jonchang

Installing diversitree on OS X Mavericks, R 3.1.0

I installed R from the installer on CRAN

If you installed R from the installer on CRAN:

The easy way

Download my compiled package from Dropbox and install it that way:

jonchang

install homebrew... http://brew.sh

install dependencies

brew install cmake boost

pull down revbayes development version

jonchang

#!/usr/bin/env python

from __future__ import print_function

import gzip
import argparse
from operator import itemgetter

def get_args():
    parser = argparse.ArgumentParser(description="selects fields from a tab-delimited file")

jonchang

import itertools

def group_ranges(L):
    """
    Collapses a list of integers into a list of the start and end of
    consecutive runs of numbers. Returns a generator of generators.

    >>> [list(x) for x in group_ranges([1, 2, 3, 5, 6, 8])]
    [[1, 3], [5, 6], [8]]
    """

jonchang

R typically installs libgfortran so packages can link to it, but for some reason it wasn't linked properly for me.

ln -s $(R RHOME)/lib/libgfortran.2.dylib $(R RHOME)/lib/libgfortran.dylib

Also for some reason R wasn't able to find its own shared library directory, so download geiger

curl -O https://dl.dropbox.com/u/8859543/geiger_1.4-4.666.tar.gz

jonchang

#!/usr/bin/env python

# convert_characters.py -- by Jonathan Chang (March 2013)

import argparse
import os.path
import multiprocessing
import functools

import dendropy

jonchang

#!/usr/bin/env python

import argparse
import os.path
import os
import errno
import multiprocessing
import functools
import subprocess
import pdb

jonchang

#!/usr/bin/env python

# canonize_synonyms.py -- by Jonathan Chang (March 2013)

import argparse
import os.path
import multiprocessing
import functools
import csv
import collections

jonchang

require 'formula'

class Shrimp < Formula
  homepage 'http://compbio.cs.toronto.edu/shrimp/'
  url 'http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_2.macosx.x86_64.tar.gz'
  sha1 'ba666ccc0aa5da0f55a8a41e6f40daabe876c3dd'
  version '2.2.2'

  def patches
    # Change shebang of Python utilities.

jonchang

#!/usr/bin/env python3

# By Jonathan Chang - September 2017

import sys, argparse, logging, re, os


def get_partitions(path):
    """Given a path, returns a dictionary with partition names as keys and a list of
    length 2, representing a range of characters."""