[med-svn] [ball] 04/04: New upstream version, most patches were taken over
Andreas Tille
tille at debian.org
Thu Jan 7 10:40:35 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ball.
commit a6a79a1695ba6c0ac32ede9ca17d3a4409633382
Author: Andreas Tille <tille at debian.org>
Date: Thu Jan 7 11:39:53 2016 +0100
New upstream version, most patches were taken over
---
debian/changelog | 4 +-
...X_PENALTY-option-to-bond-order-assignment.patch | 76 ---------------
...xed-a-bug-in-the-AssignBondOrderProcessor.patch | 58 ------------
...ilation-of-FTPBondOrderStrategy-Fixes-451.patch | 22 -----
debian/patches/0101-cmake-syntax.patch | 105 ---------------------
.../0102-fix-boost-compatibility-issue.patch | 16 ----
..._OPTIONS-CMake-macro-changed-in-CMake-2.8.patch | 38 --------
debian/patches/HelpSipAmbiguity.patch | 13 ---
debian/patches/gcc5.diff | 58 +-----------
debian/patches/link_against_x11.patch | 6 +-
debian/patches/more-gcc5_issues.patch | 72 --------------
debian/patches/nopsboxit.patch | 6 +-
debian/patches/series | 8 --
13 files changed, 9 insertions(+), 473 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 769e29b..c576766 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,7 @@
-ball (1.4.2+20140406-2) UNRELEASED; urgency=medium
+ball (1.4.3~beta1-1) UNRELEASED; urgency=medium
+ * New upstream version
+ Closes: #777791
* New homepage
* Moved to Github
* Adapt watch file to Github
diff --git a/debian/patches/0008-Added-MAX_PENALTY-option-to-bond-order-assignment.patch b/debian/patches/0008-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
deleted file mode 100644
index 33f214b..0000000
--- a/debian/patches/0008-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-From: Anna Dehof <anne at bioinf.uni-sb.de>
-Date: Mon, 26 Mar 2012 19:11:39 +0200
-Last-Update: Andreas Tille <tille at debian.org> Thu, 12 Dec 2013 14:59:51 +0100
-Subject: Added MAX_PENALTY option to bond order assignment
-
----
- include/BALL/DATATYPE/GRAPH/treeWidth.h | 28 +--
- .../STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h | 16 +-
- include/BALL/STRUCTURE/assignBondOrderProcessor.h | 30 ++-
- source/APPLICATIONS/UTILITIES/assign_bond_orders.C | 34 +++-
- source/DATATYPE/GRAPH/treeWidth.C | 2 +-
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C | 199 +++++++++-----------
- source/STRUCTURE/assignBondOrderProcessor.C | 44 +++--
- 7 files changed, 186 insertions(+), 167 deletions(-)
-
---- a/include/BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h
-+++ b/include/BALL/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.h
-@@ -1118,6 +1118,11 @@ namespace BALL
- Size num_computed_solutions_;
-
- /**
-+ * The number of solutions produced so far.
-+ */
-+ Size num_computed_solutions_;
-+
-+ /**
- * current upperbound. This algorithm will just iterate solutions which are better than this upperbound;
- */
- Penalty upper_bound_;
---- a/include/BALL/STRUCTURE/assignBondOrderProcessor.h
-+++ b/include/BALL/STRUCTURE/assignBondOrderProcessor.h
-@@ -734,6 +734,9 @@ namespace BALL
- // the max penalty score
- int max_penalty_;
-
-+ // the max penalty score
-+ int max_penalty_;
-+
- // flag to indicate, whether also non-optimal solutions should be computed
- bool compute_also_non_optimal_solutions_;
-
---- a/source/STRUCTURE/assignBondOrderProcessor.C
-+++ b/source/STRUCTURE/assignBondOrderProcessor.C
-@@ -110,6 +110,9 @@ namespace BALL
- const char* AssignBondOrderProcessor::Option::MAX_PENALTY = "max_penalty_score";
- const int AssignBondOrderProcessor::Default::MAX_PENALTY = -1;
-
-+ const char* AssignBondOrderProcessor::Option::MAX_PENALTY = "max_penalty_score";
-+ const int AssignBondOrderProcessor::Default::MAX_PENALTY = -1;
-+
- const char* AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS = "compute_also_non_optimal_solutions";
