#Ubuntu-15.10-i686 ですが、
#root@i5:/usr/local# git clone git://github.com/shirok/Gauche.git
Cloning into 'Gauche'...
remote: Counting objects: 62718, done.
remote: Total 62718 (delta 0), reused 0 (delta 0), pack-reused 62718
Receiving objects: 100% (62718/62718), 31.16 MiB | 3.30 MiB/s, done.
Resolving deltas: 100% (49763/49763), done.
Checking connectivity... done.
root@i5:/usr/local# cd Gauche
root@i5:/usr/local/Gauche# ./DIST gen
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: copying file `m4/libtool.m4'
libtoolize: copying file `m4/ltoptions.m4'
libtoolize: copying file `m4/ltsugar.m4'
libtoolize: copying file `m4/ltversion.m4'
libtoolize: copying file `m4/lt~obsolete.m4'
configure.ac:14: installing '../../compile'
configure.ac:16: error: required file '../../ltmain.sh' not found
configure.ac:8: installing '../../missing'
src/Makefile.am: installing '../../depcomp'
parallel-tests: installing '../../test-driver'
autoreconf: automake failed with exit status: 1
root@i5:/usr/local/Gauche# こうなってしまいます。
#少し前(2Wくらい前)のGaucheからltmain.shを持ってきて置くと、make test
#まで通ります。
#automakeとlibtoolのバージョンはいくつですか
#手元ではUbuntu 14.04 x86_64 automake 1.14.1 libtool 2.4.2 および Ubuntu 16.04 i686 automake 1.15 libtool 2.4.6 で動作確認できました。