biology/paml: update to version 4.9c and add license information

[jrm]

Summary

• Update biology/paml to version 4.9c
• Set LICENSE=GPLv3
• Use the variable PORTDOCS to automate the generation of the DOCS plist (as suggested by mat@).
• Install dat/ examples/ and Technical/ directories as well as files in the root directory of the distribution tarball.
• Fix broken permissions.
• Delete windows executables.
• Build and install useful binaries not built by upstream's Makefile.
• Update pkg-descr.

Test Plan

portlint -C: OK
testport: OK (poudriere: 9.3-RELEASE-p45, i386, default options)
testport: OK (poudriere: 9.3-RELEASE-p45, amd64, default options)
testport: OK (poudriere: 10.3-RELEASE-p7, i386, default options)
testport: OK (poudriere: 10.3-RELEASE-p7, amd64, default options)
testport: OK (poudriere: 11.0-RC3, i386, default options)
testport: OK (poudriere: 11.0-RC3, amd64, default options)

http://pkg.awarnach.mathstat.dal.ca/data/latest-per-pkg/paml/4.9c/

[jrm]

I've updated the diff because the author added, just since this latest version,
this note to src/README.txt.

"The software package is provided "as is" without warranty of any
kind. In no event shall the author or his employer be held responsible
for any damage resulting from the use of this software, including but
not limited to the frustration that you may experience in using the
package. The program package, including source codes, example data
sets, executables, and this documentation, is maintained by Ziheng
Yang and distributed under the GNU GPL v3."

Unfortunately, the README.txt in the top level still says this.

"PAML is distributed free of charge for academic use only."

I suspect this was accidentally left in.

[mat]

biology/paml/Makefile

20 ↗

(On Diff #20721)

This should be called PORTDOCS, and then, you could remove them from pkg-plist.

[jrm]

Changes since last diff:

• Use the variable PORTDOCS to automate the generation of the DOCS plist (as suggested by mat@).
• Install dat/ examples/ and Technical/ directories as well as files in the root directory of the distribution tarball. I chose to keep all of these files under one root and install them in ${DATADIR} because there is no logical distinction between them.
• Fix broken permissions.
• Delete windows executables.
• Build and install useful binaries not built by the distribution's Makefile.
• Update pkg-descr.

[swills]

Looks good, approved.