[med-svn] r17608 - trunk/packages/wise/trunk/debian/patches

Andreas Tille tille at moszumanska.debian.org
Mon Aug 4 17:38:17 UTC 2014 

Author: tille
Date: 2014-08-04 17:38:16 +0000 (Mon, 04 Aug 2014)
New Revision: 17608

Modified:
   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/05_glib2.patch
   trunk/packages/wise/trunk/debian/patches/06_getline.patch
   trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch
   trunk/packages/wise/trunk/debian/patches/08_mayhem.patch
Log:
Refresh quilt patches


Modified: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,13 +1,8 @@
-#! /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.
+Author: Philipp Benner <mail at philipp-benner.de>
+Description: Avoid dependency from csh
 
- 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
+--- wise-2.4.1.orig/src/makefile
++++ wise-2.4.1/src/makefile
 @@ -109,7 +109,7 @@
  bin : 
  	mkdir bin
@@ -17,9 +12,8 @@
  
  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
+--- wise-2.4.1.orig/src/welcome.csh
++++ wise-2.4.1/src/welcome.csh
 @@ -1,4 +1,4 @@
 -#!/bin/tcsh -f
 +#!/bin/sh

Modified: trunk/packages/wise/trunk/debian/patches/02_isnumber.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/02_isnumber.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/02_isnumber.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,12 +1,8 @@
-#! /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().
+Author: Philipp Benner <mail at philipp-benner.de>
+Description: 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
+--- wise-2.4.1.orig/src/models/phasemodel.c
++++ wise-2.4.1/src/models/phasemodel.c
 @@ -20,7 +20,7 @@
      if( line[0] == '#' ) {
        continue;

Modified: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,12 +1,8 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 03_doc-nodycache.dpatch by Philipp Benner <mail at philipp-benner.de>
-##
-## DP: Documentation bugfix.
+Author Philipp Benner <mail at philipp-benner.de>
+Description: 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
+--- wise-2.4.1.orig/docs/wise2.tex
++++ wise-2.4.1/docs/wise2.tex
 @@ -1617,7 +1617,8 @@
  \item[-hithelp]   more detailed help on hitlist formats
  \item[-dymem]      memory style [default/linear/explicit]

Modified: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,13 +1,8 @@
-#! /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.
+Author Philipp Benner <mail at philipp-benner.de>
+Description: 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
+--- wise-2.4.1.orig/docs/wise2.tex
++++ wise-2.4.1/docs/wise2.tex
 @@ -1,6 +1,7 @@
  
  \documentclass{article}

Modified: trunk/packages/wise/trunk/debian/patches/05_glib2.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/05_glib2.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/05_glib2.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,8 +1,8 @@
 Author: Barry deFreese <bdefreese at debian.org>
 Description: To build wise2 with the Glib version 2.0 instead of 1.2.
 Forwarded: birney at sanger.ac.uk
---- a/src/makefile
-+++ b/src/makefile
+--- wise-2.4.1.orig/src/makefile
++++ wise-2.4.1/src/makefile
 @@ -31,13 +31,13 @@
  
  
@@ -20,8 +20,8 @@
  
  
  EXTRALIBS = -lm
---- a/src/snp/makefile
-+++ b/src/snp/makefile
+--- wise-2.4.1.orig/src/snp/makefile
++++ wise-2.4.1/src/snp/makefile
 @@ -5,9 +5,9 @@
  CC = cc
  #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
@@ -43,8 +43,8 @@
  
  INCFLAGS = -I../base/ -I../dynlibsrc/
  DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
---- a/src/corba/makefile
-+++ b/src/corba/makefile
+--- wise-2.4.1.orig/src/corba/makefile
++++ wise-2.4.1/src/corba/makefile
 @@ -3,9 +3,9 @@
  CC = cc
  INCFLAGS = -I../base/ -I../dynlibsrc
@@ -81,8 +81,8 @@
  
  .c.o :
  	$(CC) $(CFLAGS) $(INCFLAGS) $?
---- a/src/models/makefile
-+++ b/src/models/makefile
+--- wise-2.4.1.orig/src/models/makefile
++++ wise-2.4.1/src/models/makefile
 @@ -62,46 +62,46 @@
  #	$(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c
  
@@ -412,8 +412,8 @@
  
  
  #
---- a/src/dnaindex/makefile
-+++ b/src/dnaindex/makefile
+--- wise-2.4.1.orig/src/dnaindex/makefile
++++ wise-2.4.1/src/dnaindex/makefile
 @@ -27,53 +27,53 @@
  
  
@@ -483,8 +483,8 @@
  
  
  .c.o :
---- a/src/dnaindex/assembly/makefile
-+++ b/src/dnaindex/assembly/makefile
+--- wise-2.4.1.orig/src/dnaindex/assembly/makefile
++++ wise-2.4.1/src/dnaindex/assembly/makefile
 @@ -3,33 +3,33 @@
  .SUFFIXES :  .dy
  
@@ -527,8 +527,8 @@
  
  
  .c.o :
---- a/src/dynlibsrc/makefile
-+++ b/src/dynlibsrc/makefile
+--- wise-2.4.1.orig/src/dynlibsrc/makefile
++++ wise-2.4.1/src/dynlibsrc/makefile
 @@ -84,11 +84,11 @@
  CC = cc
  INCFLAGS = -I../base/
@@ -607,8 +607,8 @@
  
