 166
NL-1018 WV Amsterdam

Phone: +31-(0)20-525-7456 (7451 Sectretary)
Fax:   +31-(0)20-525-7431
Email: uleopold at science.uva.nl
http://www.science.uva.nl/ibed/cbpg/index.html

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