emboss: add mirror
gmt4: update gshhg resource
gmt: update gshhg resource
getdp: update to 2.4.4

Removed the library fix (line 55) because now also corrected upstream

Closes #1061.
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