  .c.o :
  	$(CC) $(CFLAGS) $(INCFLAGS) $?
---- a/src/network/makefile
-+++ b/src/network/makefile
+--- wise-2.4.1.orig/src/network/makefile
++++ wise-2.4.1/src/network/makefile
 @@ -3,8 +3,8 @@
  
  CC = cc
@@ -629,8 +629,8 @@
  
  
  .c.o :
---- a/src/other_programs/makefile
-+++ b/src/other_programs/makefile
+--- wise-2.4.1.orig/src/other_programs/makefile
++++ wise-2.4.1/src/other_programs/makefile
 @@ -3,8 +3,8 @@
  .SUFFIXES :  .dy
  
@@ -642,8 +642,8 @@
  AR_OPTIONS = ru
  
  RANLIB_NEEDED = 0
---- a/src/base/makefile
-+++ b/src/base/makefile
+--- wise-2.4.1.orig/src/base/makefile
++++ wise-2.4.1/src/base/makefile
 @@ -19,9 +19,9 @@
  
  
@@ -657,8 +657,8 @@
  DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
  AR_OPTIONS = ru
  
---- a/src/HMMer2/Makefile
-+++ b/src/HMMer2/Makefile
+--- wise-2.4.1.orig/src/HMMer2/Makefile
++++ wise-2.4.1/src/HMMer2/Makefile
 @@ -13,7 +13,7 @@
  ## your compiler and compiler flags
  #

Modified: trunk/packages/wise/trunk/debian/patches/06_getline.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/06_getline.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/06_getline.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,7 +1,10 @@
-Index: wise-2.4.1/src/HMMer2/sqio.c
-===================================================================
---- wise-2.4.1.orig/src/HMMer2/sqio.c	2009-10-31 20:10:25.000000000 +0000
-+++ wise-2.4.1/src/HMMer2/sqio.c	2009-10-31 20:11:11.000000000 +0000
+Author: Philipp Benner <philipp at debian.org>
+Last-Update: Sat, 31 Oct 2009 21:25:52 +0000
+Bug-Debian: http://bugs.debian.org/552821
+Description: Fixed conflicting definitions of getline().
+
+--- wise-2.4.1.orig/src/HMMer2/sqio.c
++++ wise-2.4.1/src/HMMer2/sqio.c
 @@ -213,7 +213,7 @@
      }
  }

Modified: trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,11 +1,9 @@
 Description: Fix FTBFS with ld --as-needed.
 Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
 
-diff --git a/src/models/makefile b/src/models/makefile
-index 1766fee..e4634b5 100644
---- a/src/models/makefile
-+++ b/src/models/makefile
-@@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c
+--- wise-2.4.1.orig/src/models/makefile
++++ wise-2.4.1/src/models/makefile
+@@ -215,7 +215,7 @@
  	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
  
  scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
@@ -14,7 +12,7 @@
  
  scanwisep_compress.o : scanwisep.c
  	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
-@@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o
+@@ -275,7 +275,7 @@
  	$(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
  
  genewise : genewise.o $(NEWG) 
@@ -23,7 +21,7 @@
  
  cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
  	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-@@ -300,16 +300,16 @@ efgw   : genewise.o $(NEWG)
+@@ -300,16 +300,16 @@
  
  
  genewisedb : genewisedb.o $(NEWG) 
@@ -43,7 +41,7 @@
  
  
  amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
-@@ -331,7 +331,7 @@ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
+@@ -331,7 +331,7 @@
  	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
  
  pseudowise : pseudowise.o pseudowise7.o $(NEWG) 

Modified: trunk/packages/wise/trunk/debian/patches/08_mayhem.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/08_mayhem.patch	2014-08-04 17:32:23 UTC (rev 17607)
+++ trunk/packages/wise/trunk/debian/patches/08_mayhem.patch	2014-08-04 17:38:16 UTC (rev 17608)
@@ -1,5 +1,9 @@
---- a/src/models/dbac.c
-+++ b/src/models/dbac.c
+Author: Philipp Benner <philipp at debian.org>
+Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
+Description: Fix run time errors detected by Mayhem
+
+--- wise-2.4.1.orig/src/models/dbac.c
++++ wise-2.4.1/src/models/dbac.c
 @@ -535,8 +535,12 @@
     *  
     */  
@@ -15,8 +19,8 @@
    
    uppercase_Sequence(one);  
    uppercase_Sequence(two);  
---- a/src/models/estwise.c
-+++ b/src/models/estwise.c
+--- wise-2.4.1.orig/src/models/estwise.c
++++ wise-2.4.1/src/models/estwise.c
 @@ -313,7 +313,7 @@
      }
    }
@@ -49,8 +53,8 @@
  
    return ret;
  
---- a/src/models/genewise.c
-+++ b/src/models/genewise.c
+--- wise-2.4.1.orig/src/models/genewise.c
++++ wise-2.4.1/src/models/genewise.c
 @@ -550,8 +550,10 @@
        ret =  FALSE;
      }
@@ -64,8 +68,8 @@
    }
  
    if( alg_str != NULL ) {
---- a/src/models/estwisedb.c
-+++ b/src/models/estwisedb.c
+--- wise-2.4.1.orig/src/models/estwisedb.c
++++ wise-2.4.1/src/models/estwisedb.c
 @@ -688,8 +688,11 @@
  
  
@@ -80,8 +84,8 @@
  
    return ret;
  
---- a/src/models/promoterwise.c
-+++ b/src/models/promoterwise.c
+--- wise-2.4.1.orig/src/models/promoterwise.c
++++ wise-2.4.1/src/models/promoterwise.c
 @@ -147,8 +147,12 @@
  
    lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);

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