[med-svn] r17956 - in trunk/packages/rostlab/disulfinder/tags: . 1.2.11-4/debian 1.2.11-4/debian/patches

Laszlo Kajan lkajan at moszumanska.debian.org
Sun Sep 7 19:50:07 UTC 2014


Author: lkajan
Date: 2014-09-07 19:50:07 +0000 (Sun, 07 Sep 2014)
New Revision: 17956

Added:
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/unknown_escape
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/variable_length_array
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch
Removed:
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series
   trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch
Log:
[svn-buildpackage] Tagging disulfinder 1.2.11-4

Deleted: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/changelog	2014-09-05 13:29:37 UTC (rev 17947)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog	2014-09-07 19:50:07 UTC (rev 17956)
@@ -1,54 +0,0 @@
-disulfinder (1.2.11-3) unstable; urgency=low
-
-  * debian/upstream: Valid BibTeX syntax in author strings
-  * debian/control:
-     - cme fix dpkg-control
-     - Priority: s/extra/optional/
-     - canonical Vcs URLs
-     - debhelper 9
-  * debian/copyright: DEP5
-  * debian/patches/hardening.patch: Propagate hardening options
-  * debian/rules: use dh consequently
-  * README.Debian: references are now in debian/upstream - install this
-    instead into doc directory
-
- -- Andreas Tille <tille at debian.org>  Sun, 17 Nov 2013 08:46:05 +0100
-
-disulfinder (1.2.11-2) unstable; urgency=low
-
-  * added mkdir debian/disulfinder-data/usr/share/disulfinder/ to
-    debian/rules before moving Models to disulfinder-data package to
-    resolve building issue on certain architectures (Closes: #639571)
-
- -- Laszlo Kajan <lkajan at rostlab.org>  Wed, 31 Aug 2011 20:47:26 +0200
-
-disulfinder (1.2.11-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Laszlo Kajan <lkajan at rostlab.org>  Fri, 26 Aug 2011 13:02:59 +0200
-
-disulfinder (1.2.10-1) unstable; urgency=low
-
-  * New upstream release
-  * The new upstream contains a rewritten version of require.h: the new
-    require.h is no longer based on any code with restricted license,
-    it is released under the GPL (see source)
-  [Steffen]
-  * moved to dh7
-  * added data package
-
- -- Laszlo Kajan <lkajan at rostlab.org>  Thu, 18 Aug 2011 11:28:02 +0200
-
-disulfinder (1.2.9-2) UNRELEASED; urgency=low
-
-  [Steffen]
-  * Added build-arch/-indep targets to help lintian
-
- -- Laszlo Kajan <lkajan at rostlab.org>  Sun, 24 Jul 2011 15:51:08 +0200
-
-disulfinder (1.2.9-1) unstable; urgency=low
-
-  * Initial release (Closes: #634177)
-
- -- Laszlo Kajan <lkajan at rostlab.org>  Sat, 09 Jul 2011 11:54:46 +0200

