Initial import of mcl 03-185

The MCL algorithm is short for the Markov Cluster Algorithm,
a fast and scalable cluster algorithm for graphs based on
simulation of (stochastic) flow in graphs.  The algorithm was
developed by Stijn van Dongen at the Centre for Mathematics and
Computer Science (also known as CWI) in the Netherlands.

The MCL algorithm is very fast, very scalable, and has a number
of attractive properties causing it to deliver high-quality
clusterings.

WWW: http://micans.org/mcl/

from Andreas Kahari <andreas.kahari@unix.net>

math/mcl/Makefile

@@ -0,0 +1,24 @@
+# $OpenBSD: Makefile,v 1.1.1.1 2003/07/08 10:55:20 sturm Exp $
+
+COMMENT=	"clustering algorithm for graphs"
+
+V=		03-185
+DISTNAME=	mcl-${V}
+PKGNAME=	mcl-${V:S,-,_,}
+CATEGORIES=	math
+
+HOMEPAGE=	http://micans.org/mcl/
+
+MAINTAINER=	Andreas Kahari <andreas.kahari@unix.net>
+
+# GPL
+PERMIT_PACKAGE_CDROM=	Yes
+PERMIT_PACKAGE_FTP=	Yes
+PERMIT_DISTFILES_CDROM=	Yes
+PERMIT_DISTFILES_FTP=	Yes
+
+MASTER_SITES=	http://micans.org/mcl/src/
+
+CONFIGURE_STYLE=gnu
+
+.include <bsd.port.mk>

math/mcl/distinfo

@@ -0,0 +1,3 @@
+MD5 (mcl-03-185.tar.gz) = 5cfa69fece0d5b05b088d809174f5f7b
+RMD160 (mcl-03-185.tar.gz) = 74395b4e57ff52758dcfb4403f86438c1cd16d09
+SHA1 (mcl-03-185.tar.gz) = 76db5f0de8a5adc0d1ec2d02b3bc2844fe50e64a

math/mcl/patches/patch-configure

@@ -0,0 +1,29 @@
+$OpenBSD: patch-configure,v 1.1.1.1 2003/07/08 10:55:20 sturm Exp $
+--- configure.orig	Tue Jul  8 12:22:58 2003
++++ configure	Tue Jul  8 12:41:36 2003
+@@ -2956,13 +2956,13 @@ fi
+ 
+ # FIXME: Replace `main' with a function in `-lpthread':
+ 
+-echo "$as_me:$LINENO: checking for main in -lpthread" >&5
+-echo $ECHO_N "checking for main in -lpthread... $ECHO_C" >&6
++echo "$as_me:$LINENO: checking for main in -pthread" >&5
++echo $ECHO_N "checking for main in -pthread... $ECHO_C" >&6
+ if test "${ac_cv_lib_pthread_main+set}" = set; then
+   echo $ECHO_N "(cached) $ECHO_C" >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lpthread  $LIBS"
++LIBS="-pthread  $LIBS"
+ cat >conftest.$ac_ext <<_ACEOF
+ #line $LINENO "configure"
+ #include "confdefs.h"
+@@ -3004,7 +3004,7 @@ if test $ac_cv_lib_pthread_main = yes; t
+ #define HAVE_LIBPTHREAD 1
+ _ACEOF
+ 
+-  LIBS="-lpthread $LIBS"
++  LIBS="-pthread $LIBS"
+ 
+ fi
+ 

math/mcl/patches/patch-src_graphs_Makefile_in

@@ -0,0 +1,14 @@
+$OpenBSD: patch-src_graphs_Makefile_in,v 1.1.1.1 2003/07/08 10:55:20 sturm Exp $
+--- src/graphs/Makefile.in.orig	Mon Jul  7 10:49:41 2003
++++ src/graphs/Makefile.in	Mon Jul  7 10:51:02 2003
+@@ -82,7 +82,9 @@ am__include = @am__include@
+ am__quote = @am__quote@
+ install_sh = @install_sh@
+ 
+-exampledir = $(datadir)/doc/$(PACKAGE)/examples
++#exampledir = $(datadir)/doc/$(PACKAGE)/examples
++# OpenBSD wants examples in a different location...
++exampledir = $(datadir)/examples/$(PACKAGE)
+ 
+ example_DATA = falkner.mci proteins.mci small.mci small.png small.ps\
+                   data.raw data.hdr data.tab small.tab fznyy.tab

