biology/phyml3.3.20220408_1,1

biology/phyml: fix build on non-amd64

cc: error: unsupported option '-msse3' for target 'powerpc64-unknown-freebsd14.1'

biology/phyml: fix build on non-x86

- only initialise x86-only fields on x86.
 - make code compatible with platforms where char is unsigned

Obtained from:	https://github.com/stephaneguindon/phyml/commit/9c55b683c875fb9923e7cb2a1092596f72040882
MFH:		2023Q2

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/phyml: Update to 3.3.20220408

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

biology/phyml: update to 3.3.20211231

ChangeLog:
https://github.com/stephaneguindon/phyml/compare/v3.3.20211118...v3.3.20211231

Remove patches already merged into upstream.

Reported by: portscout

devel/automake: update to 1.16.5

Clean up some things

- Remove duplicate variables
- Remove nop variables
- Sort categories
- Remove redundant option descriptions that match the default ones

Reported by:	portscan

Remove # $FreeBSD$ from Makefiles.

biology/phyml: fix build on recent current

mostly backport of:
	https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a

Obtained from:	https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a

biology/phyml: update to 3.3.20200621

From ChangeLog: https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621

This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets

Reported by:	portscout

- Swap back from net/openmpi3 to net/openmpi

- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.

biology/phyml: disable -march=native

Ports shouldn't build for the host CPU, it also breaks compilation on non-x86.

Approved by:    mentors (implicit approval)

biology/phyml: update to 3.3.20190909

While here, add license.

Reported by:	portscout

- Update to 3.3.20190321

Change 4 ports from net/mpich2 to net/mpich

mpich2 is the obsolete version 2.x, mpich is at the current version 3.x

Ports:
biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis

biology/phyml: update to v3.3.20180621

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D15967

- Update to 3.3.20180214

Remove now-useless, commented-out lines.

Approved by:	portmgr (tier-2 blanket)

- Update to 3.3.20180129

Disable the extra flag "-march=native" on arm to fix builds.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run

These are also broken on aarch64 in the same way as armv6/7.

Approved by:	portmgr (tier-2 blanket)

Mark more ports broken that fail on both armv6 and armv7.

Approved by:	portmgr (tier-2 blanket)

Update to 3.3.20170530

Changes:	https://github.com/stephaneguindon/phyml/releases

Update WWW

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

- Update to 3.2.0 - Update pkg-descr

PR:		205890
Submitted by:	tkato432@yahoo.com

Convert to USES=autoreconf

- Stage support

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

- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)

- Update to 20121109.

PR:		ports/175014
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

- Reset MAINTAINER due to unrecoverable email bounce

Reported by:	portscout
Feature safe:	yes

- Get Rid MD5 support

Sync to new bsd.autotools.mk

Round one migration of ports from automake{19,110} to automake111

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast a

WWW: http://code.google.com/p/phyml/

PR:		136877
Submitted by:	Ben Allen <ben@sysadminschronicles.com>