From 1e37926ab8c1570279f5875ea9914d77fde10389 Mon Sep 17 00:00:00 2001 From: sturm Date: Tue, 8 Jul 2003 10:55:20 +0000 Subject: [PATCH] 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 --- math/mcl/Makefile | 24 ++++++ math/mcl/distinfo | 3 + math/mcl/patches/patch-configure | 29 +++++++ math/mcl/patches/patch-src_graphs_Makefile_in | 14 ++++ math/mcl/patches/patch-util_heap_c | 11 +++ math/mcl/pkg/DESCR | 11 +++ math/mcl/pkg/PLIST | 75 +++++++++++++++++++ 7 files changed, 167 insertions(+) create mode 100644 math/mcl/Makefile create mode 100644 math/mcl/distinfo create mode 100644 math/mcl/patches/patch-configure create mode 100644 math/mcl/patches/patch-src_graphs_Makefile_in create mode 100644 math/mcl/patches/patch-util_heap_c create mode 100644 math/mcl/pkg/DESCR create mode 100644 math/mcl/pkg/PLIST diff --git a/math/mcl/Makefile b/math/mcl/Makefile new file mode 100644 index 00000000000..e06f08b0737 --- /dev/null +++ b/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 + +# 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 diff --git a/math/mcl/distinfo b/math/mcl/distinfo new file mode 100644 index 00000000000..774b0332d1f --- /dev/null +++ b/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 diff --git a/math/mcl/patches/patch-configure b/math/mcl/patches/patch-configure new file mode 100644 index 00000000000..bfd86001f33 --- /dev/null +++ b/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 $LIBS" + + fi + diff --git a/math/mcl/patches/patch-src_graphs_Makefile_in b/math/mcl/patches/patch-src_graphs_Makefile_in new file mode 100644 index 00000000000..aeed841bea7 --- /dev/null +++ b/math/mcl/patches/patch-src_graphs_Makefile_in @@ -0,0 +1,14 @@ +$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 diff --git a/math/mcl/patches/patch-util_heap_c b/math/mcl/patches/patch-util_heap_c new file mode 100644 index 00000000000..3118d4b820d --- /dev/null +++ b/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 ++#include + + #include "alloc.h" + #include "heap.h" diff --git a/math/mcl/pkg/DESCR b/math/mcl/pkg/DESCR new file mode 100644 index 00000000000..88d519cc0f0 --- /dev/null +++ b/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} diff --git a/math/mcl/pkg/PLIST b/math/mcl/pkg/PLIST new file mode 100644 index 00000000000..deb0e4a147d --- /dev/null +++ b/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