math/mcl/patches/patch-util_heap_c

@@ -0,0 +1,11 @@
+$OpenBSD: patch-util_heap_c,v 1.1.1.1 2003/07/08 10:55:20 sturm Exp $
+--- util/heap.c.orig	Tue Jul  8 12:22:29 2003
++++ util/heap.c	Tue Jul  8 12:22:41 2003
+@@ -8,6 +8,7 @@
+ 
+ 
+ #include <stdio.h>
++#include <string.h>
+ 
+ #include "alloc.h"
+ #include "heap.h"

math/mcl/pkg/DESCR

@@ -0,0 +1,11 @@
+The MCL algorithm is short for the Markov Cluster Algorithm,
+a fast and scalable cluster algorithm for graphs based on
+simulation of (stochastic) flow in graphs.  The algorithm was
+developed by Stijn van Dongen at the Centre for Mathematics and
+Computer Science (also known as CWI) in the Netherlands.
+
+The MCL algorithm is very fast, very scalable, and has a number
+of attractive properties causing it to deliver high-quality
+clusterings.
+
+WWW: ${HOMEPAGE}

math/mcl/pkg/PLIST

@@ -0,0 +1,75 @@
+@comment $OpenBSD: PLIST,v 1.1.1.1 2003/07/08 10:55:20 sturm Exp $
+bin/clmdist
+bin/clmformat
+bin/clmimac
+bin/clminfo
+bin/clmmeet
+bin/clmresidue
+bin/mcl
+bin/mclpipeline
+bin/mcx
+bin/mcxassemble
+bin/mcxconvert
+bin/mcxmap
+bin/mcxsubs
+man/man1/clmdist.1
+man/man1/clmformat.1
+man/man1/clmimac.1
+man/man1/clminfo.1
+man/man1/clmmeet.1
+man/man1/clmresidue.1
+man/man1/mcl.1
+man/man1/mclpipeline.1
+man/man1/mcx.1
+man/man1/mcxassemble.1
+man/man1/mcxconvert.1
+man/man1/mcxmap.1
+man/man1/mcxsubs.1
+man/man5/mcxio.5
+man/man7/mclfaq.7
+share/doc/mcl/clmdist.html
+share/doc/mcl/clmdist.ps
+share/doc/mcl/clmformat.html
+share/doc/mcl/clmformat.ps
+share/doc/mcl/clmimac.html
+share/doc/mcl/clmimac.ps
+share/doc/mcl/clminfo.html
+share/doc/mcl/clminfo.ps
+share/doc/mcl/clmmeet.html
+share/doc/mcl/clmmeet.ps
+share/doc/mcl/clmresidue.html
+share/doc/mcl/clmresidue.ps
+share/doc/mcl/index.html
+share/doc/mcl/mcl.html
+share/doc/mcl/mcl.ps
+share/doc/mcl/mcl.txt
+share/doc/mcl/mclfaq.html
+share/doc/mcl/mclfaq.ps
+share/doc/mcl/mclfaq.txt
+share/doc/mcl/mclmcl.txt
+share/doc/mcl/mclpipeline.html
+share/doc/mcl/mclpipeline.ps
+share/doc/mcl/mcx.html
+share/doc/mcl/mcx.ps
+share/doc/mcl/mcxassemble.html
+share/doc/mcl/mcxassemble.ps
+share/doc/mcl/mcxconvert.html
+share/doc/mcl/mcxconvert.ps
+share/doc/mcl/mcxio.html
+share/doc/mcl/mcxio.ps
+share/doc/mcl/mcxmap.html
+share/doc/mcl/mcxmap.ps
+share/doc/mcl/mcxsubs.html
+share/doc/mcl/mcxsubs.ps
+share/examples/mcl/data.hdr
+share/examples/mcl/data.raw
+share/examples/mcl/data.tab
+share/examples/mcl/falkner.mci
+share/examples/mcl/fznyy.tab
+share/examples/mcl/proteins.mci
+share/examples/mcl/small.mci
+share/examples/mcl/small.png
+share/examples/mcl/small.ps
+share/examples/mcl/small.tab
+@dirrm share/examples/mcl
+@dirrm share/doc/mcl