[med-svn] r994 - in trunk/packages/probcons/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sun Dec 23 19:17:25 UTC 2007
Author: charles-guest
Date: 2007-12-23 19:17:25 +0000 (Sun, 23 Dec 2007)
New Revision: 994
Added:
trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff
trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff
trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers
trunk/packages/probcons/trunk/debian/patches/series
Removed:
trunk/packages/probcons/trunk/debian/patches/00list
trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.dpatch
trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch
Modified:
trunk/packages/probcons/trunk/debian/changelog
trunk/packages/probcons/trunk/debian/control
trunk/packages/probcons/trunk/debian/probcons-extra.manpages
trunk/packages/probcons/trunk/debian/probcons.manpages
trunk/packages/probcons/trunk/debian/rules
Log:
fixing gcc-4.3 build problem, swiched to quilt
Modified: trunk/packages/probcons/trunk/debian/changelog
===================================================================
--- trunk/packages/probcons/trunk/debian/changelog 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/changelog 2007-12-23 19:17:25 UTC (rev 994)
@@ -1,7 +1,13 @@
-probcons (1.12-4) UNRELEASED; urgency=low
+probcons (1.12-4) unstable; urgency=low
[ Charles Plessy ]
- * Moved the Homepage: field out from the package's description.
+ * debian/control:
+ - Moved the Homepage: field out from the package's description.
+ - Allowed upload by Debian Maintainers.
+ - Checked the compliance with Policy 3.7.3
+ * debian/patches:
+ - swiched to quilt
+ - added a fix to build with GCC 4.3 (Closes: #455625)
[ David Paleino ]
* debian/probcons.1, debian/probcons-RNA.1, debian/pc-compare.1,
@@ -14,7 +20,7 @@
- manpages statically built
- minor changes
- -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 11:59:43 +0100
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 23 Dec 2007 19:56:03 +0100
probcons (1.12-3) unstable; urgency=low
Modified: trunk/packages/probcons/trunk/debian/control
===================================================================
--- trunk/packages/probcons/trunk/debian/control 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/control 2007-12-23 19:17:25 UTC (rev 994)
@@ -5,8 +5,8 @@
XS-DM-Upload-Allowed: Yes
Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>,
David Paleino <d.paleino at gmail.com>
-Build-Depends: debhelper (>= 5), dpatch
-Standards-Version: 3.7.2
+Build-Depends: debhelper (>= 5), quilt
+Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/probcons/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/probcons
Homepage: http://probcons.stanford.edu/
Deleted: trunk/packages/probcons/trunk/debian/patches/00list
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/00list 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/patches/00list 2007-12-23 19:17:25 UTC (rev 994)
@@ -1,2 +0,0 @@
-10_add-RNA-in-Makefile.dpatch
-11-Rename-programs-in-Makefile.dpatch
Added: trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff 2007-12-23 19:17:25 UTC (rev 994)
@@ -0,0 +1,47 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 10_add-RNA-in-Makefile.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+## This patch is hereby released in the public domain.
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Adds probcons-RNA
+
+ at DPATCH@
+
+--- probcons-1.10/Makefile 2006-05-07 13:45:26.000000000 +0900
++++ probcons-1.10.modified/Makefile 2006-05-07 13:51:20.000000000 +0900
+@@ -16,6 +16,7 @@
+ ################################################################################
+
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
++OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12"
+
+ # debug mode
+ #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
+@@ -25,13 +26,16 @@
+
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
++
+ CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
++CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
++
+
+ ################################################################################
+ # 3) Dependencies
+ ################################################################################
+
+-TARGETS = probcons compare project makegnuplot
++TARGETS = probcons probcons-RNA compare project makegnuplot
+
+ .PHONY : all
+ all : $(TARGETS)
+@@ -42,6 +46,9 @@
+ compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+ $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+
++probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
++ $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
++
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+ $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+
Property changes on: trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.dpatch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.dpatch 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.dpatch 2007-12-23 19:17:25 UTC (rev 994)
@@ -1,47 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 10_add-RNA-in-Makefile.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
-## This patch is hereby released in the public domain.
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Adds probcons-RNA
-
- at DPATCH@
-
---- probcons-1.10/Makefile 2006-05-07 13:45:26.000000000 +0900
-+++ probcons-1.10.modified/Makefile 2006-05-07 13:51:20.000000000 +0900
-@@ -16,6 +16,7 @@
- ################################################################################
-
- OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
-+OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12"
-
- # debug mode
- #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
-@@ -25,13 +26,16 @@
-
- # release mode
- #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
-+
- CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
-+CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
-+
-
- ################################################################################
- # 3) Dependencies
- ################################################################################
-
--TARGETS = probcons compare project makegnuplot
-+TARGETS = probcons probcons-RNA compare project makegnuplot
-
- .PHONY : all
- all : $(TARGETS)
-@@ -42,6 +46,9 @@
- compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
-
-+probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
-+ $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
-+
- fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
- $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
-
Added: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff 2007-12-23 19:17:25 UTC (rev 994)
@@ -0,0 +1,47 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 11-Rename-programs-in-Makefile.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+## This patch is hereby released in the public domain.
