I'm working on a package silo-llnl. This now FTBFS with changes in autotools.
See #619830 for previous history.

Currently it fails on:

    autoreconf: running: automake --add-missing --copy --force-missing
    configure.ac:1455: required file `src/hzip/Makefile.in' not found
    configure.ac:1458: required file `src/fpzip/Makefile.in' not found
    src/Makefile.am:79: required directory src/hzip does not exist
    src/Makefile.am:83: required directory src/fpzip does not exist
    src/Makefile.am:88: required directory src/hzip does not exist
    tests/Makefile.am: Fortran 77 source seen but `F77' is undefined
    tests/Makefile.am:   The usual way to define `F77' is to add `AC_PROG_F77'
    tests/Makefile.am:   to `configure.ac' and run `autoconf' again.
    autoreconf: automake failed with exit status: 1

when running autoreconf. This is because configure.ac and src/Makefile.am contain:

692 dnl handle Peter Lindstrom's hzip compression stuff
 693 AC_MSG_CHECKING(for hzip)
 694 if test -d $srcdir/src/hzip; then
 695     AC_MSG_RESULT(found)
 696     HZIP=$DEFAULT_HZIP
 697 else
 698     AC_MSG_RESULT(hzip compression not available in BSD version)
 699     HZIP=""
 700 fi
 701 AC_ARG_ENABLE(hzip,
 702     AC_HELP_STRING([--enable-hzip],
 703         [enable Lindstrom hex/quad mesh compression @<:@default=yes@:>@]),
 704     if test "$enable_hzip" = "no"; then
 705         HZIP=""
 706     fi)
 707 AC_SUBST(HZIP)
 708
...
1454 if test -n "$HZIP"; then
1455   AC_CONFIG_FILES([src/hzip/Makefile])
1456 fi
1457 if test -n "$FPZIP"; then
1458   AC_CONFIG_FILES([src/fpzip/Makefile])
1459 fi

and Makefile:

 78 if HZIP_NEEDED
 79 DRIVER_DIRS += hzip
 80 DRIVER_LIBS += hzip/libsilo_hzip.la
 81 endif

etc: it appears that automake is failing to conditionally evaluate lines 690-- and so
not set HZIP="", and then act on this in 1454, and so on.