| non port: biology/phyml/Makefile |
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SVNWeb
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Number of commits found: 33 |
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Mon, 8 May 2023
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[ 08:25 Robert Clausecker (fuz)  ]    8e2ec28
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
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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se) ] b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
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.
(Only the first 15 lines of the commit message are shown above )
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Fri, 2 Sep 2022
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[ 07:57 Wen Heping (wen) ] 0261505
biology/phyml: Update to 3.3.20220408
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Wed, 20 Jul 2022
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[ 14:20 Tobias C. Berner (tcberner) ] 37526bb (Only the first 10 of 82 ports in this commit are shown above. )
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> (Only the first 15 lines of the commit message are shown above )
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Sun, 2 Jan 2022
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[ 17:31 Fernando Apesteguía (fernape) ] 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
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Thu, 15 Apr 2021
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[ 08:31 Tobias Kortkamp (tobik) ] ffbc3bd (Only the first 10 of 11 ports in this commit are shown above. )
Clean up some things
- Remove duplicate variables
- Remove nop variables
- Sort categories
- Remove redundant option descriptions that match the default ones
Reported by: portscan
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Fri, 10 Jul 2020
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[ 09:45 fernape ]  
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
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Tue, 21 Apr 2020
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[ 21:51 danilo ]
- Swap back from net/openmpi3 to net/openmpi
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Sun, 12 Apr 2020
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[ 09:06 danilo ]
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.
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Fri, 6 Dec 2019
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[ 13:04 pkubaj ]
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)
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Tue, 10 Sep 2019
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[ 21:04 fernape ]
biology/phyml: update to 3.3.20190909
While here, add license.
Reported by: portscout
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Mon, 20 May 2019
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[ 09:17 wen ]
- Update to 3.3.20190321
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Sat, 22 Sep 2018
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[ 18:00 yuri ]
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
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Sat, 23 Jun 2018
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[ 15:53 fernape ]
biology/phyml: update to v3.3.20180621
Approved by: tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D15967
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Tue, 15 May 2018
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[ 03:17 wen ]
- Update to 3.3.20180214
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Sat, 10 Mar 2018
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[ 23:35 linimon ]
Remove now-useless, commented-out lines.
Approved by: portmgr (tier-2 blanket)
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Thu, 1 Feb 2018
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[ 07:26 wen ]
- Update to 3.3.20180129
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Wed, 27 Dec 2017
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[ 07:36 linimon ]
Disable the extra flag "-march=native" on arm to fix builds.
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com -exp run
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Sat, 9 Dec 2017
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[ 01:39 linimon ]
These are also broken on aarch64 in the same way as armv6/7.
Approved by: portmgr (tier-2 blanket)
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[ 00:42 linimon ] (Only the first 10 of 21 ports in this commit are shown above. )
Mark more ports broken that fail on both armv6 and armv7.
Approved by: portmgr (tier-2 blanket)
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Mon, 4 Sep 2017
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[ 00:01 sunpoet ]
Update to 3.3.20170530
Changes: https://github.com/stephaneguindon/phyml/releases
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Fri, 1 Apr 2016
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[ 13:29 mat ] (Only the first 10 of 1009 ports in this commit are shown above. )
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
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Fri, 26 Feb 2016
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[ 13:03 wen ]
- Update to 3.2.0
- Update pkg-descr
PR: 205890
Submitted by: tkato432@yahoo.com
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Sun, 28 Dec 2014
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[ 19:14 bapt ]
Convert to USES=autoreconf
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Fri, 31 Jan 2014
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[ 12:32 miwi ]
- Stage support
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Fri, 20 Sep 2013
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[ 15:55 bapt ] (Only the first 10 of 94 ports in this commit are shown above. )
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Wed, 14 Aug 2013
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[ 22:35 ak ] (Only the first 10 of 1725 ports in this commit are shown above. )
- Remove MAKE_JOBS_SAFE variable
Approved by: portmgr (bdrewery)
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Mon, 4 Feb 2013
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[ 10:07 araujo ]
- Update to 20121109.
PR: ports/175014
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
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Tue, 4 Dec 2012
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[ 20:28 zi ]
- Reset MAINTAINER due to unrecoverable email bounce
Reported by: portscout
Feature safe: yes
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Sat, 4 Dec 2010
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[ 07:34 ade ] (Only the first 10 of 1730 ports in this commit are shown above. )
Sync to new bsd.autotools.mk
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Tue, 5 Oct 2010
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[ 19:57 ade ] (Only the first 10 of 235 ports in this commit are shown above. )
Round one migration of ports from automake{19,110} to automake111
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Tue, 21 Jul 2009
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[ 01:10 amdmi3 ]
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>
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Number of commits found: 33 |
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