PHP module compilation error – libtool: Version mismatch error

If you happen to get this error trying to build your own a PHP module (probably, because you need a newer version than the included one in the disto you use and because it is fairly easy):

libtool: Version mismatch error.  This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:181: geoip.lo] Error 63

Here is what you can do to recreate the configuration files for the build process:

phpize
aclocal
libtoolize --force
autoheader
autoconf
./configure
make

This sequence of commands (probably without the phpize, because it is PHP specific) could save you in similar situations with similar error in other source code not related to PHP.

Probably you saw above that we got this error trying to compile manually pecl-geoip module and here is the whole output.
Remember to delete the source and unpack it again to be sure it is clean and no cached files used from the previously failed compilation.

root@srv ~ # export CFLAGS="-march=core2 -O2 -msse3 -fomit-frame-pointer -pipe"
root@srv ~ # export CXXFLAGS="${CFLAGS}"
root@srv ~ # tar xf geoip-1.1.1.tgz 
root@srv ~ # cd geoip-1.1.1
root@srv ~/geoip-1.1.1 # ls -al
total 72
drwxr-xr-x  3 root root  4096 Oct 22 10:07 .
drwx------ 30 root root  4096 Oct 22 10:07 ..
-rw-r--r--  1  501   20  3572 Aug 18  2016 ChangeLog
-rw-r--r--  1  501   20  3218 Aug 18  2016 LICENSE
-rw-r--r--  1  501   20   348 Aug 18  2016 README
-rw-r--r--  1  501   20  4234 Aug 18  2016 config.m4
-rw-r--r--  1  501   20   626 Aug 18  2016 config.w32
-rw-r--r--  1  501   20 24916 Aug 18  2016 geoip.c
-rw-r--r--  1  501   20  1772 Aug 18  2016 geoip.def
-rw-r--r--  1  501   20  3049 Aug 18  2016 php_geoip.h
drwxr-xr-x  2 root root  4096 Oct 22 10:07 tests
root@srv ~/geoip-1.1.1 # phpize 
Configuring for:
PHP Api Version:         20131106
Zend Module Api No:      20131226
Zend Extension Api No:   220131226
root@srv ~/geoip-1.1.1 # ./configure 
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a sed that does not truncate output... /bin/sed
checking for cc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking for icc... no
checking for suncc... no
checking whether cc understands -c and -o together... yes
checking for system library directory... lib
checking if compiler supports -R... no
checking if compiler supports -Wl,-rpath,... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for PHP prefix... /usr/lib64/php5.6
checking for PHP includes... -I/usr/lib64/php5.6/include/php -I/usr/lib64/php5.6/include/php/main -I/usr/lib64/php5.6/include/php/TSRM -I/usr/lib64/php5.6/include/php/Zend -I/usr/lib64/php5.6/include/php/ext -I/usr/lib64/php5.6/include/php/ext/date/lib
checking for PHP extension directory... /usr/lib64/php5.6/lib/extensions/no-debug-non-zts-20131226
checking for PHP installed headers prefix... /usr/lib64/php5.6/include/php
checking if debug is enabled... no
checking if zts is enabled... no
checking for re2c... re2c
checking for re2c version... 1.1.1 (ok)
checking for gawk... gawk
checking for geoip support... yes, shared
checking for geoip files in default path... found in /usr
checking for GeoIP_open in -lGeoIP... yes
checking for GeoIP_setup_custom_directory in -lGeoIP... yes
checking for GeoIP_set_charset in -lGeoIP... yes
checking for GeoIP_continent_by_id in -lGeoIP... yes
checking for GeoIP_addr_to_num in -lGeoIP... yes
checking whether GEOIP_NETSPEED_EDITION_REV1 is declared... yes
checking whether GEOIP_ACCURACYRADIUS_EDITION is declared... yes
checking for LGPL compatible GeoIP libs... found 1004008
checking for ld used by cc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognize dependent libraries... pass_all
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking the maximum length of command line arguments... 1572864
checking command to parse /usr/bin/nm -B output from cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC
checking if cc PIC flag -fPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) 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 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... no