- const bool AssignBondOrderProcessor::Default::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS = false;
-
-@@ -267,6 +270,12 @@ namespace BALL
- << " : Error in options! Please check the option Option::MAX_PENALTY." << endl;
- ret = false;
- }
-+ if (max_penalty_ < -1)
-+ {
-+ Log.error() << __FILE__ << " " << __LINE__
-+ << " : Error in options! Please check the option Option::MAX_PENALTY." << endl;
-+ ret = false;
-+ }
- if ((alpha_ < 0) || ((alpha_ > 1)))
- {
- Log.error() << __FILE__ << " " << __LINE__
-@@ -1234,6 +1243,9 @@ cout << " ~~~~~~~~ added hydrogen dump ~
-
- options.setDefaultInteger(AssignBondOrderProcessor::Option::MAX_PENALTY,
- AssignBondOrderProcessor::Default::MAX_PENALTY);
-+
-+ options.setDefaultInteger(AssignBondOrderProcessor::Option::MAX_PENALTY,
-+ AssignBondOrderProcessor::Default::MAX_PENALTY);
-
- options.setDefaultBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS,
- AssignBondOrderProcessor::Default::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS);
diff --git a/debian/patches/0009-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch b/debian/patches/0009-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
deleted file mode 100644
index e8a48a9..0000000
--- a/debian/patches/0009-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
+++ /dev/null
@@ -1,58 +0,0 @@
-From: Anna Dehof <anne at bioinf.uni-sb.de>
-Date: Fri, 27 Apr 2012 18:41:52 +0200
-Last-Update: Andreas Tille <tille at debian.org> Thu, 12 Dec 2013 14:59:51 +0100
-Subject: Fixed a bug in the AssignBondOrderProcessor
-
----
- .../STRUCTURE/BONDORDERS/bondOrderAssignment.h | 2 +-
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C | 13 +++--
- source/STRUCTURE/assignBondOrderProcessor.C | 27 +++++++----
- source/TEST/AssignBondOrderProcessor_test.C | 50 +++++++++++++++-----
- 4 files changed, 67 insertions(+), 25 deletions(-)
-
---- a/source/TEST/AssignBondOrderProcessor_test.C
-+++ b/source/TEST/AssignBondOrderProcessor_test.C
-@@ -931,6 +931,34 @@ CHECK(operator() FPT vs A*)
-
- RESULT
-
-+CHECK(operator() FPT vs A*)
-+ AssignBondOrderProcessor testbop_a;
-+ testbop_a.options.set(AssignBondOrderProcessor::Option::ALGORITHM,AssignBondOrderProcessor::Algorithm::A_STAR);
-+ testbop_a.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+
-+ AssignBondOrderProcessor testbop_fpt;
-+ testbop_fpt.options.set(AssignBondOrderProcessor::Option::ALGORITHM,AssignBondOrderProcessor::Algorithm::FPT);
-+ testbop_fpt.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, true);
-+
-+ System sys4;
-+ MOL2File mol4(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_CITSED10_sol_6.mol2), std::ios::in);
-+ mol4 >> sys4;
-+ sys4.apply(testbop_a);
-+ sys4.apply(testbop_fpt);
-+ TEST_REAL_EQUAL(testbop_a.getNumberOfComputedSolutions(), testbop_fpt.getNumberOfComputedSolutions())
-+
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(0), testbop_fpt.getTotalPenalty(0)) //1.f )
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(1), testbop_fpt.getTotalPenalty(1)) //1.f )
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(2), testbop_fpt.getTotalPenalty(2)) //32.f)
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(3), testbop_fpt.getTotalPenalty(3)) //34.f)
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(4), testbop_fpt.getTotalPenalty(4)) //34.f)
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(5), testbop_fpt.getTotalPenalty(5)) //34.f)
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(6), testbop_fpt.getTotalPenalty(6)) //66.f)
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(7), testbop_fpt.getTotalPenalty(7)) //66.f)
-+ TEST_REAL_EQUAL(testbop_a.getTotalPenalty(8), testbop_fpt.getTotalPenalty(8)) //67.f)
-+
-+RESULT
-+
-
- CHECK(getTotalCharge(Position i))
- // This feature is experimental!!
