*/*: Update WWW to use HTTPS for sourceforge.net projects

Homepage link is permanent redirected to its HTTPS counterpart
Issue reported by repology : https://repology.org/repository/freebsd/problems

Approved by:	portmgr (blanket)
PR:		274888

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>

Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port

Remove # $FreeBSD$ from Makefiles.

biology/mummer: fix build on powerpc64 elfv2 and powerpc64le

Error:
src/tigr/postnuc.cc:174:37: error: non-constant-expression cannot be narrowed
from type 'signed char' to 'char' in initializer list [-Wc++11-narrowing]
        Alignments.push_back({ *Mp, CurrCp->dirB } );

Since it may also fix runtime issues on powerpc64 elfv1, bump PORTREVISION.

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

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

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, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

biology/mummer: Add USES=compiler:c++11-lang

biology/mummer: Update 3.23 -> 4.0.0beta2-2

Port changes:
* Moved to github
* It now installs itself
* It uses yaggo during build

biology/mummer: Take maintainership

- Fix installing scripts and support binaries
- Add LICENSE

PR:		223098
Submitted by:	mzaki@niid.go.jp

Fix build on mips by properly respecting compiler and flags

Cleanup plist

biology/mummer: Use OPSYS with OSVERSION

I don't think selecting clang as a function of OSVERSION is generally
desired, but if it's going to happen, make sure FreeBSD-specific
conditions are limited to FreeBSD by comparing OPSYS first.

Fix compilation on 10+ (clang)
Fix format of WWW entry in pkg-descr

PR:		190798

Reset the 99 ports still listed under sylvio@

Sylvio's last commit was 17 months ago, a full 5 months after all of his
ports could have been reset per policy.  Given the push to complete
staging (48 ports are still unstaged, something like 70+ have already
been staged by other committers) and given that PRs are automatically
assigned but never addressed, it's better just to reset all the ports and
PRs so that it's clear to others that these ports are free to maintain.

Approved by:	portmgr (implicit)

Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)

- add stage support

- Convert USE_GMAKE to USES

Remove trailing whitespaces from category biology

According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)

Convert biology to MDOCS and MEXAMPLES

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

- Update to 3.23

- Get Rid MD5 support

- Update to 3.22

Approved by:    itetcu (mentor)

- Update my mail address to FreeBSD

Approved by:    miwi (mentor)

- Update to 3.21.
- Reset maintainer to submitter.

PR:             ports/138192
Submitted by:   Sylvio Cesar <scjamorim@bsd.com.br>

MUMmer is a modular system for the rapid whole genome alignment of finished
or draft sequence. This package provides an efficient suffix tree library,
seed-and-extend alignment, SNP detection, repeat detection, and
visualization tools.

WWW:    http://mummer.sourceforge.net/

PR:             ports/118142
Submitted by:   Tony Maher