configure generates a warning about old build-aux/missing script, it looks like it should be updated
to a newer version (see http://git.savannah.gnu.org/cgit/automake.git/tree/lib and http://old.nabble.com/Re%3A--PATCH--\{master}-missing%3A-do-not-touch-timestamps--only-warn-for-out-of-date-files-td34070403.html)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/home/jakob/src/pkgbuilds/avrprog2/src/avrprog2-1.3.1/build-aux/missing: Unknown `--is-lightweight' option
Try `/home/jakob/src/pkgbuilds/avrprog2/src/avrprog2-1.3.1/build-aux/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing