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Port details
mrbayes Bayesian inference of phylogeny
3.2.7_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.2.7_2Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2007-12-15 15:13:49
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (21 items)
Collapse this list.
  1. /usr/local/share/licenses/mrbayes-3.2.7_2/catalog.mk
  2. /usr/local/share/licenses/mrbayes-3.2.7_2/LICENSE
  3. /usr/local/share/licenses/mrbayes-3.2.7_2/GPLv3
  4. bin/mb
  5. share/doc/mrbayes/COPYING
  6. share/doc/mrbayes/MBDating.pdf
  7. share/doc/mrbayes/Manual_MrBayes_v3.2.pdf
  8. share/doc/mrbayes/NEWS
  9. share/doc/mrbayes/README
  10. share/doc/mrbayes/hym.nex
  11. share/examples/mrbayes/avian_ovomucoids.nex
  12. share/examples/mrbayes/codon.nex
  13. share/examples/mrbayes/cynmix.nex
  14. share/examples/mrbayes/finch.nex
  15. share/examples/mrbayes/hymfossil.nex
  16. share/examples/mrbayes/primates.nex
  17. share/examples/mrbayes/replicase.nex
  18. share/examples/mrbayes/sceloporus.nex
  19. @owner
  20. @group
  21. @mode
Collapse this list.
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):
mrbayes
ABIlatestquarterly
FreeBSD:13:aarch643.2.7_23.2.7_2
FreeBSD:13:amd643.2.7_23.2.7_2
FreeBSD:13:armv63.2.7_23.2.7_2
FreeBSD:13:armv73.2.7_23.2.7_2
FreeBSD:13:i3863.2.7_23.2.7_2
FreeBSD:13:powerpc-3.2.7_2
FreeBSD:13:powerpc643.2.7_23.2.7_2
FreeBSD:13:powerpc64le-3.2.7_2
FreeBSD:14:aarch643.2.7_23.2.7_2
FreeBSD:14:amd643.2.7_23.2.7_2
FreeBSD:14:armv63.2.7_2-
FreeBSD:14:armv73.2.7_23.2.7_2
FreeBSD:14:i3863.2.7_23.2.7_2
FreeBSD:14:powerpc3.2.7_23.2.7_2
FreeBSD:14:powerpc64-3.2.7_2
FreeBSD:14:powerpc64le3.2.7_23.2.7_2
FreeBSD:15:aarch643.2.7_2-
FreeBSD:15:amd643.2.7_2-
FreeBSD:15:armv73.2.7_2-
FreeBSD:15:powerpc3.2.7_2-
FreeBSD:15:powerpc643.2.7_2-
FreeBSD:15:powerpc64le3.2.7_2-
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Library dependencies:
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/NBISweden/MrBayes/tar.gz/v3.2.7?dummy=/
Collapse this list.

Number of commits found: 18

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.2.7_2
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
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>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.2.7_2
15 May 2021 07:14:04
commit hash: 9671981826f7ef8b1e7fb0a430ee24d4a1f0acf2commit hash: 9671981826f7ef8b1e7fb0a430ee24d4a1f0acf2commit hash: 9671981826f7ef8b1e7fb0a430ee24d4a1f0acf2commit hash: 9671981826f7ef8b1e7fb0a430ee24d4a1f0acf2 files touched by this commit
Tobias Kortkamp (tobik) search for other commits by this committer
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
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
3.2.7_2
21 Apr 2020 21:47:58
Revision:532428Original commit files touched by this commit
danilo search for other commits by this committer
- Swap back from net/openmpi3 to net/openmpi
3.2.7_1
15 Apr 2020 19:41:27
Revision:531784Original commit files touched by this commit
danilo search for other commits by this committer
- 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
Revision:527483Original commit files touched by this commit
jrm search for other commits by this committer
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
Revision:516880Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
3.1.2_3
09 Apr 2019 14:04:50
Revision:498476Original commit files touched by this commit
sunpoet search for other commits by this committer
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
Revision:444463Original commit files touched by this commit
sunpoet search for other commits by this committer
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
Revision:364996Original commit files touched by this commit
adamw search for other commits by this committer
Fix build on -current by un-clobbering LDFLAGS. Also, don't
mute installation commands.
3.1.2_1
10 Dec 2013 17:54:12
Revision:336072Original commit files touched by this commit
bapt search for other commits by this committer
Support stage
USE_GMAKE -> USES=gmake
use USES=readline:port
3.1.2_1
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
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
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
3.1.2_1
12 May 2009 11:28:17
Original commit files touched by this commit
itetcu search for other commits by this committer
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
Original commit files touched by this commit
pav search for other commits by this committer
- 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
Original commit files touched by this commit
miwi search for other commits by this committer
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

Number of commits found: 18