[med-svn] r17955 - in trunk/packages/rostlab/disulfinder/trunk/debian: . patches
Laszlo Kajan
lkajan at moszumanska.debian.org
Sun Sep 7 19:45:54 UTC 2014
Author: lkajan
Date: 2014-09-07 19:45:53 +0000 (Sun, 07 Sep 2014)
New Revision: 17955
Added:
trunk/packages/rostlab/disulfinder/trunk/debian/patches/unknown_escape
trunk/packages/rostlab/disulfinder/trunk/debian/patches/variable_length_array
Modified:
trunk/packages/rostlab/disulfinder/trunk/debian/changelog
trunk/packages/rostlab/disulfinder/trunk/debian/control
trunk/packages/rostlab/disulfinder/trunk/debian/copyright
trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch
trunk/packages/rostlab/disulfinder/trunk/debian/patches/series
trunk/packages/rostlab/disulfinder/trunk/debian/watch
Log:
1.2.11-4: Included patch to solve FTBFS with clang; Patched out unrecognized escape sequences
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/changelog 2014-09-07 17:56:05 UTC (rev 17954)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/changelog 2014-09-07 19:45:53 UTC (rev 17955)
@@ -1,3 +1,10 @@
+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
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/control 2014-09-07 17:56:05 UTC (rev 17954)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/control 2014-09-07 19:45:53 UTC (rev 17955)
@@ -1,7 +1,7 @@
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>,
+ Laszlo Kajan <lkajan at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
@@ -9,7 +9,7 @@
libboost-dev,
libboost-graph-dev,
libf2c2-dev
-Standards-Version: 3.9.4
+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/
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/copyright
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/copyright 2014-09-07 17:56:05 UTC (rev 17954)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/copyright 2014-09-07 19:45:53 UTC (rev 17955)
@@ -9,9 +9,9 @@
Paolo Frasconi
© 2009 Laszlo Kajan <lkajan at rostlab.org>,
Technical University Munich (Munich, DE)
-License: GPL2+
+License: GPL-2+
-License: GPL2+
+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
@@ -45,4 +45,4 @@
Files: debian/*
Copyright: © 2009-2011 Laszlo Kajan <lkajan at rostlab.org>
© 2013 Andreas Tille <tille at debian.org>
-License: GPL2+
+License: GPL-2+
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch 2014-09-07 17:56:05 UTC (rev 17954)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch 2014-09-07 19:45:53 UTC (rev 17955)
@@ -1,10 +1,11 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Sun, 17 Nov 2013 08:46:05 +0100
+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 @@ MAN1PAGES := disulfinder.1
+@@ -13,7 +13,7 @@
prefix := /usr
docdir := $(prefix)/share/doc/$(PACKAGE)
@@ -22,3 +23,88 @@
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
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/series 2014-09-07 17:56:05 UTC (rev 17954)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/series 2014-09-07 19:45:53 UTC (rev 17955)
@@ -1 +1,3 @@
hardening.patch
+variable_length_array
+unknown_escape
Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/unknown_escape
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/unknown_escape (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/unknown_escape 2014-09-07 19:45:53 UTC (rev 17955)
@@ -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);
Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/variable_length_array
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/variable_length_array (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/variable_length_array 2014-09-07 19:45:53 UTC (rev 17955)
@@ -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] = "";
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/watch
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/watch 2014-09-07 17:56:05 UTC (rev 17954)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/watch 2014-09-07 19:45:53 UTC (rev 17955)
@@ -1,2 +1,2 @@
version=3
-ftp://rostlab.org/disulfinder/disulfinder-([0-9.]+)\.tar\.gz
+opts=pasv ftp://rostlab.org/disulfinder/disulfinder-([0-9.]+)\.tar\.gz
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