[R] Summary:ROracle error
Vikram Khurana
vkhurana at mail.nmfs.hawaii.edu
Fri Aug 16 04:55:43 CEST 2002
Oracle is finally up and running on RH 7.3 now. I will try to summarize
the pitfalls to avoid here for future reference.
1> Make sure you have the Pro C/C++ drivers in Oracle client installed.
This can be verified by looking for the existence of the proc directory
in $ORACLE_HOME. Existence of proc means it worked
2> Put the following in the .bashrc script in root
export ORACLE_HOME=/home/oracle/OraHome1
export PATH=$PATH:/sbin:/usr/sbin:/home/oracle:$ORACLE_HOME/bin:
/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66
The last ' /usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66' to be
replaced by your gcc directory. The way you find your gcc directory is
by doing locate stddef.h
It will return a bunch of paths. Look for the one which is similar to
the one above.
Note that Oracle is only certified for gcc 2.95 or before. RH 7.3 comes
installed with 2.96. You will have to copy gcc 2.95 from another machine
which has it
3> make sure the pcscfg.cfg file under $ORACLE_HOME/precomp/admin looks
like
sys_include=($ORACLE_HOME/precomp/public,/usr/lib/gcc-lib/i386-redhat-li
nux/egcs-2.91.66/include,/usr/include)
include=($ORACLE_HOME/precomp/public)
include=($ORACLE_HOME/rdbms/demo)
include=($ORACLE_HOME/network/public)
include=($ORACLE_HOME/plsql/public)
ltype=short
The 2nd path in the sys_include should be your gcc folder include file
4> export $LIBRARY_PATH=$ORACLE_HOME/lib
5> Run . .bashrc to set environment variables. Now you can run the R CMD
INSTALL ROracle_0.3-3.tar.gz command
6> If the error says that it cannot find stddef.h or stdarg.h, create a
soft link for
/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66/include/stddef.h and
/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66/include/stdarg.h
respectively in the directory that gcc is searching in (probably
/usr/include)
Thanks,
Vikram
-----Original Message-----
From: David James [mailto:dj at research.bell-labs.com]
Sent: Thursday, August 15, 2002 5:48 AM
To: Vikram Khurana
Subject: Re: [R] ROracle error
Hi Vikram,
I forgot to ask you. If and when you solve your problem, could you
please summarize it and send a copy to r-help? I'm sure at some
point other people may encounter the same problem, and it would be
nice if you could save them some precious time.
Thanks,
--
David
Vikram Khurana wrote:
> David,
>
> I followed all the steps in the ROracle INSTALL document. I also found
> out that gcc2.96 is incompatible with Oracle Pro C.
>
> So I copied the gcc 2.95.3 files from another RH 7.3 computer and put
> them
> under /usr/local/ on my computer. I also put the
> /usr/local/lib/gcc-lib/i686-pc-linux-gnu/2.95.3 path in PATH. However
> now I get an error
>
> R CMD SHLIB -o ROracle.so RS-DBI.o RS-Oracle.o
> make[1]: Entering directory `/tmp/R.INSTALL.15544/ROracle/src'
> gcc -shared -o ROracle.so RS-DBI.o RS-Oracle.o
> -L/home/oracle/OraHome1/lib -L/home/oracle/OraHome1/network/lib
> -lclntst8 -lnbeq8 -lnhost8 -lnus8 -lnldap8 -lldapclnt8 -lnsslb8 -ln8
> -lncrypt8 -ln8 -lncrypt8 -lnoname8 -lntcp8 -lntcps8 -lnsslb8 -lnent8
> -lntcp8 -lntns8 -ldl -lm -lpthread -ldl -lm -L/usr/lib/R/bin -lR
> ld: cannot open crtbeginS.o: No such file or directory
> make[1]: *** [ROracle.so] Error 1
> make[1]: Leaving directory `/tmp/R.INSTALL.15544/ROracle/src'
> make: *** [ROracle.so] Error 2
> ERROR: compilation failed for package 'ROracle'
>
> crtbeginS.o does exist in the
> /usr/local/lib/gcc-lib/i686-pc-linux-gnu/2.95.3 directory ??
>
> My pcscfg.cfg under $ORACLE_HOME/precomp/admin looks as follows:
>
sys_include=($ORACLE_HOME/precomp/public,/home/local/gcc-2.95.3/gcc/ginc
> lude,/usr/include)
> include=($ORACLE_HOME/precomp/public)
> include=($ORACLE_HOME/rdbms/demo)
> include=($ORACLE_HOME/network/public)
> include=($ORACLE_HOME/plsql/public)
> ltype=short
>
> Would you know what I'm doing incorrectly?
