r 3.1.2

"Pumpkin Helmet" was released October 31, 2014.

See more: https://stat.ethz.ch/pipermail/r-announce/2014/000578.html

Closes #1315.
maker: remove optional module dep

:optional, :recommended are deprecated for modules.
cantera: remove outdated devel
mathomatic: fix audit warning

Convert devel to HEAD.
mrbayes: cleanup
qrupdate: use lower-case formula name
analysis: update homepage
opencv: make eigen recommended

Closes #1287.
osgearth: fix option precedence
octave: set GNUTERM in site octaverc

Avoid Octave's default gnuplot aquaterm graphics interface.
Set GNUTERM=qt with Octave's Qt-based GUI installed.

Closes #1308.
p4est: 1.1 (new formula)

Closes #1292.
ASL: 20141030.

Fixes #1322.
phylip 3.696
littler 0.2.1
sextractor 2.19.5

Also makes formula Yosemite-compatible

Closes #1321.
octave: ship the header file for building with octave source

Fixes #1289. Closes #1319.
PaStiX: version 5.2.2.18

Fix versioned library names.

Closes #1326.
bowtie2 2.2.4

Closes #1335.
r: Add an additional rJava caveat

To fix 'fatal error: 'jni.h' file not found' after running
'R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers'
as suggested

Closes #1330.
Correct uppercase name on veclibfort

Closes #1340.