[pkgsrc/trunk]: pkgsrc/biology/mummer updated to MUMmer3.20

[schwarz <schwarz%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/3e429a8e5ac1
branches:  trunk
changeset: 548209:3e429a8e5ac1
user:      schwarz <schwarz%pkgsrc.org@localhost>
date:      Sat Oct 11 22:01:13 2008 +0000

description:
updated to MUMmer3.20

diffstat:

 biology/mummer/Makefile         |   8 ++++----
 biology/mummer/PLIST            |   4 +++-
 biology/mummer/distinfo         |  11 +++++------
 biology/mummer/patches/patch-aa |  24 +++++++++++++-----------
 biology/mummer/patches/patch-ad |  23 -----------------------
 5 files changed, 25 insertions(+), 45 deletions(-)

diffs (146 lines):

diff -r 2bee0bebf6aa -r 3e429a8e5ac1 biology/mummer/Makefile
--- a/biology/mummer/Makefile   Sat Oct 11 21:59:15 2008 +0000
+++ b/biology/mummer/Makefile   Sat Oct 11 22:01:13 2008 +0000
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.17 2008/05/25 21:42:20 joerg Exp $
+# $NetBSD: Makefile,v 1.18 2008/10/11 22:01:13 schwarz Exp $
 #
 
-DISTNAME=              MUMmer3.19
-PKGNAME=               mummer-3.19
+DISTNAME=              MUMmer3.20
+PKGNAME=               mummer-3.20
 CATEGORIES=            biology
 MASTER_SITES=          ${MASTER_SITE_SOURCEFORGE:=mummer/}
 
@@ -30,7 +30,7 @@
        ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${DESTDIR}${PREFIX}/bin
 .endfor
 .for f in run-mummer1 run-mummer3 nucmer promer exact-tandems    \
-       mapview mummerplot nucmer2xfig
+       mapview mummerplot nucmer2xfig dnadiff
        ${INSTALL_SCRIPT} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/mummer
 .endfor
        cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * \
diff -r 2bee0bebf6aa -r 3e429a8e5ac1 biology/mummer/PLIST
--- a/biology/mummer/PLIST      Sat Oct 11 21:59:15 2008 +0000
+++ b/biology/mummer/PLIST      Sat Oct 11 22:01:13 2008 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2007/01/18 19:13:10 rillig Exp $
+@comment $NetBSD: PLIST,v 1.6 2008/10/11 22:01:13 schwarz Exp $
 bin/annotate
 bin/combineMUMs
 bin/delta-filter
@@ -16,6 +16,7 @@
 bin/show-tiling
 share/doc/mummer/README
 share/doc/mummer/differences.README
+share/doc/mummer/dnadiff.README
 share/doc/mummer/mapview.README
 share/doc/mummer/maxmat3man.tex
 share/doc/mummer/maxmat3src.pdf
@@ -91,6 +92,7 @@
 share/doc/mummer/web/manual/pro_proex.gif
 share/doc/mummer/web/mummer-help.gif
 share/doc/mummer/web/mummer-users.gif
+share/mummer/dnadiff
 share/mummer/exact-tandems
 share/mummer/mapview
 share/mummer/mummerplot
diff -r 2bee0bebf6aa -r 3e429a8e5ac1 biology/mummer/distinfo
--- a/biology/mummer/distinfo   Sat Oct 11 21:59:15 2008 +0000
+++ b/biology/mummer/distinfo   Sat Oct 11 22:01:13 2008 +0000
@@ -1,9 +1,8 @@
-$NetBSD: distinfo,v 1.8 2007/01/18 19:13:10 rillig Exp $
+$NetBSD: distinfo,v 1.9 2008/10/11 22:01:13 schwarz Exp $
 
-SHA1 (MUMmer3.19.tar.gz) = 8906bab6bd43b307461de8b5f44122a115799533
-RMD160 (MUMmer3.19.tar.gz) = 54f3c692efb8bde7762c48186919754f2a8c178c
-Size (MUMmer3.19.tar.gz) = 3141991 bytes
-SHA1 (patch-aa) = e40b6538b259475def39cd8008af37d0a08e1555
+SHA1 (MUMmer3.20.tar.gz) = 68d6742de93d8524236ccf538f32ba8bb4edf7cc
+RMD160 (MUMmer3.20.tar.gz) = 7e5fefef359c6a6ee49f2ebf14dc18caa19f48fb
+Size (MUMmer3.20.tar.gz) = 3155446 bytes
+SHA1 (patch-aa) = 0f719a55e3c4f2994060f2b3f3ab4eb83519376f
 SHA1 (patch-ab) = af42da79fd287786cb83efa9c9b4fc8025abd728
 SHA1 (patch-ac) = 7f0f16bdd83bc80833f1ffdcfe1bad7c2ee76eec
-SHA1 (patch-ad) = 0804b2c966d7035c23444c4f72e1d93e45805bcf
diff -r 2bee0bebf6aa -r 3e429a8e5ac1 biology/mummer/patches/patch-aa
--- a/biology/mummer/patches/patch-aa   Sat Oct 11 21:59:15 2008 +0000
+++ b/biology/mummer/patches/patch-aa   Sat Oct 11 22:01:13 2008 +0000
@@ -1,35 +1,37 @@
-$NetBSD: patch-aa,v 1.5 2007/01/18 19:13:10 rillig Exp $
+$NetBSD: patch-aa,v 1.6 2008/10/11 22:01:13 schwarz Exp $
 
---- Makefile.orig      2003-07-09 09:49:51.000000000 -0400
-+++ Makefile   2003-09-27 18:15:34.000000000 -0400
+--- Makefile.orig      2008-10-05 16:48:07.000000000 +0200
++++ Makefile   2008-10-05 16:49:50.000000000 +0200
 @@ -22,7 +22,7 @@
  #  'make uninstall' alias for 'make clean' (for compatibility)
  #
  #-------------------------------------------------------------------------------
 -SHELL = /bin/sh
 +SHELL = ${SH}
- VERSION := 3.19
+ VERSION := 3.20
  
  
-@@ -35,15 +35,12 @@
+@@ -35,15 +35,15 @@
  TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
  KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
  
 -CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
 -CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
 -SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
+-CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
+-PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+-AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
 +#CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
 +#CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
 +#SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
--CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
 +#CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
--PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
--AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
--
--CPPFLAGS = -Wall -O3
--LDFLAGS  =
 +#PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
 +#AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
  
+-CPPFLAGS = -Wall -O3
+-LDFLAGS  =
++#CPPFLAGS = -Wall -O3
++#LDFLAGS  =
+ 
  FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
  
diff -r 2bee0bebf6aa -r 3e429a8e5ac1 biology/mummer/patches/patch-ad
--- a/biology/mummer/patches/patch-ad   Sat Oct 11 21:59:15 2008 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-$NetBSD: patch-ad,v 1.1 2006/04/19 16:50:36 joerg Exp $
-
---- src/kurtz/mm3src/Makefile.orig     2006-04-19 16:36:40.000000000 +0000
-+++ src/kurtz/mm3src/Makefile
-@@ -40,15 +40,15 @@ SPLINTALL=maxmat3.splint maxmatopt.splin
- all: $(ALL)
- 
- mummer: $(MUM3OBJECTS) $(LIBSTREE)
--      $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE)\
-+      $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-       -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
- 
- maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
--      $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE)\
-+      $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-       -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
- 
- maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
--      $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG)\
-+      $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
-       -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
- 
- include Filegoals.mf