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non port: biology/phyml/Makefile

Number of commits found: 33

Monday, 8 May 2023
08:25 Robert Clausecker (fuz) search for other commits by this committer
biology/phyml: fix build on non-x86

 - only initialise x86-only fields on x86.
 - make code compatible with platforms where char is unsigned

Obtained
from:	https://github.com/stephaneguindon/phyml/commit/9c55b683c875fb9923e7cb2a1092596f72040882
MFH:		2023Q2
commit hash: 8e2ec289a2d8891c9bd3c549319baa9c94cfda27 commit hash: 8e2ec289a2d8891c9bd3c549319baa9c94cfda27 commit hash: 8e2ec289a2d8891c9bd3c549319baa9c94cfda27 commit hash: 8e2ec289a2d8891c9bd3c549319baa9c94cfda27 8e2ec28
Wednesday, 7 Sep 2022
21:10 Stefan Eßer (se) search for other commits by this committer
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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Friday, 2 Sep 2022
07:57 Wen Heping (wen) search for other commits by this committer
biology/phyml: Update to 3.3.20220408
commit hash: 026150563ee449fc13d0363a5e25b14a888772e7 commit hash: 026150563ee449fc13d0363a5e25b14a888772e7 commit hash: 026150563ee449fc13d0363a5e25b14a888772e7 commit hash: 026150563ee449fc13d0363a5e25b14a888772e7 0261505
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
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
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Sunday, 2 Jan 2022
17:31 Fernando Apesteguía (fernape) search for other commits by this committer
biology/phyml: update to 3.3.20211231

ChangeLog:
https://github.com/stephaneguindon/phyml/compare/v3.3.20211118...v3.3.20211231

Remove patches already merged into upstream.

Reported by: portscout
commit hash: 59a8ef603d053f64e4067f3723feeeb60610bedb commit hash: 59a8ef603d053f64e4067f3723feeeb60610bedb commit hash: 59a8ef603d053f64e4067f3723feeeb60610bedb commit hash: 59a8ef603d053f64e4067f3723feeeb60610bedb 59a8ef6
Thursday, 15 Apr 2021
08:31 Tobias Kortkamp (tobik) search for other commits by this committer
Clean up some things

- Remove duplicate variables
- Remove nop variables
- Sort categories
- Remove redundant option descriptions that match the default ones

Reported by:	portscan
commit hash: ffbc3bd9376a3672e16eafddf55b233b8fed1674 commit hash: ffbc3bd9376a3672e16eafddf55b233b8fed1674 commit hash: ffbc3bd9376a3672e16eafddf55b233b8fed1674 commit hash: ffbc3bd9376a3672e16eafddf55b233b8fed1674 ffbc3bd
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Friday, 10 Jul 2020
09:45 fernape search for other commits by this committer
biology/phyml: update to 3.3.20200621

From ChangeLog:
https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621

This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets

Reported by:	portscout
Original commitRevision:541852 
Tuesday, 21 Apr 2020
21:51 danilo search for other commits by this committer
- Swap back from net/openmpi3 to net/openmpi
Original commitRevision:532429 
Sunday, 12 Apr 2020
09:06 danilo search for other commits by this committer
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.
Original commitRevision:531485 
Friday, 6 Dec 2019
13:04 pkubaj search for other commits by this committer
biology/phyml: disable -march=native

Ports shouldn't build for the host CPU, it also breaks compilation on non-x86.

Approved by:    mentors (implicit approval)
Original commitRevision:519139 
Tuesday, 10 Sep 2019
21:04 fernape search for other commits by this committer
biology/phyml: update to 3.3.20190909

While here, add license.

Reported by:	portscout
Original commitRevision:511777 
Monday, 20 May 2019
09:17 wen search for other commits by this committer
- Update to 3.3.20190321
Original commitRevision:502098 
Saturday, 22 Sep 2018
18:00 yuri search for other commits by this committer
Change 4 ports from net/mpich2 to net/mpich

mpich2 is the obsolete version 2.x, mpich is at the current version 3.x

Ports:
biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis
Original commitRevision:480425 
Saturday, 23 Jun 2018
15:53 fernape search for other commits by this committer
biology/phyml: update to v3.3.20180621

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D15967
Original commitRevision:473138 
Tuesday, 15 May 2018
03:17 wen search for other commits by this committer
- Update to 3.3.20180214
Original commitRevision:469992 
Saturday, 10 Mar 2018
23:35 linimon search for other commits by this committer
Remove now-useless, commented-out lines.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:464132 
Thursday, 1 Feb 2018
07:26 wen search for other commits by this committer
- Update to 3.3.20180129
Original commitRevision:460569 
Wednesday, 27 Dec 2017
07:36 linimon search for other commits by this committer
Disable the extra flag "-march=native" on arm to fix builds.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
Original commitRevision:457351 
Saturday, 9 Dec 2017
01:39 linimon search for other commits by this committer
These are also broken on aarch64 in the same way as armv6/7.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:455815 
00:42 linimon search for other commits by this committer
Mark more ports broken that fail on both armv6 and armv7.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:455813 
Monday, 4 Sep 2017
00:01 sunpoet search for other commits by this committer
Update to 3.3.20170530

Changes:	https://github.com/stephaneguindon/phyml/releases
Original commitRevision:449234 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Friday, 26 Feb 2016
13:03 wen search for other commits by this committer
- Update to 3.2.0
- Update pkg-descr

PR:		205890
Submitted by:	tkato432@yahoo.com
Original commitRevision:409605 
Sunday, 28 Dec 2014
19:14 bapt search for other commits by this committer
Convert to USES=autoreconf
Original commitRevision:375747 
Friday, 31 Jan 2014
12:32 miwi search for other commits by this committer
- Stage support
Original commitRevision:341987 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Wednesday, 14 Aug 2013
22:35 ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
Original commitRevision:324744 
Monday, 4 Feb 2013
10:07 araujo search for other commits by this committer
- Update to 20121109.

PR:		ports/175014
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Original commitRevision:311601 
Tuesday, 4 Dec 2012
20:28 zi search for other commits by this committer
- Reset MAINTAINER due to unrecoverable email bounce

Reported by:	portscout
Feature safe:	yes
Original commitRevision:308268 
Saturday, 4 Dec 2010
07:34 ade search for other commits by this committer
Sync to new bsd.autotools.mk
Original commit
Tuesday, 5 Oct 2010
19:57 ade search for other commits by this committer
Round one migration of ports from automake{19,110} to automake111
Original commit
Tuesday, 21 Jul 2009
01:10 amdmi3 search for other commits by this committer
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:             136877
Submitted by:   Ben Allen <ben@sysadminschronicles.com>
Original commit

Number of commits found: 33