creating libtool
appending configuration tag "CXX" to libtool
configure: creating ./config.status
config.status: creating config.h
root@srv ~/geoip-1.1.1 # make -j 12
/bin/sh /root/geoip-1.1.1/libtool --mode=compile cc  -I. -I/root/geoip-1.1.1 -DPHP_ATOM_INC -I/root/geoip-1.1.1/include -I/root/geoip-1.1.1/main -I/root/geoip-1.1.1 -I/usr/lib64/php5.6/include/php -I/usr/lib64/php5.6/include/php/main -I/usr/lib64/php5.6/include/php/TSRM -I/usr/lib64/php5.6/include/php/Zend -I/usr/lib64/php5.6/include/php/ext -I/usr/lib64/php5.6/include/php/ext/date/lib  -DHAVE_CONFIG_H  -march=core2 -O2 -msse3 -fomit-frame-pointer -pipe   -c /root/geoip-1.1.1/geoip.c -o geoip.lo 
libtool: Version mismatch error.  This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:181: geoip.lo] Error 63
root@srv ~/geoip-1.1.1 # 

Here is the successful compilation of this PHP module:

root@srv ~ # export CFLAGS="-march=core2 -O2 -msse3 -fomit-frame-pointer -pipe"
root@srv ~ # export CXXFLAGS="${CFLAGS}"
root@srv ~/geoip-1.1.1 # cd ..
root@srv ~ # rm -R geoip-1.1.1
root@srv ~ # tar xf geoip-1.1.1.tgz 
root@srv ~ # cd geoip-1.1.1
root@srv ~/geoip-1.1.1 # phpize
Configuring for:
PHP Api Version:         20131106
Zend Module Api No:      20131226
Zend Extension Api No:   220131226
root@srv ~/geoip-1.1.1 # aclocal
aclocal-1.16: warning: autoconf input should be named 'configure.ac', not 'configure.in'
root@srv ~/geoip-1.1.1 # libtoolize --force
libtoolize: putting auxiliary files in '.'.
libtoolize: linking file './ltmain.sh'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.in,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
root@srv ~/geoip-1.1.1 # autoheader
root@srv ~/geoip-1.1.1 # autoconf
root@srv ~/geoip-1.1.1 # ./configure
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a sed that does not truncate output... /bin/sed
checking for cc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking for icc... no
checking for suncc... no
checking whether cc understands -c and -o together... yes
checking for system library directory... lib
checking if compiler supports -R... no
checking if compiler supports -Wl,-rpath,... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for PHP prefix... /usr/lib64/php5.6
checking for PHP includes... -I/usr/lib64/php5.6/include/php -I/usr/lib64/php5.6/include/php/main -I/usr/lib64/php5.6/include/php/TSRM -I/usr/lib64/php5.6/include/php/Zend -I/usr/lib64/php5.6/include/php/ext -I/usr/lib64/php5.6/include/php/ext/date/lib
checking for PHP extension directory... /usr/lib64/php5.6/lib/extensions/no-debug-non-zts-20131226
checking for PHP installed headers prefix... /usr/lib64/php5.6/include/php
checking if debug is enabled... no
checking if zts is enabled... no
checking for re2c... re2c
checking for re2c version... 1.1.1 (ok)
checking for gawk... gawk
checking for geoip support... yes, shared
checking for geoip files in default path... found in /usr
checking for GeoIP_open in -lGeoIP... yes
checking for GeoIP_setup_custom_directory in -lGeoIP... yes
checking for GeoIP_set_charset in -lGeoIP... yes
checking for GeoIP_continent_by_id in -lGeoIP... yes
checking for GeoIP_addr_to_num in -lGeoIP... yes
checking whether GEOIP_NETSPEED_EDITION_REV1 is declared... yes
checking whether GEOIP_ACCURACYRADIUS_EDITION is declared... yes
checking for LGPL compatible GeoIP libs... found 1004008
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by cc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/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... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... (cached) gawk
