[pkgsrc/trunk]: pkgsrc/biology/mummer Update to version 3.15. From David Pri...

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/fe2706625df4
branches:  trunk
changeset: 485238:fe2706625df4
user:      cube <cube%pkgsrc.org@localhost>
date:      Sun Dec 05 15:24:54 2004 +0000

description:
Update to version 3.15.  From David Price in PR#28305.

3.05 - Added -k option to show-coords to only display the best frame for
       overlapping PROmer alignments. Added --[no]optimize option to nucmer
       and promer to allow alignment score optimization to be turned off, i.e
       allow alignments to extend to the ends of sequences rather than
       backtracking to optimize the alignment score. Updated docs.
3.06 - Added -F and -h option to mummer. Changed -mumcand option to
       -mumreference, but left deprecated -mumcand option available. Added
       -maxmatch option to mummer, and changed default behavior of all
       applicable programs to -mumreference (nucmer, promer and mummer).
       Added -w (screen width) option to show-aligns. Updated documentation
       with all of these changes.
3.07 - Added the 'mapview' plotting utility and appropriate documentation.
       Fixed origin wrap shadowing bug in show-tiling when using the -c option.
       NUCmer and PROmer now convert to absolute paths to avoid ambiguity.
3.08 - Added MUMmer examples web docs which gives brief walkthroughs
3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
       the issue with mummerplot being to faint.
3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed
       a bug in nucmer and promer. Fixed rounding issue in show-coords.
       Updated citations.
3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation.
       Fixed bug in show-tiling -R
3.14 - Fixed gcc3 compilation bug
3.15 - Fixed --nooptimize in nuc/promer.

diffstat:

 biology/mummer/Makefile         |  8 ++++----
 biology/mummer/PLIST            |  3 +--
 biology/mummer/distinfo         |  8 ++++----
 biology/mummer/patches/patch-aa |  6 +++---
 4 files changed, 12 insertions(+), 13 deletions(-)

diffs (79 lines):

diff -r 69ae7400f500 -r fe2706625df4 biology/mummer/Makefile
--- a/biology/mummer/Makefile   Sun Dec 05 15:24:12 2004 +0000
+++ b/biology/mummer/Makefile   Sun Dec 05 15:24:54 2004 +0000
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.3 2004/04/11 04:07:05 snj Exp $
+# $NetBSD: Makefile,v 1.4 2004/12/05 15:24:54 cube Exp $
 #
 
-DISTNAME=              MUMmer3.04
-PKGNAME=               mummer-3.04
+DISTNAME=              MUMmer3.15
+PKGNAME=               mummer-3.15
 CATEGORIES=            biology
 MASTER_SITES=          ftp://ftp.tigr.org/pub/software/MUMmer/
 
@@ -37,7 +37,7 @@
                ${PREFIX}/share/doc/html/mummer
 .endfor
        ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/mummer
-.for DOC in maxmat3man.pdf maxmat3man.tex maxmat3src.pdf nucmer.README    \
+.for DOC in maxmat3man.tex maxmat3src.pdf nucmer.README    \
        optionman.sty promer.README run-mummer1.README run-mummer3.README \
        skaff.sty
        ${INSTALL_DATA} ${WRKSRC}/docs/${DOC} ${PREFIX}/share/doc/mummer
diff -r 69ae7400f500 -r fe2706625df4 biology/mummer/PLIST
--- a/biology/mummer/PLIST      Sun Dec 05 15:24:12 2004 +0000
+++ b/biology/mummer/PLIST      Sun Dec 05 15:24:54 2004 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $
+@comment $NetBSD: PLIST,v 1.2 2004/12/05 15:24:54 cube Exp $
 bin/annotate
 bin/combineMUMs
 bin/gaps
@@ -23,7 +23,6 @@
 share/doc/html/mummer/nucex.gif
 share/doc/html/mummer/osi.gif
 share/doc/html/mummer/pro_proex.gif
-share/doc/mummer/maxmat3man.pdf
 share/doc/mummer/maxmat3man.tex
 share/doc/mummer/maxmat3src.pdf
 share/doc/mummer/nucmer.README
diff -r 69ae7400f500 -r fe2706625df4 biology/mummer/distinfo
--- a/biology/mummer/distinfo   Sun Dec 05 15:24:12 2004 +0000
+++ b/biology/mummer/distinfo   Sun Dec 05 15:24:54 2004 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $
+$NetBSD: distinfo,v 1.2 2004/12/05 15:24:54 cube Exp $
 
-SHA1 (MUMmer3.04.tar.gz) = e0f17d535a857bd9b3059d5d0a951621f89041b2
-Size (MUMmer3.04.tar.gz) = 835629 bytes
-SHA1 (patch-aa) = 39253c79e7239365dfdcee46c410f234a23c6df0
+SHA1 (MUMmer3.15.tar.gz) = c8907b0b2010e3a8d07fff0dde570c12d9cf8dea
+Size (MUMmer3.15.tar.gz) = 660102 bytes
+SHA1 (patch-aa) = bf64019cbbfa53c1883641b28186146cd7c0a946
diff -r 69ae7400f500 -r fe2706625df4 biology/mummer/patches/patch-aa
--- a/biology/mummer/patches/patch-aa   Sun Dec 05 15:24:12 2004 +0000
+++ b/biology/mummer/patches/patch-aa   Sun Dec 05 15:24:54 2004 +0000
@@ -1,4 +1,4 @@
-$NetBSD: patch-aa,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $
+$NetBSD: patch-aa,v 1.2 2004/12/05 15:24:54 cube Exp $
 
 --- Makefile.orig      2003-07-09 09:49:51.000000000 -0400
 +++ Makefile   2003-09-27 18:15:34.000000000 -0400
@@ -8,7 +8,7 @@
  #-------------------------------------------------------------------------------
 -SHELL = /bin/sh
 +SHELL = ${SH}
- VERSION := 3.04
+ VERSION := 3.15
  
  
 @@ -35,15 +35,12 @@
@@ -30,5 +30,5 @@
 +#PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
 +#AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
  
- FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README
+ FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog