Building GIT head with
mkdir obj && cd obj/ && cmake .. && make -j5 && mkdir DEST && make install DESTDIR=`pwd`/DEST
yields
(sid)ametzler@argenau:/tmp/FLANN/flann/obj$ tail -n3 DEST/usr/local/lib/pkgconfi
g/flann.pc
Libs: -L${libdir} -L/usr/lib/x86_64-linux-gnu;-llz4 -lflann -lflann_cpp
Cflags: -I${includedir}
Note the stray semicolon in Libs.
flann uses @LZ4_STATIC_LDFLAGS@ in cmake/flann.pc.in, however @LZ4_STATIC_LDFLAGS@ is a semicolon delimited list.