mcl: Upgrade to 14-137 and clean up

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 2 14:04:05 2018 -0500
Changeset:	e9fbd831bfb9ef28bb24eef4cce9a1ff83471ac5

Modified Files:
	mcl/DESCR
	mcl/Makefile
	mcl/PLIST
	mcl/distinfo

Log Message:
mcl: Upgrade to 14-137 and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e9fbd831bfb9ef28bb24eef4cce9a1ff83471ac5

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 mcl/DESCR    | 10 +++-------
 mcl/Makefile | 25 ++++++++++++++++++-------
 mcl/PLIST    | 10 +++++++++-
 mcl/distinfo |  9 +++++----
 4 files changed, 35 insertions(+), 19 deletions(-)

diffs:
diff --git a/mcl/DESCR b/mcl/DESCR
index 48188bf477..48f4823e87 100644
--- a/mcl/DESCR
+++ b/mcl/DESCR
@@ -1,7 +1,3 @@
-The MCL package is an implementation of the MCL algorithm, and offers
-utilities for manipulating sparse matrices (the essential data structure in the
-MCL algorithm) and conducting cluster experiments.
-
-MCL is currently being used in sciences like biology (protein family detection,
-genomics), computer science (node clustering in Peer-to-Peer networks),
-and linguistics (text analysis)
+The MCL algorithm is short for the Markov Cluster Algorithm, a fast and
+scalable unsupervised cluster algorithm for graphs (also known as networks)
+based on simulation of (stochastic) flow in graphs.
diff --git a/mcl/Makefile b/mcl/Makefile
index a5172e43a0..deffd4cf2c 100644
--- a/mcl/Makefile
+++ b/mcl/Makefile
@@ -1,15 +1,26 @@
-# $NetBSD: Makefile,v 1.1 2013/09/01 20:46:00 jihbed Exp $
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Fri Nov  2 13:57:58 CDT 2018               #
+###########################################################
 
-DISTNAME=	mcl-12-135
+DISTNAME=	mcl-${PV}-137
+PKGNAME=	mcl-${PV}
 CATEGORIES=	math
-MASTER_SITES=	http://micans.org/mcl/src/
+MASTER_SITES=	https://www.micans.org/mcl/src/
 
-MAINTAINER=	jihbed.research%gmail.com@localhost
-HOMEPAGE=	http://micans.org/mcl/src/
-COMMENT=	Markov Cluster algorithm
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://www.micans.org/mcl/index.html?sec_software
+COMMENT=	Fast and scalable unsupervised cluster algorithm for graphs
 LICENSE=	gnu-gpl-v3
 
 GNU_CONFIGURE=	yes
+USE_TOOLS=	bash perl:run
+
+REPLACE_BASH=	scripts/clxdo
+REPLACE_PERL=	src/shcl/mclpipeline
+
+PV=		14
 
-.include "../../mk/pthread.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/mcl/PLIST b/mcl/PLIST
index 081290c513..f3357fa544 100644
--- a/mcl/PLIST
+++ b/mcl/PLIST
@@ -1,6 +1,7 @@
-@comment $NetBSD: PLIST,v 1.1 2013/09/01 20:46:00 jihbed Exp $
+@comment $NetBSD$
 bin/clm
 bin/clmformat
+bin/clxdo
 bin/mcl
 bin/mclcm
 bin/mclpipeline
@@ -19,8 +20,10 @@ man/man1/clmdist.1
 man/man1/clmformat.1
 man/man1/clmimac.1
 man/man1/clminfo.1
+man/man1/clminfo2.1
 man/man1/clmmate.1
 man/man1/clmmeet.1
+man/man1/clmoptics.1
 man/man1/clmorder.1
 man/man1/clmresidue.1
 man/man1/clmvol.1
@@ -62,10 +65,14 @@ share/doc/mcl/clmimac.html
 share/doc/mcl/clmimac.ps
 share/doc/mcl/clminfo.html
 share/doc/mcl/clminfo.ps
+share/doc/mcl/clminfo2.html
+share/doc/mcl/clminfo2.ps
 share/doc/mcl/clmmate.html
 share/doc/mcl/clmmate.ps
 share/doc/mcl/clmmeet.html
 share/doc/mcl/clmmeet.ps
+share/doc/mcl/clmoptics.html
+share/doc/mcl/clmoptics.ps
 share/doc/mcl/clmorder.html
 share/doc/mcl/clmorder.ps
 share/doc/mcl/clmprotocols.html
@@ -100,6 +107,7 @@ share/doc/mcl/examples/friends
 share/doc/mcl/examples/fznyy.mci
 share/doc/mcl/examples/fznyy.tab
 share/doc/mcl/examples/honey.mci
+share/doc/mcl/examples/infinity.mci
 share/doc/mcl/examples/lattice.mci
 share/doc/mcl/examples/make-falkner.pl
 share/doc/mcl/examples/matula.mci
diff --git a/mcl/distinfo b/mcl/distinfo
index 7de4576294..2b5d36b473 100644
--- a/mcl/distinfo
+++ b/mcl/distinfo
@@ -1,5 +1,6 @@
-$NetBSD: distinfo,v 1.1 2013/09/01 20:46:00 jihbed Exp $
+$NetBSD$
 
-SHA1 (mcl-12-135.tar.gz) = 27e7bc08fe5f0d3361bbc98d343c9d045712e406
-RMD160 (mcl-12-135.tar.gz) = a3a3f6a9f19d65b0520c29a2116687a92fca6ca2
-Size (mcl-12-135.tar.gz) = 2970824 bytes
+SHA1 (mcl-14-137.tar.gz) = 9016240ecdc39d26e493c1e18967e46ff0742bdd
+RMD160 (mcl-14-137.tar.gz) = 063e6415a0d23dcdb2fa8663fe62a95ec4f67f5d
+SHA512 (mcl-14-137.tar.gz) = 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2
+Size (mcl-14-137.tar.gz) = 3035491 bytes