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/changelog)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/changelog	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,61 @@
+disulfinder (1.2.11-4) unstable; urgency=medium
+
+  * Included patch to solve 'FTBFS with clang' (Closes: #741559)
+  * Patched out 'unrecognized escape sequences'
+
+ -- Laszlo Kajan <lkajan at debian.org>  Sun, 07 Sep 2014 09:56:52 +0200
+
+disulfinder (1.2.11-3) unstable; urgency=low
+
+  * debian/upstream: Valid BibTeX syntax in author strings
+  * debian/control:
+     - cme fix dpkg-control
+     - Priority: s/extra/optional/
+     - canonical Vcs URLs
+     - debhelper 9
+  * debian/copyright: DEP5
+  * debian/patches/hardening.patch: Propagate hardening options
+  * debian/rules: use dh consequently
+  * README.Debian: references are now in debian/upstream - install this
+    instead into doc directory
+
+ -- Andreas Tille <tille at debian.org>  Sun, 17 Nov 2013 08:46:05 +0100
+
+disulfinder (1.2.11-2) unstable; urgency=low
+
+  * added mkdir debian/disulfinder-data/usr/share/disulfinder/ to
+    debian/rules before moving Models to disulfinder-data package to
+    resolve building issue on certain architectures (Closes: #639571)
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Wed, 31 Aug 2011 20:47:26 +0200
+
+disulfinder (1.2.11-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Fri, 26 Aug 2011 13:02:59 +0200
+
+disulfinder (1.2.10-1) unstable; urgency=low
+
+  * New upstream release
+  * The new upstream contains a rewritten version of require.h: the new
+    require.h is no longer based on any code with restricted license,
+    it is released under the GPL (see source)
+  [Steffen]
+  * moved to dh7
+  * added data package
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Thu, 18 Aug 2011 11:28:02 +0200
+
+disulfinder (1.2.9-2) UNRELEASED; urgency=low
+
+  [Steffen]
+  * Added build-arch/-indep targets to help lintian
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Sun, 24 Jul 2011 15:51:08 +0200
+
+disulfinder (1.2.9-1) unstable; urgency=low
+
+  * Initial release (Closes: #634177)
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Sat, 09 Jul 2011 11:54:46 +0200

Deleted: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/control	2014-09-05 13:29:37 UTC (rev 17947)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control	2014-09-07 19:50:07 UTC (rev 17956)
@@ -1,46 +0,0 @@
-Source: disulfinder
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Guy Yachdav <gyachdav at rostlab.org>,
-           Laszlo Kajan <lkajan at rostlab.org>,
-           Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
-               libboost-dev,
-               libboost-graph-dev,
-               libf2c2-dev
-Standards-Version: 3.9.4
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/disulfinder/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/disulfinder/trunk/
-Homepage: http://disulfind.dsi.unifi.it/
-
-Package: disulfinder
-Architecture: any
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         disulfinder-data
-Description: cysteines disulfide bonding state and connectivity predictor
- 'disulfinder' is for predicting the disulfide bonding state of cysteines
- and their disulfide connectivity starting from sequence alone. Disulfide
- bridges play a major role in the stabilization of the folding process for
- several proteins. Prediction of disulfide bridges from sequence alone is
- therefore useful for the study of structural and functional properties
- of specific proteins. In addition, knowledge about the disulfide bonding
- state of cysteines may help the experimental structure determination
- process and may be useful in other genomic annotation tasks.
- .
- 'disulfinder' predicts disulfide patterns in two computational stages:
- (1) the disulfide bonding state of each cysteine is predicted by a
- BRNN-SVM binary classifier; (2) cysteines that are known to participate
- in the formation of bridges are paired by a Recursive Neural Network
- to obtain a connectivity pattern.
-
-Package: disulfinder-data
-Architecture: all
-Depends: ${misc:Depends}
-Description: data files for predictor of disulfide bonds in proteins
- 'disulfinder' is for predicting the disulfide bonding state of cysteines
- and their disulfide connectivity starting from sequence alone.
- .
- This package contains all data files to reduce the redundancy between
- architectures in Debian.

