Steps to reproduce the bug: 1. Create the directories and the files $ mkdir -p autoconf include/common src $ touch src/main.cpp autoconf/configure.ac
2. Edit the contents of autoconf/configure.ac: AC_PREREQ([2.69]) AC_INIT([foo], 3.1, [victor.lav...@gmail.com]) LT_INIT AC_CONFIG_SRCDIR([src/main.cpp]) AC_CONFIG_HEADERS([include/common/config.h]) AC_OUTPUT 3. Run autoreconf $ autoreconf -v autoconf/configure.ac 4. Notice the error: autoheader-2.69: cannot rename /tmp/arvJbwKq/ahY1jPcF/config.hin as include/common/config.h.in: No such file or directory Also note that no file is generated in include/common 5. Now run autoheader $ autoheader-2.69 autoconf/configure.ac 6. Notice that it works, and include/common/config.h.in is generated I hope this helps