I put this here in the hope that google will find it and it will be useful for developers having problems the same problem with libtool and autoconf (I know that this is the document I would have wanted to see - it would have saved me days of work (off and on)). I had a problem building my program on a redhat 8 machine, which therefore had a development environment (automake, autoconf, aclocal, libtool) substantially older than than my usual build computer. So, I'd done a make dist on my new (FC4) machine and transfered the tar back to rh8 machine. configure went OK. This is what I got when I tried to make: then mv -f ".deps/atom-utils.Tpo" ".deps/atom-utils.Plo"; else rm -f ".deps/atom-utils.Tpo"; exit 1; fi ../libtool: line 1: s,^.*/,,g: No such file or directory ../libtool: line 1: -e: command not found *** Warning: inferring the mode of operation is deprecated. *** Future versions of Libtool will require --mode=MODE be specified. ../libtool: line 1: -e: command not found ../libtool: line 1: -e: command not found ../libtool: line 1: -e: command not found ../libtool: line 1: -e: command not found Well, lots of investigation followed. This happens because SED is not defined in the generated libtool (made by configure (and configure is made by autoconf, of course)). the libtool header (the bit that configure adds to ltmain.sh) comes from aclocal.m4 aclocal.m4 is generated using .m4 files by aclocal. so aclocal, when it runs needs to find "The Right" libtool.m4 I installed my own libtool (1.5.20) so I use the share/aclocal/libtool.m4 that comes with that (there are a bunch of variables which this libtool.m4 defines with sane defaults, including SED) by using the -I argument to aclocal (set in autogen.sh). Hope that helps.