>
> Thanks for your time,
> Vikram
>
>
>
> -----Original Message-----
> From: owner-r-help at stat.math.ethz.ch
> [mailto:owner-r-help at stat.math.ethz.ch] On Behalf Of Vikram Khurana
> Sent: Friday, August 09, 2002 4:13 PM
> To: David James
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] FW: ROracle error
>
> Thanks David,
>
> I was able to get past the proc problems. However now I'm stuck on
> another problem. Hope you can point me in the right direction here
too.
>
> My pcscfg.cfg file in $ORACLE_HOME/precomp/admin/pcscfg.cfg
> looks as follows:
>
>
sys_include=($ORACLE_HOME/precomp/public,/usr/lib/gcc-lib/i386-redhat-li
> nux/2.96/include/,/usr/include)
> include=($ORACLE_HOME/precomp/public)
> include=($ORACLE_HOME/rdbms/demo)
> include=($ORACLE_HOME/network/public)
> include=($ORACLE_HOME/plsql/public)
> ltype=short
>
> The error message on executing R CMD INSTALL ROracle_0.3-3.tar.gz
logged
>
> in as root is as follows:
>
> R CMD COMPILE RS-DBI.c
> make[1]: Entering directory `/tmp/R.INSTALL.6290/ROracle/src'
> gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES
> -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c RS-DBI.c -o
> RS-DBI.o
> make[1]: Leaving directory `/tmp/R.INSTALL.6290/ROracle/src'
> proc CODE=ANSI_C INCLUDE=/usr/lib/R/include PARSE=FULL
> RS-Oracle.pc
>
> Pro*C/C++: Release 8.1.7.0.0 - Production on Fri Aug 9 16:06:51 2002
>
> (c) Copyright 2000 Oracle Corporation. All rights reserved.
>
> System default option values taken from:
> /home/oracle/OraHome1/precomp/admin/pcscfg.cfg
>
> Error at line 36, column 10 in file /usr/lib/R/include/S.h
> #include <stddef.h>
> .........1
> PCC-S-02015, unable to open include file
> Error at line 33, column 10 in file /usr/include/stdlib.h
> #include <stddef.h>
> .........1
> PCC-S-02015, unable to open include file
> Syntax error at line 133, column 15, file /usr/include/stdlib.h:
> Error at line 133, column 15 in file /usr/include/stdlib.h
> extern size_t __ctype_get_mb_cur_max (void) __THROW;
> ..............1
> PCC-S-02201, Encountered the symbol "__ctype_get_mb_cur_max" when
> expecting one
> of the following:
>
> ; , = ( [
> The symbol ";" was substituted for "__ctype_get_mb_cur_max" to
continue.
>
> & on & on
>
> I know this is really a Pro C problem & not a R problem, but I'm
hoping
> somebody in this list might still be able to help me...
>
> Thanks,
> Vikram
>
> David James wrote:
>
> >Hello Vikram,
> >
> >(I did respond to you yesterday's email from vkhurana at noaa.gov, but
> >apparantly noaa.gov doesn't recognize your handle vkhurana.)
> >
> >Apparently you don't have the Oracle ProC/C++ precomplier "proc"
> >in your $PATH. You need to include $ORACLE_HOME/bin in your $PATH,
> >and probably $ORACLE_HOME/lib in your $LD_LIBRARY_PATH. See the
> >files INSTALL, README, and README.client in the source distribution
> >(they'll be in the "inst" directory under "ROracle" after you untar
> >the source file ROracle_0.3-3.tar.gz).
> >
> >Regards,
> >--
> >David
> >
> >Vikram Khurana wrote:
> >
> >>Howdy,
> >>
> >>When doing a
> >>install.packages("ROracle") in R I'm getting the following error:
> >>
> >>R CMD COMPILE RS-DBI.c
> >>make[1]: Entering directory `/tmp/R.INSTALL.1809/ROracle/src'
> >>gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES
> >>-mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c RS-DBI.c -o
> >>RS-DBI.o
> >>make[1]: Leaving directory `/tmp/R.INSTALL.1809/ROracle/src'
> >>proc CODE=ANSI_C INCLUDE=/usr/lib/R/include PARSE=FULL
> >>RS-Oracle.pc
> >>make: proc: Command not found
> >>make: *** [RS-Oracle.c] Error 127
> >>ERROR: compilation failed for package 'ROracle'
> >>
> >>
> >>I've tried this on 2 different RH 7.3 LINUX boxes with no luck. I
also
>
> >>searched the R search engine and google with no luck. Can someone
> please
> >>
> >>point me in the right direction as to if I'm doing something wrong?
> >>
> >>Thanks,
> >>Vikram
> >>
> >>
>
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--
David A. James
Statistics Research, Room 2C-253 Phone: (908) 582-3082
Bell Labs, Lucent Technologies Fax: (908) 582-3340
Murray Hill, NJ 09794-0636
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