[med-svn] r1697 - in trunk/packages/clustalw-mpi/trunk/debian: . patches

charles-guest at alioth.debian.org charles-guest at alioth.debian.org
Tue Apr 8 00:24:36 UTC 2008 

Author: charles-guest
Date: 2008-04-08 00:24:35 +0000 (Tue, 08 Apr 2008)
New Revision: 1697

Added:
   trunk/packages/clustalw-mpi/trunk/debian/watch
Modified:
   trunk/packages/clustalw-mpi/trunk/debian/changelog
   trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1
   trunk/packages/clustalw-mpi/trunk/debian/control
   trunk/packages/clustalw-mpi/trunk/debian/copyright
   trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch
   trunk/packages/clustalw-mpi/trunk/debian/rules
Log:
New upstream version.

Modified: trunk/packages/clustalw-mpi/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/changelog	2008-04-07 16:22:51 UTC (rev 1696)
+++ trunk/packages/clustalw-mpi/trunk/debian/changelog	2008-04-08 00:24:35 UTC (rev 1697)
@@ -1,7 +1,8 @@
-clustalw-mpi (0.13-4) unstable; urgency=low
+clustalw-mpi (0.14-1) UNRELEASED; urgency=low
 
+  [ Andreas Tille ]
   * Put package under group maintenance of Debian-Med Team
-    - XS-DM-Upload-Allowed: Yes
+    - DM-Upload-Allowed: Yes
     - Vcs tags
     - Use correct address as Uploader: Steffen Moeller <moeller at debian.org>
   * Switched to quilt
@@ -14,6 +15,20 @@
   * debian/copyright machine readable
   * Removed [Biology] from short description
 
+  [ Charles Plessy ]
+  * Bug fix version 0.14 released on Dec 19, 2005.
+    See /usr/share/doc/clustalw-mpi/History for more details.
+  * Updated debian/patches for the new upstream version.
+  * Added myself to the Hall of Fame of debian/copyright
+    and to the Uploaders in debian/control.
+  * Updated homepage in debian/copyright and debian/control.
+  * Added debian/watch file.
+  * debian/clustalw-mpi.1: incremented version number.
+  * debian/control:
+    - Dropped versionned dependancies on lam packages, as they
+      are satisfied even in Sarge.
+    - Updated homepage of Clustal.
+
  -- Andreas Tille <tille at debian.org>  Sun, 06 Apr 2008 20:23:04 +0200
 
 clustalw-mpi (0.13-3) unstable; urgency=low

Modified: trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1	2008-04-07 16:22:51 UTC (rev 1696)
+++ trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1	2008-04-08 00:24:35 UTC (rev 1697)
@@ -2,7 +2,7 @@
 .\" The man page was derived from the man page of Chet Ramey for the BASH
 .\"
 
-.TH CLUSTALW\-MPI 1 "2003\ April\ 8" "ClustalW\-MPI 0.13"
+.TH CLUSTALW\-MPI 1 "2003\ April\ 8" "ClustalW\-MPI 0.14"
 
 .SH NAME
 ClustalW-MPI \- MPI distributed ClustalW

Modified: trunk/packages/clustalw-mpi/trunk/debian/control
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/control	2008-04-07 16:22:51 UTC (rev 1696)
+++ trunk/packages/clustalw-mpi/trunk/debian/control	2008-04-08 00:24:35 UTC (rev 1697)
@@ -2,12 +2,13 @@
 Section: non-free/science
 Priority: optional
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-XS-DM-Upload-Allowed: yes
+DM-Upload-Allowed: yes
 Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 4.0), lam4-dev (>= 7.1.1-3.2), quilt
+ Andreas Tille <tille at debian.org>,
+ Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), lam4-dev, quilt
 Standards-Version: 3.7.3
-Homepage: http://www.bii.a-star.edu.sg/~kuobin/clustalw-mpi/
+Homepage: http://kmlvli.com/kuobin/clustalw-mpi/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalw-mpi/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/clustalw-mpi/trunk/
 
@@ -15,7 +16,7 @@
 Architecture: any
 Enhances: clustalw
 Suggests: seaview, clustalx
-Depends: ${shlibs:Depends}, lam-runtime (>= 7.1.1)
+Depends: ${shlibs:Depends}, lam-runtime
 Description: MPI-distributed global sequence alignment with ClustalW
  ClustalW is a popular tool for multiple sequence alignment. The
  alignment is achieved via three steps: pairwise alignment,
@@ -40,4 +41,4 @@
  is a versatile editor of alignments.
  .
  The original ClustalW/ClustalX can be found at
- URL: ftp://ftp-igbmc.u-strasbg.fr
+ URL: http://www.clustal.org/download/pre-2/

Modified: trunk/packages/clustalw-mpi/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/copyright	2008-04-07 16:22:51 UTC (rev 1696)
+++ trunk/packages/clustalw-mpi/trunk/debian/copyright	2008-04-08 00:24:35 UTC (rev 1697)
@@ -2,12 +2,13 @@
 X-Debianized-By: Steffen Moeller <moeller at debian.org>,
  Andreas Tille <tille at debian.org>
 X-Debianized-Date: Mon, 30 Jun 2003 22:54:41 +0200.
-X-Source-Downloaded-From: http://www.bii.a-star.edu.sg/~kuobin/clustalg/clustalw-mpi-0.13.tar.gz
+X-Source-Downloaded-From: http://kmlvli.com/kuobin/clustalw-mpi/clustalw-mpi-0.14.tar.gz
 X-Upstream-Author: Dr. Kuo-Bin Li <kuobin at bii.a-star.edu.sg>
 
