biology/iolib1.16.0

biology/iolib: Update 1-15-1 => 1.16.0

Approved by:	    	db@, yuri@ (Mentors, implicit)

biology/iolib: Fix building with libtool 2.6

PR:		296964
Approved by:	portmgr (fixit blanket)

biology/iolib: fix build on armv7

This port tries to use NEON if __ARM_NEON is defined.  Unfortunately it
now requires a bunch of intrinsics available on AArch64 only, breaking
the armv7 build.  Fix the build by disabling NEON on armv7.

Approved by:	portmgr (build fix blanket)
MFH:		2026Q1

biology/iolib: Update 1.14.10 => 1.15.1, take maintainership

Changelogs:
* https://github.com/jkbonfield/io_lib/blob/io_lib-1-15-1/CHANGES
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-15-0...io_lib-1-15-1
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-15...io_lib-1-15-0
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-14...io_lib-1-14-15
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-13...io_lib-1-14-14
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-12...io_lib-1-14-13
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-11...io_lib-1-14-12
* https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-10...io_lib-1-14-11

* Use release tarball
* Add WWW for source code repository
* Pet portclippy(1) and portfmt(1)
* Re-generate patches via `make makepatch` to ensure proper patch format

Approved by:		yuri@ (Mentor)
Differential Revision:	https://reviews.freebsd.org/D54568

biology/iolib: Moved man to share/man

Approved by:    portmgr (blanket)

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

Homepage link is permanent redirected to its HTTPS counterpart

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

Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)

biology/iolib: Drop maintainership

Remove # $FreeBSD$ from Makefiles.

- Fix build in head i386

Remove the incorrect typedefs to fix build on tier-2.

PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)

Remove the inccorrect typedefs to fix build on tier-2.

PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)

- Update to 1-14-10 - Move USES to make portlint happy

Mark various ports broken on mips64 and, where appropriate, mips.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

Mark some ports failing on power64.  In cases where the error message was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

Fix USE_GITHUB's GH_TAGNAME usage.

Sponsored by:	Absolight

- Update to 1.14.9 - Use github

- Update to 1.14.8

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

With hat:	portmgr
Sponsored by:	Absolight

- Update to 1.14.7

- Update to 1.14.6

- Update to 1.14.5

- Update to 1.14.4

- Update to 1.14.3

Typos, whitespace and capitalization fixes (A-F).

- Update to 1.14.2

- Update to 1.14.1

- Update to 1.14.0 - Use install-strip

- Update to 1.13.10

- Update to 1.13.9

- Update to 1.13.8

Cleanup plist

- I forgot to svn add a new patch

- Update from 1.13.5 to 1.13.7 - Add libtool to USES - Take maintainership

- Update to version 1.13.5

PR:		188863
Submitted by:	ports fury

- Back to the heap, I don't use this port anymore

Support stage Conver USE_GMAKE

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)

- Update to 7.31.0 - Bump PORTREVISION for ftp/curl shlib change - Add TEST_DEPENDS - Convert to new options framework - Adjust options:   - Add COOKIES   - Add CYASSL, NSS, POLARSSL, THREADED_RESOLVER, TLS_SRP [1]   - Add GSSAPI and SPNEGO [2]   - Remove KERBEROS4   - Rename LIBIDN to IDN   - Remove TRACKMEMORY [1] - Sort option handler - Add SLAVEDIRS: ftp/curl-hiphop - Cosmetic change - Cleanup

Changes:	http://curl.haxx.se/changes.html
PR:		ports/172325 (-exp run), ports/177369 (based on) [1]
Submitted by:	Hirohisa Yamaguchi <umq@ueo.co.jp> [1], hrs (via email) [2]
Exp run by:	miwi

- Update to 1.13.0 - Improve COMMENT (remove leading article, add missing space) - Remove unneeded BSD license file - Trim Makefile's header - Pet portlint (move LICENSE section earlier, change tab to space in WWW link)

Changes:	http://sourceforge.net/p/staden/news/2013/03/iolib-1130-released/

- Remove WITH_FBSD10_FIX, is no longer needed

- Fix build on FreeBSD 10

- Update to 1.12.5

Changes:	http://sourceforge.net/news/?group_id=100316&id=297223

Sync to new bsd.autotools.mk

Update my MAINTAINER address to culot@FreeBSD.org.

Approved by:	sahil@ (mentor)

Fix typo in maintainer mail address

Submitted by:	Frederic Culot <frederic _at_ culot.org> (maintainer)
Approved by:	jadawin@ (co-mentor)