You are having issues because you do not have the full kernel source 
installed.  The Upstream Vendor does not release the kernel-source rpm any 
more.  Please read the RELEASE-NOTES-x86-en in /usr/share/doc/sl-release*/

From RELEASE-NOTES-x86-en
-------------------------------------------------------------------------
     o In order to eliminate the redundancy inherent in providing a separate
       package for the kernel source code when that source code already
       exists in the kernel's .src.rpm file, Scientific Linux 4.x no
       longer includes the kernel-source package. Users that require access
       to the kernel sources can find them in the kernel .src.rpm file. To
       create an exploded source tree from this file, perform the following
       steps (note that <version> refers to the version specification for
       your currently-running kernel):

         1. Obtain the kernel-<version>.src.rpm file from one of the
            following sources:

               o The SRPMS directory on the appropriate "SRPMS" CD iso image

               o The FTP site where you got the kernel package

The kernel src.rpm can be obtained from
ftp://ftp.scientificlinux.org/linux/scientific/4x/SRPMS/vendor/errata/

         2. Install kernel-<version>.src.rpm (given the default RPM
            configuration, the files this package contains will be written to
            /usr/src/redhat/)

         3. Change directory to /usr/src/redhat/SPECS/, and issue the
            following command:

            rpmbuild -bp --target=<arch> kernel.spec

            (Where <arch> is the desired target architecture.)

            On a default RPM configuration, the kernel tree will be located
            in /usr/src/redhat/BUILD/.

         4. In resulting tree, the configurations for the specific kernels
            shipped in Scientific Linux 4.x are in the /configs/
            directory. For example, the i686 SMP configuration file is named
            /configs/kernel-<version>-i686-smp.config. Issue the following
            command to place the desired configuration file in the proper
            place for building:

            cp <desired-file> ./.config

         5. Issue the following command:

            make oldconfig

       You can then proceed as usual.

-----------------------------------------------------------------------------

-Connie Sieh

 On 
Wed, 9 Nov 2005, Rob Henderson wrote:

> I am currently trying to get Scientific Linux to run properly on an Acer
> TravelMate 8104WLMi. I knew it had issues with the acpi and the DSDT
> database. In order to try to fix this I need to patch the kernel and
> recompile.
> 
> I have however found that
> 
> when from directory /usr/src/kernel/2.6.9-5.0.5.EL-hugemem-i686
> I issue the command
> 
> >make zImage (I note make dep is no longer necessary)
> 
> It fails with errors even for the standard unpatched kernel. I have tried a
> range of recent SL 4.0 4.1 and they all fail
> 
> The 4.1 fails with
> 
> 
> root@lapi 2.6.9-5.0.5.EL-hugemem-i686]# make zImage
>   CHK     include/linux/version.h
>   SPLIT   include/linux/autoconf.h -> include/config/*
>   CHK     include/asm-i386/asm_offsets.h
>   HOSTCC  scripts/genksyms/genksyms.o
>   HOSTCC  scripts/genksyms/lex.o
>   HOSTCC  scripts/genksyms/parse.o
>   HOSTLD  scripts/genksyms/genksyms
>   CC      scripts/mod/empty.o
>   MKELF   scripts/mod/elfconfig.h
>   HOSTCC  scripts/mod/file2alias.o
>   HOSTCC  scripts/mod/modpost.o
>   HOSTCC  scripts/mod/sumversion.o
>   HOSTLD  scripts/mod/modpost
> make[1]: *** No rule to make target `init/main.o', needed by `init/built-in.o'.  Stop.
> make: *** [init] Error 2
> 
> 
> On an older release 3.9 I got
> 
> 
> /usr/src/linux-2.4.21-15.0.4.EL/include/net/esp.h:49: `crypto_hmac_update' undeclared (first use in this function)
> make[3]: *** [xfrm_algo.o] Error 1
> make[3]: Leaving directory `/usr/src/linux-2.4.21-15.0.4.EL/net/xfrm'
> make[2]: *** [first_rule] Error 2
> make[2]: Leaving directory `/usr/src/linux-2.4.21-15.0.4.EL/net/xfrm'
> make[1]: *** [_subdir_xfrm] Error 2
> make[1]: Leaving directory `/usr/src/linux-2.4.21-15.0.4.EL/net'
> make: *** [_dir_net] Error 2
> 
> 
> 
> 
> This seems rather fundamental as if something has fundamentally changed
> which I have missed.
> 
> I have been used to recompiling the kernel when using the old caldera distribution
> and never had any problems so I assume I am doing something fundamentally wrong.
> but without being able to recomp[ile I cannot fix problems.
> 
> Thanks for any light on this
> 
> 
> 
> 
> Dr Rob C W Henderson
> Department of Physics    Lancaster University
> Telephone : 01524 593617
>