Caffe incompatible with Boost 1.58.0

Boost 1.58.0 was released on April 17th, and it breaks compilation with Caffe on OSX (when the build reaches one of the "NVCC" steps, you get a string of errors starting with complaining about the absence of a semicolon, that look like this: /usr/local/include/boost/smart_ptr/detail/sp_counted_base_clang.hpp(27): error: expected a ";"

Googling landed me on this page which suggested an incompatibility with boost 1.58.0 (https://groups.google.com/forum/#!topic/caffe-users/fY2r6bO3_0w). However, the steps suggested in the solution (as of May 26th; it seems to have been updated since) didn't work for me. So this is what I did, and it's kindof sketchy but oh well...

[July 16th update: Ian Blenke put together a boost-1.57 brew and mentioned how to use it in the comments; it looks a lot easier and less sketchy to install, but if that does not work for you, read on...]

1) cd $(brew --prefix) (for me this cd's to /usr/local/).
2) cd Library/Formula
3) Make a backup of the files boost.rb and boost-python.rb
4) Replace the boost.rb file with the contents of https://raw.githubusercontent.com/Homebrew/homebrew/6fd6a9b6b2f56139a44dd689d30b7168ac13effb/Library/Formula/boost.rb
5) Replace the boost-python.rb file with the contents of https://raw.githubusercontent.com/Homebrew/homebrew/3141234b3473717e87f3958d4916fe0ada0baba9/Library/Formula/boost-python.rb

6) brew uninstall boost (this should uninstall the 1.58.0 version)
7) brew install boost (this should install 1.57.0 since you've replaced the rb files)

(Edit: You *may* have to do "brew link boost" after this - can't recall exactly. Also, Parang Saraf pointed out a "no rule to make target" error in the comments, which they solved with "make clean")

Also, I missed this guide the first time I went through the page, so I'm linking to it in case you did too: http://caffe.berkeleyvision.org/install_osx.html

Remember to sort when using bedtools groupby!

Learned this the hard way. At the very end of the bedtools groupby help message, in the notes section, it says: "The input file/stream should be sorted/grouped by the -grp. columns". AUGH. Note that this is absolutely NOT a constraint posed by SQL's group by, even if their bold claim of 'Akin to the SQL "group by" command' may lead you believe otherwise. Talk about false advertising!

Upgrade to bleeding edge version solved issue with Theano and Anaconda

I recently switched to using the python that comes with Anaconda (sidebar: is an Anaconda a kind of python? I would google it except, for the first time, I have the problem where googling search terms gets me the technical usage instead of the layperson one). Theano started hiccupping quite badly, both on my local Mac and on the linux server (I got different errors depending on the machine). In both cases, switching to the bleeding-edge version of theano (http://deeplearning.net/software/theano/install.html#bleeding-edge-install-instructions) made the problem go away. Googling the error on linux didn't turn up any solutions, so I am copying it here so the search engine fairy will index it:

 'Compilation failed (return status=1): /usr/bin/ld: cannot find -lf77blas. collect2: ld returned 1 exit status. '