[med-svn] r3055 - in trunk/packages/wise/trunk/debian: . patches
pbenner-guest at alioth.debian.org
pbenner-guest at alioth.debian.org
Sun Jan 25 23:18:24 UTC 2009
Author: pbenner-guest
Date: 2009-01-25 23:18:23 +0000 (Sun, 25 Jan 2009)
New Revision: 3055
Added:
trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch
trunk/packages/wise/trunk/debian/patches/02_isnumber.patch
trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch
trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch
trunk/packages/wise/trunk/debian/patches/series
Removed:
trunk/packages/wise/trunk/debian/patches/00list
trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch
trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch
trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch
trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch
Modified:
trunk/packages/wise/trunk/debian/changelog
trunk/packages/wise/trunk/debian/control
trunk/packages/wise/trunk/debian/rules
Log:
using quilt instead of dpatch
Modified: trunk/packages/wise/trunk/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/changelog 2009-01-25 23:18:23 UTC (rev 3055)
@@ -1,10 +1,12 @@
-wise (2.4.1-6) UNRELEASED; urgency=low
+wise (2.4.1-6) unstable; urgency=low
- [debian/control]
- * Updated policy to 3.8.0 (no changes required)
- * wise now suggests wise-doc (downgraded from 'recommends')
+ * Updated policy to 3.8.0 (no changes required).
+ * wise now suggests wise-doc (downgraded from 'recommends').
+ [ Steffen Moeller ]
+ * Using quilt instead of dpatch.
+ [ Philipp Benner ]
- -- Steffen Moeller <moeller at debian.org> Sun, 28 Dec 2008 14:00:29 +0100
+ -- Philipp Benner <pbenner at uni-osnabrueck.de> Sun, 25 Jan 2009 22:57:27 +0000
wise (2.4.1-5) unstable; urgency=low
Modified: trunk/packages/wise/trunk/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/control 2009-01-25 23:18:23 UTC (rev 3055)
@@ -4,9 +4,9 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>
DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 5), dpatch (>= 2.0.21), texlive-latex-base,
+Build-Depends: debhelper (>= 5), quilt, texlive-latex-base,
texlive-extra-utils, hevea, docbook-to-man, libglib1.2-dev
-Standards-Version: 3.7.3
+Standards-Version: 3.8.0
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/wise/trunk/
Homepage: http://www.ebi.ac.uk/~birney/wise2/
Deleted: trunk/packages/wise/trunk/debian/patches/00list
===================================================================
--- trunk/packages/wise/trunk/debian/patches/00list 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/patches/00list 2009-01-25 23:18:23 UTC (rev 3055)
@@ -1,4 +0,0 @@
-01_welcome-csh
-02_isnumber
-03_doc-nodycache
-04_wise2-pdflatex-update
Deleted: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -1,28 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 01_welcome-csh.dpatch by Philipp Benner <mail at philipp-benner.de>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
-
- at DPATCH@
-diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile
---- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200
-+++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200
-@@ -109,7 +109,7 @@
- bin :
- mkdir bin
- cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
-- csh welcome.csh
-+ ./welcome.csh
-
- libs :
- (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
-diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
---- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200
-+++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200
-@@ -1,4 +1,4 @@
--#!/bin/tcsh -f
-+#!/bin/sh
-
- echo ""
- echo "Welcome to Wise2.4"
Copied: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch)
===================================================================
--- trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -0,0 +1,28 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01_welcome-csh.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile
+--- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200
+@@ -109,7 +109,7 @@
+ bin :
+ mkdir bin
+ cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
+- csh welcome.csh
++ ./welcome.csh
+
+ libs :
+ (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
+diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
+--- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/bin/tcsh -f
++#!/bin/sh
+
+ echo ""
+ echo "Welcome to Wise2.4"
Property changes on: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mergeinfo
+
Deleted: trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -1,18 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 02_isnumber.dpatch by Philipp Benner <mail at philipp-benner.de>
-##
-## DP: Replace isnumber() (which does not exist on linux) by isdigit().
-
- at DPATCH@
-diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
---- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200
-+++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200
-@@ -20,7 +20,7 @@
- if( line[0] == '#' ) {
- continue;
- }
-- if( !isnumber(line[0]) ) {
-+ if( !isdigit(line[0]) ) {
- warn("Bad looking line in intron file, %s",line);
- continue;
- }
Copied: trunk/packages/wise/trunk/debian/patches/02_isnumber.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch)
===================================================================
--- trunk/packages/wise/trunk/debian/patches/02_isnumber.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/02_isnumber.patch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_isnumber.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## DP: Replace isnumber() (which does not exist on linux) by isdigit().
+
+ at DPATCH@
+diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
+--- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200
++++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200
+@@ -20,7 +20,7 @@
+ if( line[0] == '#' ) {
+ continue;
+ }
+- if( !isnumber(line[0]) ) {
++ if( !isdigit(line[0]) ) {
+ warn("Bad looking line in intron file, %s",line);
+ continue;
+ }
Property changes on: trunk/packages/wise/trunk/debian/patches/02_isnumber.patch
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mergeinfo
+
Deleted: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -1,19 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 03_doc-nodycache.dpatch by Philipp Benner <mail at philipp-benner.de>
-##
-## DP: Documentation bugfix.
