[root@localhost modsecurity-apache_2.6.5]# ./configure --with-apxs=/usr/local/apache2/bin/apxs --with-apr=/usr/local/apache2/bin/apr-1-config --with-apu=/usr/local/apache2/bin/apu-1-config
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-redhat-linux-gnu
checking host system type... i686-redhat-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 98304
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gawk... (cached) gawk
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for grep that handles long lines and -e... (cached) /bin/grep
checking for perl... /usr/bin/perl
checking for env... /bin/env
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking for pid_t... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uint8_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for atexit... yes
checking for getcwd... yes
checking for memmove... yes
checking for memset... yes
checking for strcasecmp... yes
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strncasecmp... yes
checking for strrchr... yes
checking for strstr... yes
checking for strtol... yes
checking for fchmod... yes
Checking plataform... Identified as Linux
configure: looking for Apache module support via DSO through APXS
configure: found apxs at /usr/local/apache2/bin/apxs
configure: checking httpd version
configure: httpd is recent enough
checking for libpcre config script... /usr/local/bin/pcre-config
configure: using pcre v8.30
checking for libapr config script... /usr/local/apache2/bin/apr-1-config
configure: using apr v1.4.6
checking for libapu config script... /usr/local/apache2/bin/apu-1-config
configure: using apu v1.4.1
checking for libxml2 config script... /usr/bin/xml2-config
configure: using libxml2 v2.6.26
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for liblua config script... no
checking for lua install... no
configure: optional lua library not found
checking for libcurl config script... /usr/bin/curl-config
checking if libcurl is at least v... yes, 7.15.5
checking if libcurl is linked with gnutls... no
configure: using curl v7.15.5
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tools/Makefile
config.status: creating apache2/Makefile
config.status: creating build/apxs-wrapper
config.status: creating mlogc/mlogc-batch-load.pl
config.status: creating tests/run-unit-tests.pl
config.status: creating tests/run-regression-tests.pl
config.status: creating tests/gen_rx-pm.pl
config.status: creating tests/csv_rx-pm.pl
config.status: creating tests/regression/server_root/conf/httpd.conf
config.status: creating tools/rules-updater.pl
config.status: creating mlogc/Makefile
config.status: creating tests/Makefile
config.status: creating apache2/modsecurity_config_auto.h
config.status: apache2/modsecurity_config_auto.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
[root@localhost modsecurity-apache_2.6.5]#
 

[root@localhost modsecurity-apache_2.6.5]# make
Making all in tools
make[1]: Entering directory `/Soft/modsec/modsecurity-apache_2.6.5/tools'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/Soft/modsec/modsecurity-apache_2.6.5/tools'
Making all in apache2
make[1]: Entering directory `/Soft/modsec/modsecurity-apache_2.6.5/apache2'
make all-am
make[2]: Entering directory `/Soft/modsec/modsecurity-apache_2.6.5/apache2'
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLINUX=2 -D_REENTRANT -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -I/usr/local/apache2/include -I/usr/local/apache2/include -I/usr/local/apache2/include -I/usr/local/include -I/usr/include/libxml2 -DWITH_PCRE_STUDY -DMODSEC_PCRE_MATCH_LIMIT=1500 -DMODSEC_PCRE_MATCH_LIMIT_RECURSION=1500 -g -O2 -MT mod_security2_la-mod_security2.lo -MD -MP -MF .deps/mod_security2_la-mod_security2.Tpo -c -o mod_security2_la-mod_security2.lo `test -f 'mod_security2.c' || echo './'`mod_security2.c
../libtool: line 813: X--tag=CC: command not found
../libtool: line 846: libtool: ignoring unknown tag : command not found
../libtool: line 813: X--mode=compile: command not found
../libtool: line 979: *** Warning: inferring the mode of operation is deprecated.: command not found
../libtool: line 980: *** Future versions of Libtool will require --mode=MODE be specified.: command not found
../libtool: line 1123: Xgcc: command not found
../libtool: line 1123: X-DHAVE_CONFIG_H: command not found
../libtool: line 1123: X-I.: command not found
../libtool: line 1123: X-DLINUX=2: command not found
../libtool: line 1123: X-D_REENTRANT: command not found
../libtool: line 1123: X-D_GNU_SOURCE: command not found
../libtool: line 1123: X-D_LARGEFILE64_SOURCE: command not found
../libtool: line 1123: X-I/usr/local/apache2/include: No such file or directory
../libtool: line 1123: X-I/usr/local/apache2/include: No such file or directory
../libtool: line 1123: X-I/usr/local/apache2/include: No such file or directory
../libtool: line 1123: X-I/usr/local/include: No such file or directory
../libtool: line 1123: X-I/usr/include/libxml2: No such file or directory
../libtool: line 1123: X-DWITH_PCRE_STUDY: command not found
../libtool: line 1123: X-DMODSEC_PCRE_MATCH_LIMIT=1500: command not found
../libtool: line 1123: X-DMODSEC_PCRE_MATCH_LIMIT_RECURSION=1500: command not found
../libtool: line 1123: X-g: command not found
../libtool: line 1123: X-O2: command not found
../libtool: line 1123: X-MT: command not found
../libtool: line 1123: Xmod_security2_la-mod_security2.lo: command not found
../libtool: line 1123: X-MD: command not found
../libtool: line 1123: X-MP: command not found
../libtool: line 1123: X-MF: command not found
../libtool: line 1123: X.deps/mod_security2_la-mod_security2.Tpo: No such file or directory
../libtool: line 1123: X-c: command not found
../libtool: line 1175: Xmod_security2_la-mod_security2.lo: command not found
../libtool: line 1180: libtool: compile: cannot determine name of library object from `': command not found
make[2]: *** [mod_security2_la-mod_security2.lo] Error 1
make[2]: Leaving directory `/Soft/modsec/modsecurity-apache_2.6.5/apache2'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/Soft/modsec/modsecurity-apache_2.6.5/apache2'
make: *** [all-recursive] Error 1
[root@localhost modsecurity-apache_2.6.5]# 

modsecurity version 2.6.5 là bản ổn định mới nhất hiện nay, có thể libtool trên CentOS 5.6 của bạn đã lỗi thời (out-of-date) cho nên không phù hợp để biên dịch.

Bạn thử upgrage libtool lên version mới hơn xem sao.

Theo mình thì bạn nên upgrade lên CentOS 5.8. 

modsecurity version 2.6.5 là bản ổn định mới nhất hiện nay, có thể libtool trên CentOS 5.6 của bạn đã lỗi thời (out-of-date) cho nên không phù hợp để biên dịch.

Bạn thử upgrage libtool lên version mới hơn xem sao.

Theo mình thì bạn nên upgrade lên CentOS 5.8.