I created a support request for this: https://sourceforge.net/tracker/?func=detail&aid=2856824&group_id=13478&atid=213478
(that may not have been the right thing to do, sourceforge tracker is a littel confusing :)
The issue is that 'make install' fails if the doc/html/api/ directory is empty. This patch calls 'install' only if that directory is not empty.
Configure flac with --disable-doxygen-docs. 'make' works fine, but 'make install' fails at the following:
...
make[3]: Leaving directory `/home/sam/flac/doc/html/images'
make[3]: Entering directory `/home/sam/flac/doc/html'
make[4]: Entering directory `/home/sam/flac/doc/html'
make[4]: Nothing to be done for `install-exec-am'.
/bin/bash ../../mkinstalldirs...