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.

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>

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

- Reassign to the heap at maintainer's request

- update png to 1.5.10

Chase pdflib.so version and bump PORTREVISION accordingly.

- unbreak

Feature safe:   yes

- Mark BROKEN: does not compile with new fltk

Reported by:    pointyhat

- Get Rid MD5 support

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- Chase x11-toolkits/fltk update

- update to jpeg-8

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+

Thanks to all Helpers:
        Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
        ehaupt, nox, itetcu, flz, pav

PR:             116263
Tested on:      pointyhat
Approved by:    portmgr (pav)

- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

Chase pdf library and bump PORTREVISION.

- Update to 2006.02.13

PR:             95281
Submitted by:   maintainer

Update to 2006.01.25.

PR:             ports/93051
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- New upstream version; two patches incorporated.

PR:             90140
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    clement (mentor)

- Update to 2005.13.07 to make fetchable again

PR:             89976
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    clement (mentor)

BROKEN: Size mismatch

- Update to 2004.12.16

PR:             ports/75205
Submitted by:   maintainer

Not a real update with the last patch.
The real update here.

- This update brings seaview to the latest release (dated 09.24.04
in the FTP site).

- While here add a modeline for vi, and fix a tab (cosmetic)

- Make portlint happy.

PR:             ports/74897
Submitted by:   maintainer

unbreak, only minor changes in the distfiles (see PR)

Since the distfile has no version number, put it in
DIST_SUBDIR=    ${PORTNAME}-${PORTVERSION}

PR:             66817
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (new maintainer)

BROKEN: Checksum mismatch

- Update to version 2003.11.25

- Update to new version 2003.11.17
- Unbreak this port

Mark BROKEN: distfile has changed.

Upgrade to 2003.01.21.  Appears to only add some more file export/print
options.  Additional patches were necessary since the fltk port seems
to have been upgraded and thus also broken this port (which would
been already broken due to the checksum failure).

Add back the WWW which was inexplicably deleted in a previous
revision.  Make a few organisational improvements.  However, be
too lazy to move to pkg-message a note that really shouldn't
be necessary for the end user at all.

De-pkg-comment.

unbroke by upgrade to 20021018
drop maintainership

PR:             45466
Submitted by:   old maintainer

Update WWW

Bump XForms lib. version.

BROKEN: Checksum is incorrect

Change PKGDIR from pkg/ to .  Also fix places where ${PKGDIR} is   spelled out
(many of which are ${PKGDIR}/MESSAGE -> ${PKGMESSAGE} type   fixes that
shouldn't have been necessary) and the string "/pkg/"   appear.    

Convert category biology to new layout.