BSD Ports

math/jags 5.0.0 FreeBSD

Just Another Gibbs Sampler

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
f80dfca614
License
GPLv2
Categories
math
Package size
1643.0 KiB, 3788.9 KiB installed

Description

JAGS is Just Another Gibbs Sampler -- a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

The functionality of JAGS is based on the BUGS program created by the MRC Biostatistics Unit (http://www.mrc-bsu.cam.ac.uk/). There is a short manual that describes the differences between JAGS and BUGS.

Some of the BUGS examples have been modified to run with JAGS, and have been turned into a test suite.

Install

Binary package:

pkg install mcmc-jags

From the ports tree:

cd /usr/ports/math/jags/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	mcmc-jags>0:math/jags
LIB_DEPENDS=	libjags.so:math/jags

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest5.0.05.0.0-4.3.1_55.0.0
FreeBSD:14:quarterly5.0.05.0.0n/a4.3.1_55.0.0
FreeBSD:15:latest5.0.05.0.0n/a4.3.1_54.3.1_5
FreeBSD:15:quarterly5.0.05.0.0n/an/an/a
FreeBSD:16:latest5.0.05.0.0n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Library 1

Test 1

The full lists below include those, and their dependencies in turn.

Build dependencies 17
Run dependencies 10

No port depends on this one.

Configuration

Options name: math_mcmc-jags

OptionDefaultDescription
DOCSoffBuild and/or install documentation
EXAMPLESoffBuild and/or install examples
NETLIBoffBLAS implementation from Netlib
OPENBLASonOpenBLAS BLAS implementation
USES
bison compiler:features fortran gmake libtool localbase pathfix pkgconfig
Service scripts
none

Message after installing

Please note that the name of the jags script has been changed
from "jags" to "mcmc-jags" on this platform, to avoid a conflict
with net/jags, and usage should be adjusted accordingly.

===>   NOTICE:

