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non port: biology/phyml/Makefile
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Number of commits found: 29

Sun, 2 Jan 2022
[ 17:31 Fernando ApesteguĂ­a (fernape) search for other commits by this committer ]    commit hash:59a8ef603d053f64e4067f3723feeeb60610bedb  59a8ef6 
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
Thu, 15 Apr 2021
[ 08:31 Tobias Kortkamp (tobik) search for other commits by this committer ]    commit hash:ffbc3bd9376a3672e16eafddf55b233b8fed1674  ffbc3bd  (Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
Clean up some things

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

Reported by:	portscan
Tue, 6 Apr 2021
[ 14:31 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148  (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
Fri, 10 Jul 2020
[ 09:45 fernape search for other commits by this committer ] Original commit   Revision:541852
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
Tue, 21 Apr 2020
[ 21:51 danilo search for other commits by this committer ] Original commit   Revision:532429
- Swap back from net/openmpi3 to net/openmpi
Sun, 12 Apr 2020
[ 09:06 danilo search for other commits by this committer ] Original commit   Revision:531485
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.
Fri, 6 Dec 2019
[ 13:04 pkubaj search for other commits by this committer ] Original commit   Revision:519139
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)
Tue, 10 Sep 2019
[ 21:04 fernape search for other commits by this committer ] Original commit   Revision:511777
biology/phyml: update to 3.3.20190909

While here, add license.

Reported by:	portscout
Mon, 20 May 2019
[ 09:17 wen search for other commits by this committer ] Original commit   Revision:502098
- Update to 3.3.20190321
Sat, 22 Sep 2018
[ 18:00 yuri search for other commits by this committer ] Original commit   Revision:480425
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
Sat, 23 Jun 2018
[ 15:53 fernape search for other commits by this committer ] Original commit   Revision:473138
biology/phyml: update to v3.3.20180621

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D15967
Tue, 15 May 2018
[ 03:17 wen search for other commits by this committer ] Original commit   Revision:469992
- Update to 3.3.20180214
Sat, 10 Mar 2018
[ 23:35 linimon search for other commits by this committer ] Original commit   Revision:464132
Remove now-useless, commented-out lines.

Approved by:	portmgr (tier-2 blanket)
Thu, 1 Feb 2018
[ 07:26 wen search for other commits by this committer ] Original commit   Revision:460569
- Update to 3.3.20180129
Wed, 27 Dec 2017
[ 07:36 linimon search for other commits by this committer ] Original commit   Revision:457351
Disable the extra flag "-march=native" on arm to fix builds.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
Sat, 9 Dec 2017
[ 01:39 linimon search for other commits by this committer ] Original commit   Revision:455815
These are also broken on aarch64 in the same way as armv6/7.

Approved by:	portmgr (tier-2 blanket)
[ 00:42 linimon search for other commits by this committer ] Original commit   Revision:455813 (Only the first 10 of 21 ports in this commit are shown above. View all ports for this commit)
Mark more ports broken that fail on both armv6 and armv7.

Approved by:	portmgr (tier-2 blanket)
Mon, 4 Sep 2017
[ 00:01 sunpoet search for other commits by this committer ] Original commit   Revision:449234
Update to 3.3.20170530

Changes:	https://github.com/stephaneguindon/phyml/releases
Fri, 1 Apr 2016
[ 13:29 mat search for other commits by this committer ] Original commit   Revision:412344 (Only the first 10 of 1009 ports in this commit are shown above. View all ports for this commit)
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Fri, 26 Feb 2016
[ 13:03 wen search for other commits by this committer ] Original commit   Revision:409605
- Update to 3.2.0
- Update pkg-descr

PR:		205890
Submitted by:	tkato432@yahoo.com
Sun, 28 Dec 2014
[ 19:14 bapt search for other commits by this committer ] Original commit   Revision:375747
Convert to USES=autoreconf
Fri, 31 Jan 2014
[ 12:32 miwi search for other commits by this committer ] Original commit   Revision:341987
- Stage support
Fri, 20 Sep 2013
[ 15:55 bapt search for other commits by this committer ] Original commit   Revision:327709 (Only the first 10 of 94 ports in this commit are shown above. View all ports for this commit)
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Wed, 14 Aug 2013
[ 22:35 ak search for other commits by this committer ] Original commit   Revision:324744 (Only the first 10 of 1725 ports in this commit are shown above. View all ports for this commit)
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
Mon, 4 Feb 2013
[ 10:07 araujo search for other commits by this committer ] Original commit   Revision:311601
- Update to 20121109.

PR:		ports/175014
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Tue, 4 Dec 2012
[ 20:28 zi search for other commits by this committer ] Original commit   Revision:308268
- Reset MAINTAINER due to unrecoverable email bounce

Reported by:	portscout
Feature safe:	yes
Sat, 4 Dec 2010
[ 07:34 ade search for other commits by this committer ] Original commit  (Only the first 10 of 1730 ports in this commit are shown above. View all ports for this commit)
Sync to new bsd.autotools.mk
Tue, 5 Oct 2010
[ 19:57 ade search for other commits by this committer ] Original commit  (Only the first 10 of 235 ports in this commit are shown above. View all ports for this commit)
Round one migration of ports from automake{19,110} to automake111
Tue, 21 Jul 2009
[ 01:10 amdmi3 search for other commits by this committer ] Original commit 
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>

Number of commits found: 29