Add new port math/fbm.

A software for Flexible Bayesian Modelling and Markov Chain
Sampling(The software is for education and research use only).

PR:		53650
Submitted by:	Pedro F. Giffuni <giffunip@yahoo.com>

8 files changed, 648 insertions, 0 deletions

diff --git a/math/Makefile b/math/Makefile
index 655535f06dae..aabcd397da0c 100644
--- a/math/Makefile
+++ b/math/Makefile
@@ -31,6 +31,7 @@
     SUBDIR += entropy
     SUBDIR += eukleides
     SUBDIR += eval
+    SUBDIR += fbm
     SUBDIR += femlab
     SUBDIR += fftpack
     SUBDIR += fftw
diff --git a/math/fbm/Makefile b/math/fbm/Makefile
new file mode 100644
index 000000000000..d73b593a07e4
--- /dev/null
+++ b/math/fbm/Makefile
@@ -0,0 +1,68 @@
+# New ports collection makefile for:	fbm
+# Date created:         31 June 2003
+# Whom:			Pedro F. Giffuni <giffunip@asme.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	fbm
+PORTVERSION=	20010803
+CATEGORIES=	math
+MASTER_SITES=	ftp://ftp.cs.utoronto.ca/pub/radford/
+DISTNAME=	${PORTNAME}.2001-08-31
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	ports@FreeBSD.org
+COMMENT=	Flexible Bayesian Modeling and Markov Chain Sampling
+
+NO_CDROM=	'Free for educational use and research'
+
+USE_REINPLACE=  yes
+
+SCRIPTS = 	bvg-circ bvg-wrap dist-circ dist-wrap gp-circ	\
+		gp-wrap mix-circ mix-wrap net-circ net-wrap
+PROGRAMS =	bvg-grad-test bvg-hist bvg-initial bvg-mc	\
+		bvg-plt bvg-spec bvg-stepsizes bvg-tbl calc	\
+		combine data-spec dist-display dist-est		\
+		dist-gen dist-genp dist-grad-test dist-hist	\
+		dist-initial dist-mc dist-plt dist-spec 	\
+		dist-stepsizes dist-tbl extract	find-min 	\
+		gp-cov gp-display gp-eigen gp-eval gp-gen 	\
+		gp-genp gp-grad-test gp-hist gp-mc gp-plt 	\
+		gp-pred gp-spec gp-stepsizes gp-tbl grid 	\
+		log-append log-copy log-equal log-last		\
+		log-records mc-ais mc-spec mc-temp-filter	\
+		mc-temp-sched mix-cases mix-display mix-gen	\
+		mix-hist mix-mc mix-plt mix-spec mix-tbl	\
+		model-spec net-display net-dvar net-eval	\
+		net-gd net-gen net-genp net-grad-test net-hist	\
+		net-mc net-plt net-pred net-rej net-spec	\
+		net-stepsizes net-tbl rand-seed series
+TEXT=		mix-genp
+
+post-patch:
+	@${REINPLACE_CMD} -e 's+%%CC%%+${CC}+g;' ${WRKSRC}/make.include
+	@${REINPLACE_CMD} -e 's+%%CFLAGS%%+${CFLAGS}+g;' ${WRKSRC}/make.include
+do-build:
+	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${SH} make-all)
+
+do-install:
+	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${SH} install-arch)
+.for i in ${SCRIPTS}
+	@${INSTALL_SCRIPT} ${WRKSRC}/bin.${ARCH}/${i} ${PREFIX}/bin
+.endfor
+.for i in ${PROGRAMS}
+	@${INSTALL_PROGRAM} ${WRKSRC}/bin.${ARCH}/${i} ${PREFIX}/bin
+.endfor
+	@${MKDIR} ${PREFIX}/share/fbm
+	@${INSTALL_DATA} ${WRKSRC}/util/randfile ${PREFIX}/share/fbm
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+	@${CP} -R $(WRKSRC)/doc/* ${DOCSDIR}
+	@${MKDIR} ${DOCSDIR}/html
+	@${MV} ${DOCSDIR}/*.html ${DOCSDIR}/html
+	@${MKDIR} ${EXAMPLESDIR}
+	@${CP} -R $(WRKSRC)/ex-* ${EXAMPLESDIR}
+.endif
+
+.include <bsd.port.mk>
diff --git a/math/fbm/distinfo b/math/fbm/distinfo
new file mode 100644
index 000000000000..13b64ce19fb3
--- /dev/null
+++ b/math/fbm/distinfo
@@ -0,0 +1 @@
+MD5 (fbm.2001-08-31.tar.Z) = 70e122eaee198811a29dfbd2d4cae1da
diff --git a/math/fbm/files/patch-install-arch b/math/fbm/files/patch-install-arch
new file mode 100644
index 000000000000..da3fff151e30
--- /dev/null
+++ b/math/fbm/files/patch-install-arch
@@ -0,0 +1,10 @@
+--- install-arch.orig	Sun Jun 22 21:29:53 2003
++++ install-arch	Sun Jun 22 21:30:21 2003
+@@ -5,6 +5,6 @@
+ # the programs were last compiled for this architecture.  A program called
+ # "arch" that returns the name of the architecture is assumed to exist.
+ 
+-a=`arch`
++a=${ARCH}
+ mkdir -p bin.$a
+ cp bin/* bin.$a
diff --git a/math/fbm/files/patch-make.include b/math/fbm/files/patch-make.include
new file mode 100644
index 000000000000..ca048d84f470
--- /dev/null
+++ b/math/fbm/files/patch-make.include
@@ -0,0 +1,12 @@
+--- make.include.orig	Sat Sep  1 05:21:58 2001
++++ make.include	Sat Jul 12 12:46:16 2003
+@@ -2,6 +2,6 @@
+ #
+ # You may wish to modify this file to fit your local installation.
+ 
+-CC     = cc  # C compiler to use
+-CFLAGS = -O  # C compiler options when compiling .c files to .o files
+-LFLAGS =     # Options when linking .o files
++CC     = %%CC%%      # C compiler to use
++CFLAGS = %%CFLAGS%%  # C compiler options when compiling .c files to .o files
++LFLAGS = ${LDFLAGS}  # Options when linking .o files
diff --git a/math/fbm/files/patch-util+util.make b/math/fbm/files/patch-util+util.make
new file mode 100644
index 000000000000..f5501557c57b
--- /dev/null
+++ b/math/fbm/files/patch-util+util.make
@@ -0,0 +1,8 @@
+--- util/util.make.orig	Sun Jun 22 23:10:08 2003
++++ util/util.make	Sun Jun 22 23:16:12 2003
+@@ -92,4 +92,4 @@
+ phi.o:		phi.c
+ 
+ rand.o:		rand.c		rand.h
+-	$(CC) $(CFLAGS) -DRAND_FILE=\"`pwd`/../util/randfile\" -c rand.c
++	$(CC) $(CFLAGS) -DRAND_FILE=\"${PREFIX}/share/fbm/randfile\" -c rand.c
diff --git a/math/fbm/pkg-descr b/math/fbm/pkg-descr
new file mode 100644
index 000000000000..3d661c7711f4
--- /dev/null
+++ b/math/fbm/pkg-descr
@@ -0,0 +1,19 @@
+Software for Flexible Bayesian Modeling and Markov Chain Sampling
+
+This software supports Bayesian regression and classification models
+based on neural networks and Gaussian processes, and Bayesian mixture
+models.  It also supports a variety of Markov chain sampling methods,
+which may be applied to distributions specified by simple formulas,
+including simple Bayesian models defined by formulas for the prior
+and likelihood.
+
+Before trying to use the software, you may need to read various 
+references that describe the models and the Markov chain methods used.
+
+Some of the programs in this package are designed for use with the xgraph 
+plot package for X-Windows, though the data can instead be plotted by 
+whatever plot program you have available.
+
+WWW:	http://www.cs.utoronto.ca/~radford/fbm.software.html
+
+Radford Neal
diff --git a/math/fbm/pkg-plist b/math/fbm/pkg-plist
new file mode 100644
index 000000000000..551502aa7b2f
--- /dev/null
+++ b/math/fbm/pkg-plist
@@ -0,0 +1,529 @@
+bin/bvg-circ
+bin/bvg-grad-test
+bin/bvg-hist
+bin/bvg-initial
+bin/bvg-mc
+bin/bvg-plt
+bin/bvg-spec
+bin/bvg-stepsizes
+bin/bvg-tbl
+bin/bvg-wrap
+bin/calc
+bin/combine
+bin/data-spec
+bin/dist-circ
+bin/dist-display
+bin/dist-est
+bin/dist-gen
+bin/dist-genp
+bin/dist-grad-test
+bin/dist-hist
+bin/dist-initial
+bin/dist-mc
+bin/dist-plt
+bin/dist-spec
+bin/dist-stepsizes
+bin/dist-tbl
+bin/dist-wrap
+bin/extract
+bin/find-min
+bin/gp-circ
+bin/gp-cov
+bin/gp-display
+bin/gp-eigen
+bin/gp-eval
+bin/gp-gen
+bin/gp-genp
+bin/gp-grad-test
+bin/gp-hist
+bin/gp-mc
+bin/gp-plt
+bin/gp-pred
+bin/gp-spec
+bin/gp-stepsizes
+bin/gp-tbl
+bin/gp-wrap
+bin/grid
+bin/log-append
+bin/log-copy
+bin/log-equal
+bin/log-last
+bin/log-records
+bin/mc-ais
+bin/mc-spec
+bin/mc-temp-filter
+bin/mc-temp-sched
+bin/mix-cases
+bin/mix-circ
+bin/mix-display
+bin/mix-gen
+@comment bin/mix-genp
+bin/mix-hist
+bin/mix-mc
+bin/mix-plt
+bin/mix-spec
+bin/mix-tbl
+bin/mix-wrap
+bin/model-spec
+bin/net-circ
+bin/net-display
+bin/net-dvar
+bin/net-eval
+bin/net-gd
+bin/net-gen
+bin/net-genp
+bin/net-grad-test
+bin/net-hist
+bin/net-mc
+bin/net-plt
+bin/net-rej
+bin/net-pred
+bin/net-spec
+bin/net-stepsizes
+bin/net-tbl
+bin/net-wrap
+bin/rand-seed
+bin/series
+share/fbm/randfile
+@dirrm share/fbm
+%%PORTDOCS%%%%DOCSDIR%%/Acknowledgements.doc
+%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
+%%PORTDOCS%%%%DOCSDIR%%/Contents.doc
+%%PORTDOCS%%%%DOCSDIR%%/Copyright.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-bayes-e.doc
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+%%PORTDOCS%%%%DOCSDIR%%/Ex-dist.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-gdes.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-intro.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-mix-b.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-mix-r.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-mix.doc
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+%%PORTDOCS%%%%DOCSDIR%%/Ex-netgp.doc
+%%PORTDOCS%%%%DOCSDIR%%/Ex-surv.doc
+%%PORTDOCS%%%%DOCSDIR%%/Facilities.doc
+%%PORTDOCS%%%%DOCSDIR%%/Guide.doc
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