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Renames compare, project and makegnuplot to pc-compare, pc-project and
+## DP: pc-makegnuplot
+
+ at DPATCH@
+
+--- probcons-1.10-orig/Makefile 2006-06-04 22:01:10.000000000 +0900
++++ probcons-1.10/Makefile 2006-06-04 21:53:30.000000000 +0900
+@@ -35,7 +35,7 @@
+ # 3) Dependencies
+ ################################################################################
+
+-TARGETS = probcons probcons-RNA compare project makegnuplot
++TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
+
+ .PHONY : all
+ all : $(TARGETS)
+@@ -43,8 +43,8 @@
+ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+ $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
+
+-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
++pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
++ $(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
+
+ probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+ $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
+@@ -52,11 +52,11 @@
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+ $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+
+-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
++pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
++ $(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
+
+-makegnuplot : MakeGnuPlot.cc
+- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
++pc-makegnuplot : MakeGnuPlot.cc
++ $(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
+
+ .PHONY : clean
+ clean:
Property changes on: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.diff
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch 2007-12-23 19:17:25 UTC (rev 994)
@@ -1,47 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 11-Rename-programs-in-Makefile.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
-## This patch is hereby released in the public domain.
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Renames compare, project and makegnuplot to pc-compare, pc-project and
-## DP: pc-makegnuplot
-
- at DPATCH@
-
---- probcons-1.10-orig/Makefile 2006-06-04 22:01:10.000000000 +0900
-+++ probcons-1.10/Makefile 2006-06-04 21:53:30.000000000 +0900
-@@ -35,7 +35,7 @@
- # 3) Dependencies
- ################################################################################
-
--TARGETS = probcons probcons-RNA compare project makegnuplot
-+TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
-
- .PHONY : all
- all : $(TARGETS)
-@@ -43,8 +43,8 @@
- probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
- $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
-
--compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
-+pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-+ $(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
-
- probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
- $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
-@@ -52,11 +52,11 @@
- fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
- $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
-
--project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
-- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
-+pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
-+ $(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
-
--makegnuplot : MakeGnuPlot.cc
-- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
-+pc-makegnuplot : MakeGnuPlot.cc
-+ $(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
-
- .PHONY : clean
- clean:
Added: trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers 2007-12-23 19:17:25 UTC (rev 994)
@@ -0,0 +1,33 @@
+--- a/CompareToRef.cc
++++ b/CompareToRef.cc
+@@ -7,7 +7,7 @@
+
+ #include "SafeVector.h"
+ #include "MultiSequence.h"
+-#include <string>
++#include <string.h>
+ #include <sstream>
+ #include <iomanip>
+ #include <iostream>
+--- a/Main.cc
++++ b/Main.cc
+@@ -11,7 +11,7 @@
+ #include "ProbabilisticModel.h"
+ #include "EvolutionaryTree.h"
+ #include "SparseMatrix.h"
+-#include <string>
++#include <string.h>
+ #include <sstream>
+ #include <iomanip>
+ #include <iostream>
+--- a/ProjectPairwise.cc
++++ b/ProjectPairwise.cc
+@@ -7,7 +7,7 @@
+
+ #include "SafeVector.h"
+ #include "MultiSequence.h"
+-#include <string>
++#include <string.h>
+ #include <sstream>
+ #include <iomanip>
+ #include <iostream>
Added: trunk/packages/probcons/trunk/debian/patches/series
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/series (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/series 2007-12-23 19:17:25 UTC (rev 994)
@@ -0,0 +1,3 @@
+10_add-RNA-in-Makefile.diff
+11-Rename-programs-in-Makefile.diff
+fix-gcc-4.3-headers
Modified: trunk/packages/probcons/trunk/debian/probcons-extra.manpages
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-extra.manpages 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/probcons-extra.manpages 2007-12-23 19:17:25 UTC (rev 994)
@@ -1,3 +1,3 @@
-pc-makegnuplot.1
-pc-compare.1
-pc-project.1
+debian/pc-makegnuplot.1
+debian/pc-compare.1
+debian/pc-project.1
Modified: trunk/packages/probcons/trunk/debian/probcons.manpages
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.manpages 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/probcons.manpages 2007-12-23 19:17:25 UTC (rev 994)
@@ -1,2 +1,2 @@
-probcons.1
-probcons-RNA.1
+debian/probcons.1
+debian/probcons-RNA.1
Modified: trunk/packages/probcons/trunk/debian/rules
===================================================================
--- trunk/packages/probcons/trunk/debian/rules 2007-12-23 18:07:20 UTC (rev 993)
+++ trunk/packages/probcons/trunk/debian/rules 2007-12-23 19:17:25 UTC (rev 994)
@@ -24,7 +24,7 @@
CFLAGS += -O2
endif
-include /usr/share/dpatch/dpatch.make
+include /usr/share/quilt/quilt.make
build: patch build-stamp
build-stamp:
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