RODBC connection to Oracle on 64-bit RHEL box failing

Wed, Mar 24, 2010 6:44 AM

On Mar 23, 2010, at 2:47 PM, Harlan Harris wrote:

Is Actual making a 64 bit Oracle ODBC driver available?  I had not seen anything on that and had in fact queried them some time ago specifically on the availability of one. I use their 32 bit version on Snow Leopard.

We need to be able to run our software on a 64-bit Redhat Linux box now. We
installed instantclient_11_2_0_1_0-linux-64bit with ODBC support. That
works. We also compiled and installed unixODBC version 2.2.14, and that
works too. (Version 2.2.11, which is shipped with RedHat, does NOT work.)

I then installed the RODBC source, as follows (we have to install packages
in the user directory, for uninteresting reasons):

Sys.info()[c(1:3,5)]

                             sysname                               release
                             "Linux"                  "2.6.18-164.6.1.el5"
                             version                               machine
"#1 SMP Tue Oct 27 11:28:30 EDT 2009"                              "x86_64"

sessionInfo()

R version 2.10.1 (2009-12-14)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] tools_2.10.1

install.packages("RODBC", "~/R/x86_64-redhat-linux-gnu-library/2.10/")

trying URL '
http://cran.revolution-computing.com/src/contrib/RODBC_1.3-1.tar.gz'
Content type 'application/x-gzip' length 990220 bytes (967 Kb)
opened URL
==================================================
downloaded 967 Kb

* installing *source* package ?RODBC? ...
checking for gcc... gcc -m64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sql.h usability... yes
checking sql.h presence... yes
checking for sql.h... yes
checking sqlext.h usability... yes
checking sqlext.h presence... yes
checking for sqlext.h... yes
checking for library containing SQLTables... -lodbc
checking for SQLLEN... yes
checking for SQLULEN... yes
checking for long... yes
checking size of long... 8
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I. -I/home/rproj/unixODBC/include/
-I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
-c RODBC.c -o RODBC.o
In file included from /home/rproj/unixODBC/include/sql.h:19,
                from RODBC.c:41:
/home/rproj/unixODBC/include/sqltypes.h:400: warning: type defaults to ?int?
in declaration of ?SQLBIGINT?
/home/rproj/unixODBC/include/sqltypes.h:403: warning: type defaults to ?int?
in declaration of ?SQLUBIGINT?
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o RODBC.so RODBC.o -lodbc
-L/home/rproj/unixODBC/lib/ -L/usr/lib64/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
 converting help for package ?RODBC?
   finding HTML links ... done
   RODBC-internal                          html
   RODBC-package                           html
   odbc                                    html
   odbcClose                               html
   odbcConnect                             html
   odbcDataSources                         html
   odbcGetInfo                             html
   odbcSetAutoCommit                       html
   setSqlTypeInfo                          html
   sqlColumns                              html
   sqlCopy                                 html
   sqlDrop                                 html
   sqlFetch                                html
   sqlQuery                                html
   sqlSave                                 html
   sqlTables                               html
   sqlTypeInfo                             html
** building package indices ...
* DONE (RODBC)

The downloaded packages are in
   ?/tmp/RtmpLzupy7/downloaded_packages?

library(RODBC)
hdl <- odbcConnect("ktparep")

*** caught segfault ***
address (nil), cause 'unknown'

Traceback:
1: .Call(C_RODBCDriverConnect, as.character(connection), id,
as.integer(believeNRows),     as.logical(readOnlyOptimize))
2: odbcDriverConnect("DSN=ktparep")
3: eval(expr, envir, enclos)
4: eval(expr, p)
5: eval.parent(Call)
6: odbcConnect("ktparep")


Anyone have any ideas? This sort of seg fault seems like a 64-bit/32-bit
issue, but as far as I can see, everything in the chain is 64-bit...

Also, unixODBC does not seem to be under active development or support. Are
there alternatives for accessing Oracle servers? ROracle seems even less
active than unixODBC...

Thank you!

-Harlan

Two comments:

1. The segfault is indeed typically a consequence of a mix of 32/64 bit tools. That being said, I am not seeing anything obvious to suggest that one component or another is 32 bit.  You might want to check your environment variables (eg. LD_LIBRARY_PATH, PATH or one of the Oracle variables) or that there is an entry in /etc/ld.so.conf that is pointing to a 32 bit version of either Oracle's files or unixODBC. Also, be sure that any relevant entries in odbcinst.ini and odbc.ini are also pointing to the proper Oracle ODBC drivers.

2. If you manage to solve the above problem, you have another potential hurdle in front of you, which is that there have been reports of problems connecting to Oracle using 64 bit R/RODBC on 64 bit Linux. It would be helpful, if you do solve the above issue, to try to connect and to see what level of success you have. Prof. Ripley is aware of the issue and either is or will shortly be testing the 64 bit toolchain on Linux to see if he can identify the etiology of the problem and perhaps offer a fix or workaround.


I have not used ROracle, but others have and seem to have good luck with it. I would not let the last version dates of either unixODBC or ROracle sway your opinion. If the components are pretty stable and are not influenced by updates on the R or Oracle end of things, there may very well be no reason to update them. But I would certainly defer to the respective maintainers on those points.

HTH,

Marc Schwartz

RODBC connection to Oracle on 64-bit RHEL box failing

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