To build arts (3.5.12) from the stable repository, with autoconf, I applied a little sed substitution :
$ cp -vp /usr/share/aclocal/libtool.m4 admin/libtool.m4.in && $ cp -vp /usr/share/libtool/config/ltmain.sh admin/ltmain.sh && $ make -f admin/Makefile.common && $ sed -e 's/qiomanager_p.h qiomanager_p.moc/qiomanager_p.h > qiomanager_p.moc/' -i qtmcop/Makefile.in
and then ./configure ... && make && make install
It may help. ( See http://trinity-devel.pearsoncomputing.net/?0::116 )