| Port details |
- mrbayes Bayesian inference of phylogeny
- 3.2.7_2 biology
 =2      3.2.7_2Version of this port present on the latest quarterly branch. - Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2007-12-15 15:13:49
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://nbisweden.github.io/MrBayes/
- Description:
- MrBayes is a program for the Bayesian estimation of phylogeny.
Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished
using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- mrbayes>0:biology/mrbayes
- To install the port:
- cd /usr/ports/biology/mrbayes/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/mrbayes
- pkg install mrbayes
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: mrbayes
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1583009863
SHA256 (NBISweden-MrBayes-v3.2.7_GH0.tar.gz) = 64da39c01f606d0413ce90a1dd3c1ce2cbdef4cbad99aee8a4b2391a2e8db244
SIZE (NBISweden-MrBayes-v3.2.7_GH0.tar.gz) = 9825172
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Library dependencies:
-
- libreadline.so.8 : devel/readline
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for mrbayes-3.2.7_2:
AVX=off: Use AVX optimized routines
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
FMA=off: Use FMA optimized routines
SSE=on: Use SSE optimized routines
====> MPI (Message Passing Interface) support: you can only select none or one of them
MPICH=off: Parallel processing support via MPICH 3
OPENMPI=off: Parallel processing support via Open MPI
===> Use 'make config' to modify these settings
- Options name:
- biology_mrbayes
- USES:
- readline
- pkg-message:
- For install:
- If MrBayes core dumps with "illegal hardware instruction (core dumped) mb", then
it should be built on the target system.
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
07 Sep 2022 21:58:51
 |
Stefan Eßer (se) |
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) |
3.2.7_2
07 Sep 2022 21:10:59
|
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.
(Only the first 15 lines of the commit message are shown above  ) |
3.2.7_2
20 Jul 2022 14:20:57
|
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> (Only the first 15 lines of the commit message are shown above ) |
3.2.7_2
15 May 2021 07:14:04
|
Tobias Kortkamp (tobik)
Author: Yasuhiro Kimura |
*: Remove unnecessary 'port' argument from USES=readline
PR: 248459
Exp-run by: antoine |
3.2.7_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
3.2.7_2
21 Apr 2020 21:47:58
 |
danilo |
- Swap back from net/openmpi3 to net/openmpi |
3.2.7_1
15 Apr 2020 19:41:27
|
danilo |
- Move OpenMPI support to net/openmpi3. OpenMPI 1 and 2 were deprecated.
Approved by: maintainer (e-mail) |
3.2.7
29 Feb 2020 23:24:40
|
jrm |
biology/mrbayes: Update to version 3.2.7
PR: 243237
Submitted by: mzaki@e-mail.ne.jp (maintainer, with modifications) |
3.1.2_3
06 Nov 2019 12:48:32
 |
antoine |
Mark a few ports BROKEN, unfetchable |
3.1.2_3
09 Apr 2019 14:04:50
|
sunpoet |
Update devel/readline to 8.0
- Bump PORTREVISION of dependent ports for shlib change
Changes: https://tiswww.case.edu/php/chet/readline/CHANGES
PR: 236156
Exp-run by: antoine |
3.1.2_2
27 Jun 2017 13:46:53
|
sunpoet |
Update devel/readline to 7.0 patch 3
- Bump PORTREVISION for shlib change
Changes: https://cnswww.cns.cwru.edu/php/chet/readline/CHANGES
https://lists.gnu.org/archive/html/bug-bash/2016-09/msg00107.html
https://lists.gnu.org/archive/html/bug-readline/2017-01/msg00002.html
Differential Revision: https://reviews.freebsd.org/D11172
PR: 219947
Exp-run by: antoine |
3.1.2_1
15 Aug 2014 16:37:37
|
adamw |
Fix build on -current by un-clobbering LDFLAGS. Also, don't
mute installation commands. |
3.1.2_1
10 Dec 2013 17:54:12
|
bapt |
Support stage
USE_GMAKE -> USES=gmake
use USES=readline:port |
3.1.2_1
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
3.1.2_1
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
3.1.2_1
12 May 2009 11:28:17
|
itetcu |
Fix LIB_DEPENDS on devel/readline: its sh lib version was bumped recently from
5 to 6.
Forgotten by: araujo@
Reported by: QAT |
3.1.2
17 May 2008 16:52:34
|
pav |
- Update maintainer's email address
Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) |
3.1.2
15 Dec 2007 15:13:41
|
miwi |
MrBayes is a program for the Bayesian estimation of phylogeny.
Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished
using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
WWW: http://mrbayes.csit.fsu.edu/
PR: ports/118542
Submitted by: mzaki at biol.s.u-tokyo.ac.jp |
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