The mcmc-jags port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

Manual pages 1
  • jags(1)
pkg-plist 126
  • bin/mcmc-jags
  • include/JAGS/Console.h
  • include/JAGS/JRmath.h
  • include/JAGS/compiler/Compiler.h
  • include/JAGS/compiler/Counter.h
  • include/JAGS/compiler/CounterTab.h
  • include/JAGS/compiler/LogicalFactory.h
  • include/JAGS/compiler/NodeFactory.h
  • include/JAGS/compiler/ObsFuncTab.h
  • include/JAGS/compiler/ParseTree.h
  • include/JAGS/distribution/ArrayDist.h
  • include/JAGS/distribution/DistError.h
  • include/JAGS/distribution/DistPtr.h
  • include/JAGS/distribution/DistTab.h
  • include/JAGS/distribution/Distribution.h
  • include/JAGS/distribution/RScalarDist.h
  • include/JAGS/distribution/ScalarDist.h
  • include/JAGS/distribution/VectorDist.h
  • include/JAGS/function/ArrayFunction.h
  • include/JAGS/function/ArrayLogDensity.h
  • include/JAGS/function/DFunction.h
  • include/JAGS/function/DPQFunction.h
  • include/JAGS/function/FuncError.h
  • include/JAGS/function/FuncTab.h
  • include/JAGS/function/Function.h
  • include/JAGS/function/FunctionPtr.h
  • include/JAGS/function/LinkFunction.h
  • include/JAGS/function/PFunction.h
  • include/JAGS/function/QFunction.h
  • include/JAGS/function/ScalarFunction.h
  • include/JAGS/function/ScalarLogDensity.h
  • include/JAGS/function/ScalarVectorFunction.h
  • include/JAGS/function/VectorFunction.h
  • include/JAGS/function/VectorLogDensity.h
  • include/JAGS/graph/AggNode.h
  • include/JAGS/graph/ArrayLogicalNode.h
  • include/JAGS/graph/ArrayStochasticNode.h
  • include/JAGS/graph/ConstantNode.h
  • include/JAGS/graph/DeterministicNode.h
  • include/JAGS/graph/Graph.h
  • include/JAGS/graph/GraphMarks.h
  • include/JAGS/graph/LinkNode.h
  • include/JAGS/graph/LogicalNode.h
  • include/JAGS/graph/MixTab.h
  • include/JAGS/graph/MixtureNode.h
  • include/JAGS/graph/MixtureNodeError.h
  • include/JAGS/graph/Node.h
  • include/JAGS/graph/NodeError.h
  • include/JAGS/graph/ScalarLogicalNode.h
  • include/JAGS/graph/ScalarStochasticNode.h
  • include/JAGS/graph/StochasticNode.h
  • include/JAGS/graph/VSLogicalNode.h
  • include/JAGS/graph/VectorLogicalNode.h
  • include/JAGS/graph/VectorStochasticNode.h
  • include/JAGS/matrix/blas.h
  • include/JAGS/matrix/lapack.h
  • include/JAGS/matrix/matrix.h
  • include/JAGS/model/BUGSModel.h
  • include/JAGS/model/CovMonitor.h
  • include/JAGS/model/ESSWeight.h
  • include/JAGS/model/MeanMonitor.h
  • include/JAGS/model/Model.h
  • include/JAGS/model/Monitor.h
  • include/JAGS/model/MonitorControl.h
  • include/JAGS/model/MonitorFactory.h
  • include/JAGS/model/MonitorInfo.h
  • include/JAGS/model/MonitorStat.h
  • include/JAGS/model/NodeArray.h
  • include/JAGS/model/NodeArraySubset.h
  • include/JAGS/model/StochasticIndex.h
  • include/JAGS/model/SymTab.h
  • include/JAGS/model/TraceMonitor.h
  • include/JAGS/model/TraceWeight.h
  • include/JAGS/model/VarMonitor.h
  • include/JAGS/model/WeightMonitor.h
  • include/JAGS/model/WeightedTraceMonitor.h
  • include/JAGS/module/Module.h
  • include/JAGS/module/ModuleError.h
  • include/JAGS/rng/RNG.h
  • include/JAGS/rng/RNGFactory.h
  • include/JAGS/rng/RmathRNG.h
  • include/JAGS/rng/TruncatedNormal.h
  • include/JAGS/sampler/GraphView.h
  • include/JAGS/sampler/ImmutableSampleMethod.h
  • include/JAGS/sampler/ImmutableSampler.h
  • include/JAGS/sampler/Linear.h
  • include/JAGS/sampler/Metropolis.h
  • include/JAGS/sampler/MutableSampleMethod.h
  • include/JAGS/sampler/MutableSampler.h
  • include/JAGS/sampler/RWMetropolis.h
  • include/JAGS/sampler/SampleMethodNoAdapt.h
  • include/JAGS/sampler/Sampler.h
  • include/JAGS/sampler/SamplerFactory.h
  • include/JAGS/sampler/SingletonFactory.h
  • include/JAGS/sampler/SingletonGraphView.h
  • include/JAGS/sampler/Slicer.h
  • include/JAGS/sampler/StepAdapter.h
  • include/JAGS/sampler/TemperedMetropolis.h
  • include/JAGS/sarray/Range.h
  • include/JAGS/sarray/RangeIterator.h

The first 100 are listed.

distinfo 5
FileSizeSHA256
mcmc-jags/JAGS-5.0.0.tar.gz2.158256e+0664fcd4883b8a8ee907722f49366cc9f277477a0647ada61356f17568f84ffff8
mcmc-jags/jags_developer_manual.pdf713196e7c707b94ffc931807198cc162e8b254859bb774695ae39ef1c1c175560259b
mcmc-jags/jags_installation_manual.pdf17487309bba065a1d2d2c902e17a6c867cfa46748fb1b218509ada52892d6578cdcf98
mcmc-jags/jags_user_manual.pdf52022762b82131398c223fd50d8e9b0919f5731676462528db01662bd1d6c0ca52651d
mcmc-jags/classic-bugs.tar.gz86183cbecdd184516ed1e0ed26993335c7ce6b50b85875c66a059a4ad51780547e580
Master sites 4
  • SF/mcmc-jags/JAGS/${PORTVERSION:C|\..*||}.x/Source/:1
  • SF/mcmc-jags/Examples/4.x/:2
  • SF/mcmc-jags/Manuals/5.x/:3
  • SF/mcmc-jags/Manuals/${PORTVERSION:C|\..*||}.x/:4

Commit history 1

DateCommitCreditsLog message
f80dfca614 Thierry Thomas math/jags: upgrade to 5.0.0
News at https://martynplummer.wordpress.com/2026/08/03/whats-new-in-jags-5-0-0-part-1-initial-values/ https://martynplummer.wordpress.com/2026/08/04/whats-new-in-jags-5-0-0-part-2-reproducibility/