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/control)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/control	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,46 @@
+Source: disulfinder
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Guy Yachdav <gyachdav at rostlab.org>,
+           Laszlo Kajan <lkajan at debian.org>,
+           Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               libboost-dev,
+               libboost-graph-dev,
+               libf2c2-dev
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/disulfinder/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/disulfinder/trunk/
+Homepage: http://disulfind.dsi.unifi.it/
+
+Package: disulfinder
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         disulfinder-data
+Description: cysteines disulfide bonding state and connectivity predictor
+ 'disulfinder' is for predicting the disulfide bonding state of cysteines
+ and their disulfide connectivity starting from sequence alone. Disulfide
+ bridges play a major role in the stabilization of the folding process for
+ several proteins. Prediction of disulfide bridges from sequence alone is
+ therefore useful for the study of structural and functional properties
+ of specific proteins. In addition, knowledge about the disulfide bonding
+ state of cysteines may help the experimental structure determination
+ process and may be useful in other genomic annotation tasks.
+ .
+ 'disulfinder' predicts disulfide patterns in two computational stages:
+ (1) the disulfide bonding state of each cysteine is predicted by a
+ BRNN-SVM binary classifier; (2) cysteines that are known to participate
+ in the formation of bridges are paired by a Recursive Neural Network
+ to obtain a connectivity pattern.
+
+Package: disulfinder-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: data files for predictor of disulfide bonds in proteins
+ 'disulfinder' is for predicting the disulfide bonding state of cysteines
+ and their disulfide connectivity starting from sequence alone.
+ .
+ This package contains all data files to reduce the redundancy between
+ architectures in Debian.

Deleted: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/copyright	2014-09-05 13:29:37 UTC (rev 17947)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright	2014-09-07 19:50:07 UTC (rev 17956)
@@ -1,48 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Contact: Laszlo Kajan <lkajan at rostlab.org>
-Source: ftp://rostlab.org/disulfinder/
-
-Files: *
-Copyright: © 2011 Alessio Ceroni,
-                  Andrea Passerini <passerini at disi.unitn.it>,
-                  Alessandro Vullo,
-                  Paolo Frasconi
-           © 2009 Laszlo Kajan <lkajan at rostlab.org>,
-                  Technical University Munich (Munich, DE)
-License: GPL2+
-
-License: GPL2+
- This suite of programs is free software. You can redistribute it
- and/or modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of the
- License, or (at your option) any later version.
- .
- In other words, you are free to modify, copy, or redistribute this
- source code and its documentation in any way you like, but you must
- distribute all derivative versions as free software under the same
- terms that I've provided my code to you (i.e. the GNU General Public
- License). This precludes any use of the code in proprietary or
- commercial software unless your source code is made freely available.
- .
- If you wish to use Disulfinder code under a different Open Source 
- license that's not compatible with the GPL (like the Artistic License, 
- BSD license, or the Netscape Public License), please contact me
- (passerini at disi.unitn.it) for permission.
- .
- This software is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this Disulfinder release, in the file LICENSE; if not, 
- write to the Free Software Foundation, Inc., 51 Franklin St, Fifth
- Floor, Boston, MA  02110-1301 USA
- .
- On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL-2'.
-
-Files: debian/*
-Copyright: © 2009-2011 Laszlo Kajan <lkajan at rostlab.org>
-           © 2013 Andreas Tille <tille at debian.org>
-License: GPL2+

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/copyright)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/copyright	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,48 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Laszlo Kajan <lkajan at rostlab.org>
+Source: ftp://rostlab.org/disulfinder/
+
+Files: *
+Copyright: © 2011 Alessio Ceroni,
+                  Andrea Passerini <passerini at disi.unitn.it>,
+                  Alessandro Vullo,
+                  Paolo Frasconi
+           © 2009 Laszlo Kajan <lkajan at rostlab.org>,
+                  Technical University Munich (Munich, DE)
+License: GPL-2+
+
+License: GPL-2+
+ This suite of programs is free software. You can redistribute it
+ and/or modify it under the terms of the GNU General Public License as
+ published by the Free Software Foundation; either version 2 of the
+ License, or (at your option) any later version.
+ .
+ In other words, you are free to modify, copy, or redistribute this
+ source code and its documentation in any way you like, but you must
+ distribute all derivative versions as free software under the same
+ terms that I've provided my code to you (i.e. the GNU General Public
+ License). This precludes any use of the code in proprietary or
+ commercial software unless your source code is made freely available.
+ .
+ If you wish to use Disulfinder code under a different Open Source 
+ license that's not compatible with the GPL (like the Artistic License, 
+ BSD license, or the Netscape Public License), please contact me
+ (passerini at disi.unitn.it) for permission.
+ .
+ This software is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this Disulfinder release, in the file LICENSE; if not, 
+ write to the Free Software Foundation, Inc., 51 Franklin St, Fifth
+ Floor, Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-2'.
+
+Files: debian/*
+Copyright: © 2009-2011 Laszlo Kajan <lkajan at rostlab.org>
+           © 2013 Andreas Tille <tille at debian.org>
+License: GPL-2+