 Files: debian/*
-Copyright: © 2003—2008 Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
+Copyright: © 2003—2008 Steffen Moeller <moeller at debian.org>
+           © 2003—2008 Andreas Tille <tille at debian.org>
+           © 2008 Charles Plessy <charles-debian-nospam at plessy.org>
 License: GPL-2+
 X-Comment: On Debian systems, the complete text of the GNU General
  Public License can be found in `/usr/share/common-licenses/GPL'.

Modified: trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch	2008-04-07 16:22:51 UTC (rev 1696)
+++ trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch	2008-04-08 00:24:35 UTC (rev 1697)
@@ -1,5 +1,5 @@
---- clustalw-mpi-0.13.orig/Makefile
-+++ clustalw-mpi-0.13/Makefile
+--- a/Makefile
++++ b/Makefile
 @@ -1,7 +1,13 @@
 -install: clustalw-mpi
 +#!/usr/bin/make
@@ -10,21 +10,19 @@
 +DOCDIR	= $(DESTDIR)/usr/share/doc/clustalw-mpi
 +BINDIR	= $(DESTDIR)/usr/bin
 +MANDIR	= $(DESTDIR)/usr/share/man/man1
-+DOCS	= README.clustalw-mpi dele.input
++DOCS	= README.clustalw-mpi dele.input History
 +BINS	= clustalw-mpi
 +
 +RM	= /bin/rm -f
  
  OBJECTS = clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o \
          malign_mpi_pdiff.o util.o trees.o gcgcheck.o \
-@@ -25,29 +31,45 @@
- PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN 
+@@ -26,9 +32,16 @@
  #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
  
--CFLAGS  = -c -O3
+ CFLAGS  = -c -g
 -#CFLAGS  = -c -O3 -funroll-all-loops
-+CFLAGS	= -O3
-+#CFLAGS	= -O3 -funroll-all-loops
++#CFLAGS  =  -O3 -funroll-all-loops
  LFLAGS	= -lm 
  
 +all:		clustalw-mpi
@@ -37,24 +35,9 @@
  clustalw-mpi: $(OBJECTS) 
  	$(CC) -o $@ $(OBJECTS) $(LFLAGS)
  
- interface.o : interface.c $(HEADERS) param.h
--	$(CC) $(CFLAGS) $*.c
-+	$(CC) -c $(CFLAGS) $*.c
- 
- readmat.o : readmat.c $(HEADERS) matrices.h
--	$(CC) $(CFLAGS) $*.c
-+	$(CC) -c $(CFLAGS) $*.c
- 
- trees.o : trees.c $(HEADERS) dayhoff.h
--	$(CC) $(TREES_FLAG) $(CFLAGS) $*.c
-+	$(CC) -c $(TREES_FLAG) $(CFLAGS) $*.c
- 
- pairalign_new.o : pairalign_new.c $(HEADERS)
--	$(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
-+	$(CC) -c $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
+@@ -46,8 +59,17 @@
  parallel_compare.o : parallel_compare.c $(HEADERS) dayhoff.h
--	$(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
-+	$(CC) -c $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
+ 	$(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
  
 +.PHONY:		clean distclean
 +
@@ -62,12 +45,11 @@
  
  
  .c.o :
--	$(CC) $(CFLAGS) $?
-+	$(CC) -c $(CFLAGS) $?
+ 	$(CC) $(CFLAGS) $?
+ 
 +
-+
 +clean:
 +	$(RM) -f *.o
- 
++
 +distclean:	clean
 +	$(RM) $(BINS)

Modified: trunk/packages/clustalw-mpi/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/rules	2008-04-07 16:22:51 UTC (rev 1696)
+++ trunk/packages/clustalw-mpi/trunk/debian/rules	2008-04-08 00:24:35 UTC (rev 1697)
@@ -76,7 +76,7 @@
 	dh_builddeb
 
 get-orig-source:
-	wget http://www.bii.a-star.edu.sg/~kuobin/clustalg/clustalw-mpi-0.13.tar.gz && mv clustalw-mpi-0.13.tar.gz clustalw-mpi_0.13.orig.tar.gz
+	wget http://kmlvli.com/kuobin/clustalw-mpi/clustalw-mpi-0.14.tar.gz && mv clustalw-mpi-0.14.tar.gz clustalw-mpi_0.14.orig.tar.gz
 
 binary: binary-indep binary-arch
 .PHONY: build clean binary-indep binary-arch binary install configure get-orig-source

Added: trunk/packages/clustalw-mpi/trunk/debian/watch
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/watch	2008-04-08 00:24:35 UTC (rev 1697)
@@ -0,0 +1,3 @@
+version=3
+http://kmlvli.com/kuobin/clustalw-mpi/index.html clustalw-mpi-([\d\.]+)\.tar\.gz
+#http://kmlvli.com/kuobin/clustalw-mpi/clustalw-mpi-0.14.tar.gz

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