On Windows Cygwin make of some program gives
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
libtoolize: copying file 'build-aux/ltmain.sh'
libtoolize: error: AC_CONFIG_MACRO_DIRS([build-aux/m4]) conflicts with ACLOCAL.AMFLAGS=-I build-aux/m4
Look here:
http://pete.akeo.ie/2010/12/that-darn-libtoolize-acconfigmacrodirm4.html
Maybe u can do like this:
find . -name \*.m4|xargs dos2unix
find . -name \*.ac|xargs dos2unix
find . -name \*.am|xargs dos2unix