Deleted: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch	2014-09-05 13:29:37 UTC (rev 17947)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch	2014-09-07 19:50:07 UTC (rev 17956)
@@ -1,24 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Sun, 17 Nov 2013 08:46:05 +0100
-Description: Propagate hardening options
-
---- a/Makefile
-+++ b/Makefile
-@@ -13,7 +13,7 @@ MAN1PAGES := disulfinder.1
- prefix := /usr
- docdir := $(prefix)/share/doc/$(PACKAGE)
- 
--CXXFLAGS := -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\"
-+CXXFLAGS += -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\"
- export CXXFLAGS
- 
- .PHONY: all
---- a/disulfind/src/Makefile
-+++ b/disulfind/src/Makefile
-@@ -1,5 +1,5 @@
- LIBS=-lCommon 
--LDFLAGS=-LCommon/
-+LDFLAGS+=-LCommon/
- TARGETS=disulfinder disultrainer
- ifndef CXX
- CXX=g++

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/hardening.patch	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,110 @@
+Author: Andreas Tille <tille at debian.org>,
+		Laszlo Kajan <lkajan at debian.org>
+LastChanged: Sun, 07 Sep 2014 21:36:07 +0200
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -13,7 +13,7 @@
+ prefix := /usr
+ docdir := $(prefix)/share/doc/$(PACKAGE)
+ 
+-CXXFLAGS := -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\"
++CXXFLAGS += -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\"
+ export CXXFLAGS
+ 
+ .PHONY: all
+--- a/disulfind/src/Makefile
++++ b/disulfind/src/Makefile
+@@ -1,5 +1,5 @@
+ LIBS=-lCommon 
+-LDFLAGS=-LCommon/
++LDFLAGS+=-LCommon/
+ TARGETS=disulfinder disultrainer
+ ifndef CXX
+ CXX=g++
+@@ -45,7 +45,7 @@
+ all: SVM NN brnn disulfinder disultrainer
+ 
+ %.o : %.cpp
+-	$(CXX) $(CXXFLAGS) -c $< -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
+ 
+ $(COMMONDIR)/libCommon.a: COMMON
+ 
+--- a/disulfind/src/BRNN/Makefile
++++ b/disulfind/src/BRNN/Makefile
+@@ -29,7 +29,7 @@
+ LD            	= $(CXX) #$(LDFLAGS)
+ 
+ .cpp.o:
+-	$(CXX) $(CINCLUDES) $(CODEOPT) $(DEBUG) $(CXXFLAGS) $(PROFILE) -c $< -o $@
++	$(CXX) $(CINCLUDES) $(CODEOPT) $(DEBUG) $(CPPFLAGS) $(CXXFLAGS) $(PROFILE) -c $< -o $@
+ SOURCES.cpp= \
+ 	$(RNNDIR)/Node.cpp \
+ 	$(RNNDIR)/StructureSearch.cpp \
+@@ -65,7 +65,7 @@
+ 	$(LD) $(OBJECTS) disulfind-conn.o -o $@ $(PROFILE) $(LDFLAGS)
+ 
