Adventures installing gkmersvm

gkmersvm is an svm kernel implementation from the Beer lab: http://www.beerlab.org/gkmsvm/

I ran into a couple of issues when trying to compile it, and I thought I'd describe them here.

When I first typed in make, I got: fatal error: 'tr1/unordered_map' file not found

This was fixed by upgrading my gcc using the instructions on: http://stackoverflow.com/questions/837992/update-gcc-on-osx

Then make resulted in: "'getopt' was not declared in this scope"

This was fixed by adding "#include <getopt.h>" to src/mainSVMclassify.cpp:

When I did this on our linux server, I also got a bunch of errors about "intptr_t" has not been declared. This was fixed by adding #include <stdint.h> to the following files:

src/CountKLmersGeneral.cpp:19

src/MLEstimKLmers.cpp

src/LKTree.cpp

src/LTree.cpp

src/LKTree.h 

After this, "make" produced the necessary binaries gkmsvm_classify, gkmsvm_kernel and gkmsvm_train. Curiously enough, there's no "make install", so I manually copied the binaries to /usr/local/bin.

Finally, when I tried to run the modshogun script, I got the error "Cannot create new instances of type 'Labels'". I think this is because I was using shogun 4.0.0, and the script was written for Shogun version 0.9.2 ~ 1.1.0. Changing every instance of "Labels" to "BinaryLabels" fixed the issue. Note, if you are getting a segfault with the modular interface, or are having trouble installing it, see my post about shogun.

Also...after that gcc upgrade, I ran into the following error with a line containing "dispatch_block_t", which once again requires modifying some source code: http://hamelot.co.uk/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/