Adventures installing shogun and shogun's python modular interface

First of all, whatever instructions they have on their main website seem to be out of date, because there is no "configure", so ./configure does not do anything.

Second, I think there used to be a file called "INSTALL", but there isn't anymore. And the README is utterly unhelpful. This is all I could find, and following it seemed to work. That github repo also seems to be the most up to date in terms of documentation.

If ccmake is installed, use it - it will give you insight into all the instructions. If not, well, you need to "cmake .. -DCmdLineStatic=ON -DPythonModular=ON" to get both the static command line interfaces and the python modular interface (and I even tossed in a -DPythonStatic=ON although I'm not sure it did anything...I was driving blind due to no ccmake, and for whatever reason none of this easily accessible online!). Also, my colleague pointed me to this quickstart, also on the GitHub.

I had to install swig for the python modular interface. IMPORTANT: with swig 3.0.2, the python modular interface gave me a segfault; but downgrading to 2.0.12 worked. I've done it in the past without root access, but that time I had ccmake and could easily tell shogun where to find swig - this time, I didn't have ccmake, so I couldn't figure out what to specify (seriously, this is awful documentation even by open source standards!). If you can't get root access, playing around with CMakeCache.txt in the build directory might be a start (note that the build directory has one CMakeChache.txt and the main directory also has one; you should modify the one in the build directory).

Finally, shogun installed completely error-free, but "import shogun" was not working. It was because shogun had installed to /usr/local/lib/python2.7/site-packages/, which wasn't even in my actual python's path, let alone anaconda's. To get it to work with anaconda, I copied the folder shogun and the files modshogup.py and _modshogun.so to /path/to/anaconda/lib/python2.7/site-packages.

To diagnose the issue with your particular installation of python, start the python shell, do "import sys", and then do "print sys.path" - if the place that shogun decided to put the python libraries (displayed on the screen when you do "make install", and also present in CMakeCache.txt in the build folder) is not in that list, well, that's the problem. By hook or by crook, get it on that list. One thing you can do is go back and recompile shogun, but with PYTHON_PACKAGES_PATH set to the right value - as I don't have ccmake, the only way I can think to set this is to open up CMakeCache.txt in your build folder and modify it there. I also hear something funky with the "PYTHONPATH" environment variable is supposed to work but for whatever reason, it never does for me. As a last resort, you can do "sys.path.insert(0, /path/to/shogun's/python/packages/folder/)"

I was then confronted with a whiny "ImportError: libshogun.so.17: cannot open shared object file: No such file or directory". I looked at the messages when shogun was installed and confirmed that libshogun.so.17 did in fact live in /usr/local/lib. Turns out I had to do "sudo ldconfig" to get that to behave. NO ONE MENTIONED THAT ANYWHERE.

Error: 'SecTrustEvaluateAsync' undeclared

I got this error when trying to compile cmake on my mac. It apparently concerns curl in some way. It was fixed by commenting out some of the lines form 2003 to 2048 in Utilities/cmcurl/lib/vtls/curl_darwinssl.c - but I'm not sure whether to take the first or the second block (for now I'm taking the first block of the if statement).

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/

Copying files via the terminal gets around "read only" error from USB in Ubuntu

This was very weird. I was recently trying to get files off an old laptop that had suffered a fall. The internet connection was not working. Bluetooth was not working. And it looked like an old USB I found, which I erased and reformatted multiple times, wasn't working either. When I tried pasting files into the drive via the GUI, I got the following error (yes I know how to take screenshots, but remember that whether or not I could get files off this computer was an open question):

And yet, copying into /media/[drive name] via the terminal worked, although it was slow:

[shakes head]