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Did another rosinstall and got the latest build of perception_pcl which seems to work. I'm not sure what the problem was though.

flann still has the name_install_tool section commented out; I'm not sure why since it's necessary to have the correct location for libflann_cpp or , so I think you have to do it manually if the Makefile doesn't. So my Makefile has for that:

if [ `uname` = Darwin ]; then \
    install_name_tool -id `rospack find flann`/lib/libflann_cpp.1.6.dylib lib/libflann_cpp.1.6.7.dylib; \
fi

Note that you have to fix the whole path. Can somebody confirm and fix this in svn? I see it's still in flann 1.6.8.

Also I removed all refs to lib64 in the flann manifest.xml. pcl_ros still refers to it and complains in the log file, but it doesn't have any effect that I have so far observed on pcd_viewer. Not sure about other things. Here's what my manifest.xml for flann has in the <export> section (I removed the angle brackets which were affecting display of the code):

cpp cflags="-I${prefix}/include" lflags="-Wl,-rpath,${prefix}/lib -Wl,-rpath,${prefix}/lib -L${prefix}/lib -L${prefix}/lib -lflann_cpp -lhdf5_cpp -lhdf5"

Again if flann isn't actually using a lib64 directory, this should be removed from the manifest.xml in svn.