checking command to parse /usr/bin/nm -B output from cc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
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 cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) 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 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... no
configure: creating ./config.status
config.status: creating config.h
config.status: executing libtool commands
root@srv ~/geoip-1.1.1 # make -j 12 
/bin/sh /root/geoip-1.1.1/libtool --mode=compile cc  -I. -I/root/geoip-1.1.1 -DPHP_ATOM_INC -I/root/geoip-1.1.1/include -I/root/geoip-1.1.1/main -I/root/geoip-1.1.1 -I/usr/lib64/php5.6/include/php -I/usr/lib64/php5.6/include/php/main -I/usr/lib64/php5.6/include/php/TSRM -I/usr/lib64/php5.6/include/php/Zend -I/usr/lib64/php5.6/include/php/ext -I/usr/lib64/php5.6/include/php/ext/date/lib  -DHAVE_CONFIG_H  -march=core2 -O2 -msse3 -fomit-frame-pointer -pipe   -c /root/geoip-1.1.1/geoip.c -o geoip.lo 
libtool: compile:  cc -I. -I/root/geoip-1.1.1 -DPHP_ATOM_INC -I/root/geoip-1.1.1/include -I/root/geoip-1.1.1/main -I/root/geoip-1.1.1 -I/usr/lib64/php5.6/include/php -I/usr/lib64/php5.6/include/php/main -I/usr/lib64/php5.6/include/php/TSRM -I/usr/lib64/php5.6/include/php/Zend -I/usr/lib64/php5.6/include/php/ext -I/usr/lib64/php5.6/include/php/ext/date/lib -DHAVE_CONFIG_H -march=core2 -O2 -msse3 -fomit-frame-pointer -pipe -c /root/geoip-1.1.1/geoip.c  -fPIC -DPIC -o .libs/geoip.o
/bin/sh /root/geoip-1.1.1/libtool --mode=link cc -DPHP_ATOM_INC -I/root/geoip-1.1.1/include -I/root/geoip-1.1.1/main -I/root/geoip-1.1.1 -I/usr/lib64/php5.6/include/php -I/usr/lib64/php5.6/include/php/main -I/usr/lib64/php5.6/include/php/TSRM -I/usr/lib64/php5.6/include/php/Zend -I/usr/lib64/php5.6/include/php/ext -I/usr/lib64/php5.6/include/php/ext/date/lib  -DHAVE_CONFIG_H  -march=core2 -O2 -msse3 -fomit-frame-pointer -pipe   -o geoip.la -export-dynamic -avoid-version -prefer-pic -module -rpath /root/geoip-1.1.1/modules  geoip.lo -lGeoIP
libtool: link: cc -shared  -fPIC -DPIC  .libs/geoip.o   -lGeoIP  -march=core2 -O2 -msse3   -Wl,-soname -Wl,geoip.so -o .libs/geoip.so
libtool: link: ( cd ".libs" && rm -f "geoip.la" && ln -s "../geoip.la" "geoip.la" )
/bin/sh /root/geoip-1.1.1/libtool --mode=install cp ./geoip.la /root/geoip-1.1.1/modules
libtool: install: cp ./.libs/geoip.so /root/geoip-1.1.1/modules/geoip.so
libtool: install: cp ./.libs/geoip.lai /root/geoip-1.1.1/modules/geoip.la
libtool: finish: PATH="/usr/lib/llvm/7/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/sbin" ldconfig -n /root/geoip-1.1.1/modules
----------------------------------------------------------------------
Libraries have been installed in:
   /root/geoip-1.1.1/modules

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------

Build complete.
Don't forget to run 'make test'.

root@srv ~/geoip-1.1.1 # ls -altr /root/geoip-1.1.1/modules
total 44
drwxr-xr-x 8 root root  4096 Oct 22 10:09 ..
-rwxr-xr-x 1 root root 28728 Oct 22 10:09 geoip.so
-rw-r--r-- 1 root root   905 Oct 22 10:09 geoip.la
drwxr-xr-x 2 root root  4096 Oct 22 10:09 .
root@srv ~/geoip-1.1.1 # make install

You can execute “make install” to install it in the default directory or copy the module manually from “/root/geoip-1.1.1/modules” to whatever directory you like.

Similar error

We have the following compilation error with another software compilation:

libtool: line 467: CDPATH: command not found

The solution is the same as above!

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