+ disulfind-conn.o: $(SOURCES.cpp) disulfind-conn.cpp $(SOURCES.h)
+-	$(CXX) $(CINCLUDES) $(WARNINGS) $(CODEOPT) $(DEBUG) $(CXXFLAGS) $(PROFILE) -c disulfind-conn.cpp
++	$(CXX) $(CINCLUDES) $(WARNINGS) $(CODEOPT) $(DEBUG) $(CPPFLAGS) $(CXXFLAGS) $(PROFILE) -c disulfind-conn.cpp
+ 
+ clean:
+ 	rm -f *.o core
+--- a/disulfind/src/Common/Makefile
++++ b/disulfind/src/Common/Makefile
+@@ -18,7 +18,7 @@
+ 	g++ -o $@ $+ ${LIBS}
+ 
+ %.o: %.cpp
+-	g++ $(CXXFLAGS) -c $< -o $@
++	g++ $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
+ 
+ clean:
+ 	$(MAKE) -C eig clean
+--- a/disulfind/src/Common/eig/Makefile
++++ b/disulfind/src/Common/eig/Makefile
+@@ -9,7 +9,7 @@
+ 	$(MAKELIB) ${TARGETLIB} $+
+ 
+ %.o: %.c
+-	g++ $(CXXFLAGS) -O3 -c $< -o $@
++	g++ $(CPPFLAGS) $(CXXFLAGS) -O3 -c $< -o $@
+ 
+ clean:
+ 	rm *.o $(TARGETLIB) *~ -f 
+--- a/disulfind/src/NN/Makefile
++++ b/disulfind/src/NN/Makefile
+@@ -5,10 +5,10 @@
+ all : brnn-train brnn-test
+ 
+ %.standalone.o:%.cpp
+-	g++ $(CXXFLAGS) -DSTANDALONE -c $< -o $@
++	g++ $(CPPFLAGS) $(CXXFLAGS) -DSTANDALONE -c $< -o $@
+ 
+ %.o:%.cpp
+-	g++ $(CXXFLAGS) -c $< -o $@
++	g++ $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
+  
+ brnn-train : multi-array.o array.o brnn-model.o brnn-train.standalone.o brnn-test.standalone.o 
+ 	g++ $(CXXFLAGS) -o brnn-train brnn-train.standalone.o brnn-model.o array.o multi-array.o $(LDFLAGS)
+--- a/disulfind/src/SVM/Makefile
++++ b/disulfind/src/SVM/Makefile
+@@ -1,6 +1,6 @@
+ TARGETBIN = SVMClassifier
+ OPT = -O3
+-CXXFLAGS=$(OPT) $(CFLAGS) -Wno-deprecated 
++CXXFLAGS+=$(OPT) -Wno-deprecated 
+ CXX = g++ 
+ LIBS=-lCommon 
+ LDFLAGS=-L../Common/
+@@ -14,7 +14,7 @@
+ 	${CXX} -DSVMCLASSIFIER -c $< -o $@
+ 
+ %.o : %.cpp
+-	${CXX} -c $< -o $@ 
++	${CXX} $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@ 
+ 
+ clean:	
+ 	rm *~ *.o *.a *.exe ${TARGETBIN} -f 

Deleted: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/series	2014-09-05 13:29:37 UTC (rev 17947)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series	2014-09-07 19:50:07 UTC (rev 17956)
@@ -1 +0,0 @@
-hardening.patch

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/patches/series)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/series	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,3 @@
+hardening.patch
+variable_length_array
+unknown_escape

