biology/wise2.4.1_1

all: drop support for expired FreeBSD 14.0

Simplify expressions for FreeBSD 13.X

Reviewed by:	many

Differential Revision:	https://reviews.freebsd.org/D46601

*/*: Fix build with llvm16 on 13.2-STABLE

As like as HEAD(14.0-RELEASE) llvm16 was merged in base for 13.2-STABLE
with the OSVERSION 1302507.

- Utilize USE_CXXSTD=c++14 or similar solution where applicable
- Update conditionals to addtionally check for OSVERSION greater than
  1302507 and less than 1400000

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation

biology/wise: Fix build with llvm16

Sponsored by:	The FreeBSD Foundation

*/*: llvm15 build fixes

llvm15 was also merged into 13.2-STABLE effective from OSVERSION
1302505. Fix the ports that failed to build with llvm15.

Approved by:	portmgr (blanket)

biology/wise: Unbreak on HEAD

- Add LICENSE BSD3CLAUSE GPLv2
- Pet portclippy

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

Remove # $FreeBSD$ from Makefiles.

a-b: Add missing USES={gnome,php,sdl,xorg}

Convert to UCL & cleanup pkg-message (categories a-c)

Remove libintl.so.9 compatibility link that was added in r374303 to prevent massive PORTREVISION bumps.  Bump dependent ports that have not been bumped since.

- Switch to options helpers - Regenerate patches with `make makepatch`

Prevent collision with getline(3)

Cleanup plist

- Add staging support - Unmute install commands

biology/wise: Add dragonfly support

Add NO_STAGE all over the place in preparation for the staging support (cat: biology)

- Convert to new perl framework - Remove MAKE_JOBS_SAFE=yes, it's the default.

Fix build by adding an explicit dep on pkgconf

- Update to 2.4.1

PR:		176552
Submitted by:	Ports Fury

- Get Rid MD5 support

Fix plist.

Reported by:	QAT

- SBU_FILES += pkg-message

PR:             ports/142409
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>

Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response to email.

Hat:		portmgr

Remove USE_REINPLACE from all categories starting with B

SHA256ify

Approved by:    krion@

Fix maintainer address

From: Tony Maher <anthony.maher@uts.edu.au>
    To: Edwin Groothuis <edwin@FreeBSD.org>
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:	Tony Maher <anthony.maher@uts.edu.au>

SIZEify (maintainer timeout)

Cosmetic fix: use %%DOCSDIR%% macro. No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@etrust.ru>
A part of PR:	57992

Port update (maintainer): biology/wise

Fenner's porsurvey show wise no longer available at original
	site.  Original site readme shows it has moved so update
	the MASTER_SITES accordingly.

PR:		ports/57154
Submmited by:	Tony Maher <tonymaher@optushome.com.au>

De-pkg-comment.

Add missing file

Modify replace RE to match syntax of sed now ("\)" -> ")" Noticed by: bento

PERL -> REINPLACE And some ports have USE_PERL5=yes now.

"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns."