diff options
| -rw-r--r-- | math/Makefile | 1 | ||||
| -rw-r--r-- | math/fbm/Makefile | 68 | ||||
| -rw-r--r-- | math/fbm/distinfo | 1 | ||||
| -rw-r--r-- | math/fbm/files/patch-install-arch | 10 | ||||
| -rw-r--r-- | math/fbm/files/patch-make.include | 12 | ||||
| -rw-r--r-- | math/fbm/files/patch-util+util.make | 8 | ||||
| -rw-r--r-- | math/fbm/pkg-descr | 19 | ||||
| -rw-r--r-- | math/fbm/pkg-plist | 529 |
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 +%%PORTDOCS%%%%DOCSDIR%%/Ex-bayes-p.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-bayes-r.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-bayes-t.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-bayes.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-circ.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-dist-f.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-dist-g.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-dist-n.doc +%%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 +%%PORTDOCS%%%%DOCSDIR%%/Ex-netgp-b.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-netgp-c.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-netgp-o.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-netgp-r.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-netgp.doc +%%PORTDOCS%%%%DOCSDIR%%/Ex-surv.doc +%%PORTDOCS%%%%DOCSDIR%%/Facilities.doc +%%PORTDOCS%%%%DOCSDIR%%/Guide.doc +%%PORTDOCS%%%%DOCSDIR%%/Hints.doc +%%PORTDOCS%%%%DOCSDIR%%/Install.doc +%%PORTDOCS%%%%DOCSDIR%%/Overview.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1995-08-09.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1996-08-26.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1997-01-18.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1997-07-22.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1998-08-02.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1998-09-01.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1999-03-13.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.1999-12-06.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.2000-08-21.doc +%%PORTDOCS%%%%DOCSDIR%%/Release.2001-08-31.doc +%%PORTDOCS%%%%DOCSDIR%%/bvg-initial.doc +%%PORTDOCS%%%%DOCSDIR%%/bvg-mc.doc +%%PORTDOCS%%%%DOCSDIR%%/bvg-plt.doc +%%PORTDOCS%%%%DOCSDIR%%/bvg-spec.doc +%%PORTDOCS%%%%DOCSDIR%%/bvg.doc +%%PORTDOCS%%%%DOCSDIR%%/calc.doc +%%PORTDOCS%%%%DOCSDIR%%/catff 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