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

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

def parse_fasta(path):
    """Given a path tries to parse a fasta file. Returns an iterator which
    yields a (name, sequence) tuple"""
    with open(path) as handle:
        name = sequence = ""
        for line in handle:
            line = line.strip()
            if line.startswith(">"):
                if name:
                    yield name, sequence

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

#!/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

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

import argparse
import os.path
import multiprocessing
import functools

import dendropy

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

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

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