ssake: update sha1

Closes #1260.
tasr: update sha1

Closes #1259.
hlaminer: update sha1

Closes #1258.
r: Link libraries, headers, & frameworks

Link headers, libraries, & framework into normal locations on OS X
to allow other software to easily find them implicitly rather than
needing an explicit path upon compilation.

Prefer install_symlink over ln_s

Closes #1261.
octave: use opt lib path
openblas 0.2.12

Updates 0.2.11 to 0.2.12 and addresses issue #1157

Closes #1265.
sga 0.10.13: Install scripts
amos: fix Perl module dependency, cleanup

Bump clang version
Check configure args against build.with?

Fixes #1254.
insighttoolkit 4.6.1

Closes #1273.
nextflow 0.10.3: Add post_install

Run nextflow -download in post_install.
prokka 1.10: Depends on XML::Simple
vtk: modernize options
CONTRIBUTING: update gist-logs usage
sbagen 1.4.5 (new formula)

Closes #1266.
root: link against up-to-date OpenSSL

System OpenSSL is deprecated.
swetest: update resource sha1

Closes #1278.
clustal-w: bump clang, use double quotes

Closes #1281.
edirect: update sha1
root: general cleanup

Closes #1283.
octave: build gnuplot with Qt

Fixes #1275.