R 3.1.1

Release notes: https://stat.ethz.ch/pipermail/r-announce/2014/000575.html

Closes #1058.
arpack: fix symlink overwriting pkgconfig directory

Closes #1059.
bwa 0.7.10
genometools 1.5.3
openbr: fix version
jellyfish 2.1.3

Builds with newer compilers.
edirect 1.80
cap3: fix linux shasum
gdcm: use mirror selector
cufflinks 2.2.1
openblas 0.2.10
galfit 3.0.5 (new formula)

Closes #1017.
kissplice 2.2.0
update vips to latest stable, 7.40.4

this set of minor fixes help the ruby-vips gem pass all spec tests, see:

https://github.com/jcupitt/libvips/blob/master/ChangeLog

Closes #1064.
Adol-C: upgrade to 2.5.1.
augustus: add mirror
rml-mmc 274
kissplice: Use --disable-epsv

Use --disable-epsv rather than --no-epsv. The latter does not work with older
versions of curl.
fastqc: update to 0.11.2

Closes #1072.
R: option to build libRmath only.

Closes #1067.