Add ghmm 0.7.0a, general Hidden Markov Model Library in C.

PR:		ports/100886
Submitted by:	Cheng-Lung Sung <clsung at FreeBSD.org>

6 files changed, 97 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 1bfa6b4010ed..0b1f2721cec6 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -38,6 +38,7 @@
     SUBDIR += gerris
     SUBDIR += getdp
     SUBDIR += ghemical
+    SUBDIR += ghmm
     SUBDIR += gnudatalanguage
     SUBDIR += gramps
     SUBDIR += gromacs
diff --git a/science/ghmm/Makefile b/science/ghmm/Makefile
new file mode 100644
index 000000000000..c6c3359ccc67
--- /dev/null
+++ b/science/ghmm/Makefile
@@ -0,0 +1,24 @@
+# New ports collection makefile for:	ghmm
+# Date created:		2006-07-26
+# Whom:			Cheng-Lung Sung <clsung@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	ghmm
+PORTVERSION=	0.7.0a
+CATEGORIES=	science math
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
+MASTER_SITE_SUBDIR=	${PORTNAME}
+
+MAINTAINER=	clsung@FreeBSD.org
+COMMENT=	General Hidden Markov Model Library in C
+
+GNU_CONFIGURE=	yes
+INSTALLS_SHLIB=	yes
+WRKSRC=	${WRKDIR}/${PORTNAME}-0.7.0
+
+post-patch:
+	@${REINPLACE_CMD} 's|tests doc VisualC|tests VisualC|' ${WRKSRC}/configure
+
+.include <bsd.port.mk>
diff --git a/science/ghmm/distinfo b/science/ghmm/distinfo
new file mode 100644
index 000000000000..4ec1b8d0ccdd
--- /dev/null
+++ b/science/ghmm/distinfo
@@ -0,0 +1,3 @@
+MD5 (ghmm-0.7.0a.tar.gz) = 7bbaf9bf6d7e0f7658e0809c2eddb674
+SHA256 (ghmm-0.7.0a.tar.gz) = 93bce7423a1f81da83f457fef7aa3f4190669700eb635f641960f9480797195e
+SIZE (ghmm-0.7.0a.tar.gz) = 756779
diff --git a/science/ghmm/files/patch-ltmain.sh b/science/ghmm/files/patch-ltmain.sh
new file mode 100644
index 000000000000..ce8f5d90ce30
--- /dev/null
+++ b/science/ghmm/files/patch-ltmain.sh
@@ -0,0 +1,15 @@
+--- ltmain.sh.orig	Thu Oct 13 16:30:04 2005
++++ ltmain.sh	Wed Jul 26 11:29:48 2006
+@@ -5772,10 +5772,12 @@
+ 	fi
+ 
+ 	# Install the pseudo-library for information purposes.
++	if /usr/bin/false ; then
+ 	name=`$echo "X$file" | $Xsed -e 's%^.*/%%'`
+ 	instname="$dir/$name"i
+ 	$show "$install_prog $instname $destdir/$name"
+ 	$run eval "$install_prog $instname $destdir/$name" || exit $?
++        fi
+ 
+ 	# Maybe install the static library, too.
+ 	test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library"
diff --git a/science/ghmm/pkg-descr b/science/ghmm/pkg-descr
new file mode 100644
index 000000000000..75d4acd35ea7
--- /dev/null
+++ b/science/ghmm/pkg-descr
@@ -0,0 +1,7 @@
+The General Hidden Markov Model Library (GHMM) is a C library 
+with additional Python bindings implementing a wide range of 
+types of Hidden Markov Models and algorithms: 
+discrete, continous emissions, basic training, 
+HMM clustering, HMM mixtures.
+
+WWW:	http://ghmm.sourceforge.net/
diff --git a/science/ghmm/pkg-plist b/science/ghmm/pkg-plist
new file mode 100644
index 000000000000..c33e9f706e5e
--- /dev/null
+++ b/science/ghmm/pkg-plist
@@ -0,0 +1,47 @@
+@comment $FreeBSD$
+bin/probdist
+bin/cluster
+bin/scluster
+bin/smix_hmm
+bin/ghmm-config
+include/ghmm/ghmm.h
+include/ghmm/foba.h
+include/ghmm/model.h
+include/ghmm/cluster.h
+include/ghmm/scluster.h
+include/ghmm/root_finder.h
+include/ghmm/reestimate.h
+include/ghmm/sequence.h
+include/ghmm/viterbi.h
+include/ghmm/sfoba.h
+include/ghmm/sviterbi.h
+include/ghmm/smodel.h
+include/ghmm/sdmodel.h
+include/ghmm/sdfoba.h
+include/ghmm/sreestimate.h
+include/ghmm/sgenerate.h
+include/ghmm/smixturehmm.h
+include/ghmm/scanner.h
+include/ghmm/gauss_tail.h
+include/ghmm/smap_classify.h
+include/ghmm/kbest.h
+include/ghmm/gradescent.h
+include/ghmm/discrime.h
+include/ghmm/psequence.h
+include/ghmm/pmodel.h
+include/ghmm/linkedlist.h
+include/ghmm/pviterbi.h
+include/ghmm/pviterbi_propagate.h
+include/ghmm/vector.h
+include/ghmm/matrix.h
+include/ghmm/const.h
+include/ghmm/rng.h
+include/ghmm/mes.h
+include/ghmm/randvar.h
+include/ghmm/internal.h
+lib/libghmm.so.0
+lib/libghmm.so
+lib/libghmm.a
+%%DATADIR%%/PHI_001_20.dat
+@dirrmtry %%DATADIR%%
+@dirrmtry include/ghmm