Hi! Admittedly, what prompts this report is arguably a bug in a package: It passes _all_ the configure flags to AM_DISTCHECK_CONFIGURE_FLAGS. Not a bright idea I guess, but simple.
Unfortunately distcheck reads: # This target untars the dist file and tries a VPATH configuration. Then # it guarantees that the distribution is self-contained by making another # tarfile. distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ … && ../configure --srcdir=.. --prefix="$$dc_install_base" \ $(AM_DISTCHECK_CONFIGURE_FLAGS) \ $(DISTCHECK_CONFIGURE_FLAGS) \ && $(MAKE) $(AM_MAKEFLAGS) \ So the "local" flags, --srcdir and especially --prefix, are provided by distcheck, and then overridden by the user's DISTCHECK_CONFIGURE_FLAGS. Since I use --prefix, boom. Very much agreed, --prefix should not have made it into (AM_)DISTCHECK_CONFIGURE_FLAGS; however it seems simple to just pass --srcdir and --prefix last to be protected against such cases. Thanks!