biology/hmmer3.4

biology/hmmer: add powerpc64le support

Swap vec_sld operands on little-endian so the Altivec code keeps its
big-endian element order, and drop the configure check that rejects
VMX on little-endian.

biology/hmmer: update to 3.4

Now builds and runs on armv7/aarch64!

Changelog: http://cryptogenomicon.org/hmmer-3-4-release.html

See also file RELEASE-3.4.md in distfile for an extended change log.

Approved by:	mzaki@e-mail.ne.jp (maintainer timeout, two weeks)
PR:		282111

biology/hmmer: Moved man to share/man

Approved by:    portmgr (blanket)

all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>

biology/hmmer: Update to 3.3.2

No release notes.  See commits for changes:
https://github.com/EddyRivasLab/hmmer

PR:             266968
Reported by:    mzaki@e-mail.ne.jp

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.

biology/hmmer: disable on powerpc64le and powerpcspe

Altivec/VSX code in this port works only on big-endian POWER.
powerpcspe has neither SSE2 nor Altivec.

Also enable on powerpc64le.

Approved by:	portmgr (tier-2 blanket)

biology/hmmer: update to 3.3

PR:	243244
Submitted by:	mzaki@e-mail.ne.jp (maintainer)

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

Bump PORTREVISION for ports depending on the canonical version of GCC as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

vec_splats function is not supported by base GCC.  Add USES=compiler:c11 to fix build on powerpc platforms.

PR:		235514
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)

biology/hmmer: update to 3.2.1

PR:		229693
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer)

Back out previous commits by jbeich demand.

Bah.  Remove spare line from cut-and-paste.

Attempt to fix build on non-x86 archs.  Untested, but does no harm on x86.

Approved by:	portmgr (tier-2 blanket)

- Update to 3.1b2 - Pass maintainership to submitter

PR:		223561
Submitted by:	mzaki@niid.go.jp
Approved by:	bacon4000@gmail.com(previous maintainer)

Remove dead master sites

Begin deorbit burn of ia64.  We have not attempted to build packages for it for many years.

While here, alphabetize ARCHs, pet portlint, and modernize usages.

Approved by:	portmgr (tier-2 blanket)

- Update maintainer mail address - Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

- Remove deprecated option - Tweak compiler flags - Add LICENSE - Pass maintainership to submitter

PR:		199066
Submitted by:	jwbacon@tds.net

Cleanup plist

Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.

While here, use OPTIONS helpers and re-enable manpage installation.

Stage support

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

- Convert to new perl framework - Trim Makefile header

- Update to 3.0 - Convert to optionsNG - Drop maintainership

- Take maintainership

- Reassign to the heap at maintainer's request

- Get Rid MD5 support

- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run

SHA256ify

Approved by:    krion@

- Remove a junk white space.

- Update to 2.3.2 - Add WITH_PVM knob - Pass maintainership to submitter

PR:		ports/74331
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>

With portmgr hat on, reset inactive maintainer.  These ports are now up for adoption.

SIZEify (maintainer timeout)

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

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

Clear moonlight beckons. Requiem mors pacem pkg-comment, And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

- Add patch that will, for -CURRENT only, change:  -pthread -> -lc_r - Bump $PORTREVISION

Prompted by:	Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>

- Update port to version 2.2g

- General clean-up of port. - Install PDF and HTML documentation. - Take over maintainership.

Approved by:	Silence from previous maintainer; no objections from -ports

- Add %%PORTDOCS%% support to pkg-plist. - $INSTALL_MAN -> $INSTALL_DATA in Makefile where appropriate.

PR:		28668
Submitted by:	Patrick Li <pat@databits.net>

update with the new PORTNAME/PORTVERSION variables

fix some pkg/MESSAGE stuff

Change Id->FreeBSD.

As threatened, enforce the "Capital, no period" rule.  Ellipses are permitted.  Note that, given current numeric motif of PW, this is done in four equally-sized commits of 393 files each.

Weasal and Wabbits and BIG FOOT.