Hi, I believe I created this port in the distant past, and I'm taking over maintainership (?) of it again.
math/mcl (a clustering algorithm for graphs) has not been updated in a long while, so here's a diff that brings it up to date with the most recent release of mcl. The diff is straight forward. The port installs one scripts that uses bash, but that's the only new dependency that I can find (that bash script also need a patch as it picks up perl from /usr/local). It compiles and runs. The diff and the patch are attached. Cheers, Andreas -- Andreas Kusalananda Kähäri, Bioinformatics Developer (NBIS) Uppsala University, Uppsala, Sweden NBIS: http://nbis.se OpenPGP: url=https://db.tt/2zaB1E7y; id=46082BDF ------------------------------------------------------------------------
? patches
Index: Makefile
===================================================================
RCS file: /cvs/ports/math/mcl/Makefile,v
retrieving revision 1.12
diff -u -p -u -r1.12 Makefile
--- Makefile 11 Mar 2013 11:23:55 -0000 1.12
+++ Makefile 19 Apr 2016 13:39:07 -0000
@@ -2,17 +2,21 @@
COMMENT= clustering algorithm for graphs
-V= 09-308
+V= 14-137
DISTNAME= mcl-${V}
PKGNAME= mcl-${V:S,-,_,}
CATEGORIES= math
HOMEPAGE= http://micans.org/mcl/
-# GPLv2
+MAINTAINER= Andreas Kusalananda Kahari <andreas.kah...@icm.uu.se>
+
+# GPLv3
PERMIT_PACKAGE_CDROM= Yes
MASTER_SITES= ${HOMEPAGE}/src/
+
+RUN_DEPENDS= shells/bash
WANTLIB= c m pthread
Index: distinfo
===================================================================
RCS file: /cvs/ports/math/mcl/distinfo,v
retrieving revision 1.11
diff -u -p -u -r1.11 distinfo
--- distinfo 18 Jan 2015 03:14:27 -0000 1.11
+++ distinfo 19 Apr 2016 13:39:07 -0000
@@ -1,2 +1,2 @@
-SHA256 (mcl-09-308.tar.gz) = gNV73uAtWFWsIf7ql6ko/z1DLRXtKv8CubvohVHUBxI=
-SIZE (mcl-09-308.tar.gz) = 2785872
+SHA256 (mcl-14-137.tar.gz) = tXhol6ioyhGes1WlYwgGpNpy6oQkPbqFsZqG8UdXtJc=
+SIZE (mcl-14-137.tar.gz) = 3035491
Index: pkg/PLIST
===================================================================
RCS file: /cvs/ports/math/mcl/pkg/PLIST,v
retrieving revision 1.8
diff -u -p -u -r1.8 PLIST
--- pkg/PLIST 23 Dec 2009 22:08:58 -0000 1.8
+++ pkg/PLIST 19 Apr 2016 13:39:07 -0000
@@ -1,6 +1,7 @@
@comment $OpenBSD: PLIST,v 1.8 2009/12/23 22:08:58 jasper Exp $
@bin bin/clm
@bin bin/clmformat
+bin/clxdo
@bin bin/mcl
@bin bin/mclcm
bin/mclpipeline
@@ -19,8 +20,10 @@ bin/mclpipeline
@man man/man1/clmformat.1
@man man/man1/clmimac.1
@man man/man1/clminfo.1
+@man man/man1/clminfo2.1
@man man/man1/clmmate.1
@man man/man1/clmmeet.1
+@man man/man1/clmoptics.1
@man man/man1/clmorder.1
@man man/man1/clmresidue.1
@man man/man1/clmvol.1
@@ -36,6 +39,7 @@ bin/mclpipeline
@man man/man1/mcxctty.1
@man man/man1/mcxdiameter.1
@man man/man1/mcxdump.1
+@man man/man1/mcxerdos.1
@man man/man1/mcxi.1
@man man/man1/mcxload.1
@man man/man1/mcxmap.1
@@ -43,6 +47,7 @@ bin/mclpipeline
@man man/man1/mcxrand.1
@man man/man1/mcxsubs.1
@man man/man5/clmprotocols.5
+@man man/man5/clmprotocols2.5
@man man/man5/mcxio.5
@man man/man7/mclfamily.7
@man man/man7/mclfaq.7
@@ -61,14 +66,20 @@ 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
share/doc/mcl/clmprotocols.ps
+share/doc/mcl/clmprotocols2.html
+share/doc/mcl/clmprotocols2.ps
share/doc/mcl/clmresidue.html
share/doc/mcl/clmresidue.ps
share/doc/mcl/clmvol.html
@@ -107,6 +118,8 @@ share/doc/mcl/mcxdiameter.html
share/doc/mcl/mcxdiameter.ps
share/doc/mcl/mcxdump.html
share/doc/mcl/mcxdump.ps
+share/doc/mcl/mcxerdos.html
+share/doc/mcl/mcxerdos.ps
share/doc/mcl/mcxi.html
share/doc/mcl/mcxi.ps
share/doc/mcl/mcxio.html
@@ -149,6 +162,7 @@ share/examples/mcl/friends
share/examples/mcl/fznyy.mci
share/examples/mcl/fznyy.tab
share/examples/mcl/honey.mci
+share/examples/mcl/infinity.mci
share/examples/mcl/lattice.mci
share/examples/mcl/make-falkner.pl
share/examples/mcl/matula.mci
$OpenBSD$
--- scripts/clxdo.orig Tue Apr 19 15:35:30 2016
+++ scripts/clxdo Tue Apr 19 15:36:28 2016
@@ -83,7 +83,7 @@ clm vol -nff-fac $fac $@ | mcxsubs 'val(gt(1)), out(-)
require_num 1 "<cls-file>+"
mx=$2
mcxdump -imx $mx --no-values --dump-lines -o - \
-| /usr/local/bin/perl -ane '$ct{@F-1}++; END { print map { "$_ $ct{$_}\n" }
sort { $a <=> $b } keys %ct; }'
+| perl -ane '$ct{@F-1}++; END { print map { "$_ $ct{$_}\n" } sort { $a <=> $b
} keys %ct; }'
;;
@@ -116,7 +116,7 @@ export CLXDO_VAL1=$2
shift 2
for mx in $@; do
mcxdump -imx $mx --no-values --dump-lines -o - \
- | /usr/local/bin/perl -ane '$ct{@F-1}++; END {%i = map { ($_, 1) } grep {
$_ >= $ENV{CLXDO_VAL1}; } keys %ct; ($lt, $n_lt, $gq, $n_gq) = (0,0,0,0); for
my $x (keys %ct) { if ($i{$x}) { $n_gq += $ct{$x}; $gq += $x * $ct{$x}; } else
{ $n_lt += $ct{$x}; $lt += $x * $ct{$x} } } print "$n_lt $lt $n_gq $gq\n"; }'
+ | perl -ane '$ct{@F-1}++; END {%i = map { ($_, 1) } grep { $_ >=
$ENV{CLXDO_VAL1}; } keys %ct; ($lt, $n_lt, $gq, $n_gq) = (0,0,0,0); for my $x
(keys %ct) { if ($i{$x}) { $n_gq += $ct{$x}; $gq += $x * $ct{$x}; } else {
$n_lt += $ct{$x}; $lt += $x * $ct{$x} } } print "$n_lt $lt $n_gq $gq\n"; }'
done
;;
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