[R-sig-DB] RODBC connection to Oracle on 64-bit RHEL box failing

[Harlan Harris]

Hi, we've been using the following pathway to an Oracle server from R
successfully for quite a while:

32-bit R 2.9.2 on Mac OS X -> RODBC -> ODBC Manager -> Actual Oracle -> DB

(We've also been able to get this working with 64-bit R 2.10.1 and a beta
version of the Actual Oracle driver...)

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

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