biology/seaview5.1,1

biology/seaview: Return to pool

- Remove PORTSCOUT

biology/seaview: Update version 5.0.5=>5.1

Changelog: https://doua.prabi.fr/software/seaview_data/CHANGES

biology/seaview: unbreak the port's build against FLTK 1.3.10

Currently used formula tries to fold FLTK version triple into
an integer (100 * FL_MAJOR_VERSION + 10 * FL_MINOR_VERSION +
FL_PATCH_VERSION < 140) but this fails once the patch version
had reached 10.  Drop it from the calculation entirely because
FLTK hasn't been breaking API and ABI for last several 1.3.x
releases, and accounting for it now makes little to no sense.

Reported by:	pkg-fallout

MANPREFIX: eliminate its usage

While here move manpages to share/man

*/*: Bump jpeg-turbo users treewide

New major version 3.0.0

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

biology/seaview: Update version 5.0.4=>5.0.5

Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES

biology/seaview: in preparation to FLTK update, unbreak the port

Ensure there is only one variable definition per each object, as
the C (and C++) standards mandated for years and is now enforced
by modern toolchains.

Remove # $FreeBSD$ from Makefiles.

Mark BROKEN in 13/14 (via latest llvm update).

biology/seaview: Update version 5.0.3=>5.0.4

Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES

biology/seaview: Update version 5.0.2=>5.0.3

Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES

biology/seaview: Update version 5.0=>5.0.2

Relnotes:	http://doua.prabi.fr/software/seaview

biology/seaview: Update version 4.7=>5.0

Relnotes:http://doua.prabi.fr/software/seaview

Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.

biology/seaview: Fix build with Clang 6

seaview.cxx:3352:24: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
                strcat(suggested, "."PDF_OR_PS_EXT);
                                     ^

http://beefy12.nyi.freebsd.org/data/head-amd64-default/p479076_s338486/logs/errors/seaview-4.7,1.log

PR:		230881
Submitted by:	tobik
Approved by:	bofh (maintainer timeout, 2 weeks)

biology/seaview: Updatye version 4.6.5=>4.7

Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES

biology/seaview: Update version 4.6.3=>4.6.5

- Pet portlint

biology/seaview: Update version 4.6.2=>4.6.3

- Added pkg-plist to pet portlint

Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES

biology/seaview: Update version 4.6.1=>4.6.2

biology/seaview: Update version 4.6=>4.6.1

- Add PORTSCOUT to ignore non-existent 4.6.1.3 version

biology/seaview: Update version 4.5.4.8=>4.6

- UNBREAK

Deprecate ports broken for more than 6 months

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

With hat:	portmgr
Sponsored by:	Absolight

biology/seaview: Broken, Does not fetch (checksum mismatch)

biology/seaview: Update version 4.5.4.7=>4.5.4.8

biology/seaview: Update version 4.5.4.6=>4.5.4.7

biology/seaview: Update version 4.5.4.4=>4.5.4.6

biology/seaview: Update version 4.5.4=>4.5.4.4

biology/seaview: Unbreak -- it fetches fine

The second MASTER_SITES entry worked fine, so this must have been a
transient fetch problem.  I removed the first entry which is still
failing though.

Approved by:	blanket

Mark as broken unfetchable ports

biology/seaview: Update version 4.5.3.4=>4.5.4

- Remove dependency for libpdf as removed by upstream

biology/seaview: UNBREAK

- Update version 4.5.2=>4.5.3.4
- Add LICENSE (GPLv3)
- Remove PDFLIBS as OPTIONS as it is no loner an optional requirement

PR:		198602
Submitted by:	pi
Approved by:	bapt marino (implicit)

Mark BROKEN: Fails to link, tries to use internal fltk symbols

c++ -o seaview   seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o  \
      -L/usr/local/lib -lfltk_images -lfltk  \
     -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama -L/usr/local/lib -lpdf \
         -lX11 -lm -lz -pthread
seaview.o: In function `clipboard_contains_alignment(char const*)':
seaview.cxx:(.text+0x1c14): undefined reference to `fl_selection_buffer'

Reported by:	pkg-fallout

Change my non-FreeBSD MAINTAINER mail to bofh@

Approved by:	bapt

Cleanup plist

Update the default version of GCC in the Ports Collection from GCC 4.7.4 to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

- Update to 4.5.2 - Pass maintainership to submitter

PR:		190564

- Update to 4.5.1

PR:		187975
Submitted by:	Ports Fury

- Stage support - Update to version 4.4.3

PR:		187041
Submitted by:	ports fury

In preparation for making libtool generate libraries with a sane name, fix all LIB_DEPENDS in biology

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 4.4.2

PR:		180515
Submitted by:	Ports Fury

- Update to 4.4.1

PR:		177257
Submitted by:	Ports Fury

Bump PORTREVISION after DESKTOP_ENTRIES update

- Update DESKTOP_ENTRIES:   * rephrase Comment field or use port ${COMMENT} if appropriate   * adjust Icon field according to the Desktop Entry Specification   * update Categories field: remove deprecated category Application;     set main category, if missing - Remove indefinite article and/or rephrase COMMENT - Trim Makefile header - Other minor changes

- Update to version 4.4.0 - Mark MAKE_JOBS_SAFE - Make dependency on print/pdflib optional - Switch to PLIST_FILES

While here:
- Add missing deps
- Add desktop entry

PR:		ports/172498
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Feature safe:	yes