21:23 Rene Ladan (rene) 

biology/recombine: Remove expired port

2024-01-17 biology/recombine: Upstream advises to use biology/lamarc

    2f8680e

13:11 Muhammad Moinur Rahman (bofh) 

biology/recombine: Mark DEPRECATED

- Upstream last release was in 2002
- Upstream advises to use bioloby/lamarc
- Set EXPIRATION_DATE 2024-01-17
- Pet portclippy

    62d0176

21:10 Stefan Eßer (se) 

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)

    b7f0544

14:20 Tobias C. Berner (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

    37526bb

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

05:00 cy 

Fix after gets(3) retirement using gets_s(3).

Bump PORTREVISION as this is a security issue too.

PR:		222796
MFH:		2019Q3

 

16:40 lwhsu 

Add a patch to remove use of gets(3)

PR:		238685
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Reported by:	emaste
Sponsored by:	The FreeBSD Foundation

 

11:04 mat 

When there is a do-install target, do not use a post-install target, do
everything at once.  Sometime, rename post-install into a options helper
target.

I did not fix ports that were such a mess that I could not figure out
what they really wanted to do.  I also did not change ports that had
some version of an auto-plist code in post-install, for the same reason.

With hat:	portmgr
Sponsored by:	Absolight

 

11:39 ehaupt 

- Support staging
- Use shebangfix

 

15:55 bapt 

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

 

19:15 bsam 

. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. mute mkdir;
. use PLIST_FILES and PORTDOCS at Makefile;
. remove pkg-plist;
. trim Makefile headers;
. remove article from COMMENT;
. pet portlint -- use opne space after WWW: at pkg-descr.

 

12:22 vd 

Fix master sites, un-deprecate and update biology/recombine to 1.41.

12:36 gabor 

- Deprecate
- Set EXPIRATION_DATE

Approved by:    erwin (mentor)

08:09 linimon 

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

05:56 ade 

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

E Nomini Patri, E Fili, E Spiritu Sancti.

15:49 wjv 

Add recombine 1.40, a program to fit population models across sites.