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/unknown_escape (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/patches/unknown_escape)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/unknown_escape	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/unknown_escape	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,37 @@
+Author: Laszlo Kajan <lkajan at debian.org>
+LastChanged: Sun, 07 Sep 2014 20:49:59 +0200
+Description: remove unknown escape sequences
+
+--- a/disulfind/src/Common/Accuracy.h
++++ b/disulfind/src/Common/Accuracy.h
+@@ -60,10 +60,10 @@
+   }
+ 
+   void Output(ostream &os) {
+-    os<<"Accuracy= "  << (GetAccuracy()*100.)<<"\%\n";
+-    os<<"Precision= " << (GetPrecision()*100.)<<"\%\n";
+-    os<<"Recall= "    << (GetRecall()*100.)<<"\%\n";		     
+-    os<<"FMeasure= "  << (GetFMeasure()*100.)<<"\%\n";
++    os<<"Accuracy= "  << (GetAccuracy()*100.)<<"%\n";
++    os<<"Precision= " << (GetPrecision()*100.)<<"%\n";
++    os<<"Recall= "    << (GetRecall()*100.)<<"%\n";		     
++    os<<"FMeasure= "  << (GetFMeasure()*100.)<<"%\n";
+   }
+ };
+ 
+--- a/disulfind/src/Common/ConfusionMatrix.cpp
++++ b/disulfind/src/Common/ConfusionMatrix.cpp
+@@ -43,10 +43,10 @@
+ 
+ void ConfusionMatrix::Output( ostream &out )
+ {
+-  out << "Accuracy = " << (Accuracy()*100.) << "\%\n";
++  out << "Accuracy = " << (Accuracy()*100.) << "%\n";
+   for( int c=0; c<m_noclasses; c++ ) {
+-    out << "Precision class " << c << " = " << (Precision(c)*100.) << "\%\n";
+-    out << "Recall class    " << c << " = " << (Recall(c)*100.)    << "\%\n";
++    out << "Precision class " << c << " = " << (Precision(c)*100.) << "%\n";
++    out << "Recall class    " << c << " = " << (Recall(c)*100.)    << "%\n";
+   }
+   
+   //out.setf(ios_base::left,ios_base::adjustfield);

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/variable_length_array (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/patches/variable_length_array)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/variable_length_array	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/patches/variable_length_array	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,35 @@
+Author: Laszlo Kajan <lkajan at debian.org>
+LastChanged: Sun, 07 Sep 2014 20:49:59 +0200
+Description: reimplement variable length arrays properly for C++
+
+--- a/disulfind/src/Input/buildXfolds.cpp
++++ b/disulfind/src/Input/buildXfolds.cpp
+@@ -13,7 +13,7 @@
+   std::ifstream in(example_file);
+   assert(in.good());
+   std::list<std::string> examples;
+-  std::vector<std::string> fold_examples[folds_number];
++  std::vector< std::vector<std::string> > fold_examples(folds_number);
+   std::list<std::string>::iterator iter;
+   std::string buf;
+   
+--- a/disulfind/src/Output/utils.cpp
++++ b/disulfind/src/Output/utils.cpp
+@@ -55,7 +55,7 @@
+   if( nobridges==0 )
+     return bridges;
+   
+-  unsigned int start_bridge[nobridges], end_bridge[nobridges];
++  std::vector<unsigned int> start_bridge(nobridges), end_bridge(nobridges);
+ 
+   for(unsigned int i=0; i < nobridges; i++){
+     start_bridge[i] = ind_bridges[i].first;
+@@ -80,7 +80,7 @@
+ 
+   // make bridges representations
+   bridges.resize(nocrossings+1);
+-  unsigned int activebridges[nobridges];
++  std::vector<unsigned int> activebridges(nobridges);
+   for(unsigned int i=0; i<nocrossings; i++ ) {
+     activebridges[i] = 0;
+     bridges[i] = "";

Deleted: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/watch	2014-09-05 13:29:37 UTC (rev 17947)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch	2014-09-07 19:50:07 UTC (rev 17956)
@@ -1,2 +0,0 @@
-version=3
-ftp://rostlab.org/disulfinder/disulfinder-([0-9.]+)\.tar\.gz

Copied: trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch (from rev 17955, trunk/packages/rostlab/disulfinder/trunk/debian/watch)
===================================================================
--- trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/tags/1.2.11-4/debian/watch	2014-09-07 19:50:07 UTC (rev 17956)
@@ -0,0 +1,2 @@
+version=3
+opts=pasv ftp://rostlab.org/disulfinder/disulfinder-([0-9.]+)\.tar\.gz




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