-
- at DPATCH@
-diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
---- wise-2.4.0~/docs/wise2.tex 2003-03-26 12:47:08.000000000 +0100
-+++ wise-2.4.0/docs/wise2.tex 2007-07-16 01:05:34.000000000 +0200
-@@ -1617,7 +1617,8 @@
- \item[-hithelp] more detailed help on hitlist formats
- \item[-dymem] memory style [default/linear/explicit]
- \item[-kbyte] memory amount to use [4000]
--\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
-+\item[-dycache] implicitly cache dy matrix usage (default)
-+\item[-nodycache] do not implicitly cache dy matrix usage
- \item[-dydebug] drop into dynamite dp matrix debugger
- \item[-paldebug] print PackAln after debugger run if used
- \item[-help] show help options
Copied: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch)
===================================================================
--- trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 03_doc-nodycache.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## DP: Documentation bugfix.
+
+ at DPATCH@
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex 2003-03-26 12:47:08.000000000 +0100
++++ wise-2.4.0/docs/wise2.tex 2007-07-16 01:05:34.000000000 +0200
+@@ -1617,7 +1617,8 @@
+ \item[-hithelp] more detailed help on hitlist formats
+ \item[-dymem] memory style [default/linear/explicit]
+ \item[-kbyte] memory amount to use [4000]
+-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
++\item[-dycache] implicitly cache dy matrix usage (default)
++\item[-nodycache] do not implicitly cache dy matrix usage
+ \item[-dydebug] drop into dynamite dp matrix debugger
+ \item[-paldebug] print PackAln after debugger run if used
+ \item[-help] show help options
Property changes on: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mergeinfo
+
Deleted: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -1,43 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 04_wise2-pdflatex-update.dpatch by Philipp Benner <mail at philipp-benner.de>
-##
-## DP: Make wise2.tex pdflatex compatible.
-
- at DPATCH@
-
-diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
---- wise-2.4.0~/docs/wise2.tex 2007-08-06 10:25:05.000000000 +0200
-+++ wise-2.4.0/docs/wise2.tex 2007-08-06 10:25:08.000000000 +0200
-@@ -1,6 +1,7 @@
-
- \documentclass{article}
--\usepackage{epsfig}
-+%\usepackage{epsfig}
-+\usepackage{graphicx}
-
- \begin{document}
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -707,8 +708,9 @@
- \begin{figure}
- \begin{center}
- \leavevmode
--\epsfxsize 300pt
--\epsfbox{genewise21.eps}
-+%\epsfxsize 300pt
-+%\epsfbox{genewise21.eps}
-+%\includegraphics[scale=0.75]{genewise21.pdf}
- \newline
- \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
- arrows between them transitions. Black transitions are standard
-@@ -898,8 +900,9 @@
- \begin{figure}
- \begin{center}
- \leavevmode
--\epsfxsize 300pt
--\epsfbox{genewise6.eps}
-+%\epsfxsize 300pt
-+%\epsfbox{genewise6.eps}
-+%\includegraphics[scale=0.75]{genewise6.pdf}
- \newline
- \caption{GeneWise6:23}
- \label{Figure:genewise623}
Copied: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch)
===================================================================
--- trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch 2009-01-25 23:18:23 UTC (rev 3055)
@@ -0,0 +1,43 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_wise2-pdflatex-update.dpatch by Philipp Benner <mail at philipp-benner.de>
+##
+## DP: Make wise2.tex pdflatex compatible.
+
+ at DPATCH@
+
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex 2007-08-06 10:25:05.000000000 +0200
++++ wise-2.4.0/docs/wise2.tex 2007-08-06 10:25:08.000000000 +0200
+@@ -1,6 +1,7 @@
+
+ \documentclass{article}
+-\usepackage{epsfig}
++%\usepackage{epsfig}
++\usepackage{graphicx}
+
+ \begin{document}
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -707,8 +708,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode
+-\epsfxsize 300pt
+-\epsfbox{genewise21.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise21.eps}
++%\includegraphics[scale=0.75]{genewise21.pdf}
+ \newline
+ \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
+ arrows between them transitions. Black transitions are standard
+@@ -898,8 +900,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode
+-\epsfxsize 300pt
+-\epsfbox{genewise6.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise6.eps}
++%\includegraphics[scale=0.75]{genewise6.pdf}
+ \newline
+ \caption{GeneWise6:23}
+ \label{Figure:genewise623}
Property changes on: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mergeinfo
+
Added: trunk/packages/wise/trunk/debian/patches/series
===================================================================
--- trunk/packages/wise/trunk/debian/patches/series (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/series 2009-01-25 23:18:23 UTC (rev 3055)
@@ -0,0 +1,4 @@
+01_welcome-csh.patch
+02_isnumber.patch
+03_doc-nodycache.patch
+04_wise2-pdflatex-update.patch
Modified: trunk/packages/wise/trunk/debian/rules
===================================================================
--- trunk/packages/wise/trunk/debian/rules 2009-01-25 09:02:24 UTC (rev 3054)
+++ trunk/packages/wise/trunk/debian/rules 2009-01-25 23:18:23 UTC (rev 3055)
@@ -12,8 +12,7 @@
CFLAGS += -O2
endif
-.NOTPARALLEL:
-include /usr/share/dpatch/dpatch.make
+include /usr/share/quilt/quilt.make
configure: configure-stamp
configure-stamp:
@@ -22,8 +21,7 @@
touch configure-stamp
build: patch build-stamp
-
-build-stamp: configure-stamp
+build-stamp: $(QUILT_STAMPFN) configure-stamp
dh_testdir
$(MAKE) -C src all
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