-@@ -977,7 +1005,7 @@ CHECK(computeNextSolution() using A*)
- MOL2File mol_in(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_AN06.mol2), std::ios::in);
- mol_in >> sys;
- sys.apply(testbop);
-- TEST_EQUAL(testbop.getNumberOfComputedSolutions(),1)
-+ TEST_EQUAL(testbop.getNumberOfComputedSolutions(), 1)
- TEST_REAL_EQUAL(testbop.getTotalPenalty(0), 2.f)//0.00625)// 2.)
- bool testbop_result = testbop.computeNextSolution();
- TEST_EQUAL(testbop_result, true)
diff --git a/debian/patches/0010-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch b/debian/patches/0010-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch
deleted file mode 100644
index c939fa6..0000000
--- a/debian/patches/0010-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Anna Dehof <anne at bioinf.uni-sb.de>
-Date: Fri, 8 Jun 2012 19:28:12 +0200
-Last-Update: Andreas Tille <tille at debian.org> Thu, 12 Dec 2013 14:59:51 +0100
-Subject: Fix compilation of FTPBondOrderStrategy (Fixes #451)
-
-This patch is due to Daniel Stoeckel.
----
- source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C | 33 +++++++++++---------
- 1 file changed, 18 insertions(+), 15 deletions(-)
-
---- a/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-+++ b/source/STRUCTURE/BONDORDERS/FPTBondOrderStrategy.C
-@@ -576,6 +576,9 @@ namespace BALL
- bag_properties.table->insert(DPConfig_(1, 0), 0);
- }
- }
-+
-+#define convertToCRow(tmp)\
-+ std::make_pair(boost::reference_wrapper<const DPConfig_>((tmp).first), (tmp).second)
-
- std::vector<MolecularGraphTraits::EdgeType> FPTBondOrderStrategy::FPTBondOrderAssignment_::getBondsInBag(TreeDecompositionBag& bag)
- {
diff --git a/debian/patches/0101-cmake-syntax.patch b/debian/patches/0101-cmake-syntax.patch
deleted file mode 100644
index f7df0de..0000000
--- a/debian/patches/0101-cmake-syntax.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 12 Dec 2013 16:55:11 +0100
-Description: Fix some cmake syntax issues
-
---- a/cmake/BALLDoc.cmake
-+++ b/cmake/BALLDoc.cmake
-@@ -30,15 +30,15 @@ IF (DOXYGEN_FOUND)
- ## doc
- ADD_CUSTOM_TARGET(doc ${AUTO_BUILD_DOC}
- COMMAND ${CMAKE_COMMAND} -E echo ""
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation";
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation"
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html
- COMMAND ${CMAKE_COMMAND} -E chdir doc ${DOXYGEN_EXECUTABLE} Doxyfile
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created.";
-- COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/html/index.html' in a web browser.";
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
-+ COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/html/index.html' in a web browser."
- COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMENT "Build the doxygen documentation"
- COMPONENT "${COMPONENT_DOCUMENTATION_HTML}"
-@@ -58,17 +58,17 @@ IF (DOXYGEN_FOUND)
- ## doc_tidy
- ADD_CUSTOM_TARGET(doc_tidy
- COMMAND ${CMAKE_COMMAND} -E echo ""
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation";
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation"
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html
- COMMAND ${CMAKE_COMMAND} -E chdir doc ${DOXYGEN_EXECUTABLE} Doxyfile
-- COMMAND ${CMAKE_COMMAND} -E echo "Running tidy...";
-+ COMMAND ${CMAKE_COMMAND} -E echo "Running tidy..."
- COMMAND ${CMAKE_COMMAND} -E chdir doc/html tidy -m -i -asxml -q -bare -clean *htm* 2>/dev/null | true
-- COMMAND ${CMAKE_COMMAND} -E echo "Finshed Tunning tidy...";
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created.";
-- COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/html/index.html' in a web browser.";
-+ COMMAND ${CMAKE_COMMAND} -E echo "Finshed Tunning tidy..."
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
-+ COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/html/index.html' in a web browser."
- COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMENT "Build the doxygen documentation"
- VERBATIM)
-@@ -78,15 +78,15 @@ IF (DOXYGEN_FOUND)
- ## doc_dot target
- ADD_CUSTOM_TARGET(doc_dot
- COMMAND ${CMAKE_COMMAND} -E echo ""
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "Creating DOT html documentation";
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "Creating DOT html documentation"
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html-dot
- COMMAND ${CMAKE_COMMAND} -E chdir doc ${DOXYGEN_EXECUTABLE} Doxyfile_dot
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created.";
-- COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/html-dot/index.html' in a web browser.";
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
-+ COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/html-dot/index.html' in a web browser."
- COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMENT "Build the doxygen documentation"
- VERBATIM)
-@@ -104,19 +104,19 @@ IF (LATEX_COMPILER AND DVIPS_CONVERTER)
- # doc_tutorials target
- ADD_CUSTOM_TARGET(doc_tutorial ${AUTO_BUILD_DOC}
- COMMAND ${CMAKE_COMMAND} -E echo ""
-- COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
-- COMMAND ${CMAKE_COMMAND} -E echo "Creating BALL pdf tutorial";
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-+ COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-+ COMMAND ${CMAKE_COMMAND} -E echo "Creating BALL pdf tutorial"
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMAND ${CMAKE_COMMAND} -E chdir ${PROJECT_SOURCE_DIR}/doc/TUTORIAL/ ${PDFLATEX_COMPILER} tutorial.tex
- COMMAND ${CMAKE_COMMAND} -E chdir ${PROJECT_SOURCE_DIR}/doc/TUTORIAL/ ${BIBTEX_COMPILER} tutorial
- COMMAND ${CMAKE_COMMAND} -E chdir ${PROJECT_SOURCE_DIR}/doc/TUTORIAL/ ${MAKEINDEX_COMPILER} tutorial.idx
- COMMAND ${CMAKE_COMMAND} -E chdir ${PROJECT_SOURCE_DIR}/doc/TUTORIAL/ ${PDFLATEX_COMPILER} tutorial.tex
- COMMAND ${CMAKE_COMMAND} -E chdir ${PROJECT_SOURCE_DIR}/doc/TUTORIAL/ ${PDFLATEX_COMPILER} tutorial.tex
- COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/TUTORIAL/tutorial.pdf doc/tutorial.pdf
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-- COMMAND ${CMAKE_COMMAND} -E echo "The BALL tutorial in PDF format has been successfully created:";
-- COMMAND ${CMAKE_COMMAND} -E echo "doc/tutorial.pdf";
-- COMMAND ${CMAKE_COMMAND} -E echo "";
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
-+ COMMAND ${CMAKE_COMMAND} -E echo "The BALL tutorial in PDF format has been successfully created:"
-+ COMMAND ${CMAKE_COMMAND} -E echo "doc/tutorial.pdf"
-+ COMMAND ${CMAKE_COMMAND} -E echo ""
- COMMENT "Build the BALL pdf tutorial"
- VERBATIM)
-
diff --git a/debian/patches/0102-fix-boost-compatibility-issue.patch b/debian/patches/0102-fix-boost-compatibility-issue.patch
deleted file mode 100644
index 8adb0f7..0000000
--- a/debian/patches/0102-fix-boost-compatibility-issue.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Author: Gert Wollny <gw.fossdev at gmail.com>
-Last-Update: Thu, 12 Dec 2013 19:43:34 +0100
-Bug-Debian: http://bugs.debian.org/720681
-Description: Fix build issue with more recent boost versions
-
---- a/source/FORMAT/PDBFileDetails.C
-+++ b/source/FORMAT/PDBFileDetails.C
-@@ -901,7 +901,7 @@ namespace BALL
- {
- if (!(current_protein_->hasProperty("CRYSTALINFO")))
- {
-- boost::shared_ptr<CrystalInfo> temp_ptr(new CrystalInfo());
-+ boost::shared_ptr<PersistentObject> temp_ptr(new CrystalInfo());
- current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr));
- }
-
diff --git a/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
deleted file mode 100644
index d4e261d..0000000
--- a/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
+++ /dev/null
@@ -1,38 +0,0 @@
->From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001
-From: Luis de la Garza <delagarza at informatik.uni-tuebingen.de>
-Date: Fri, 22 Nov 2013 15:18:55 +0100
-Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12;
- fixed BALLMacros.cmake
-
----
- cmake/BALLMacros.cmake | 14 ++++++++++----
- 1 file changed, 10 insertions(+), 4 deletions(-)
-
---- a/cmake/BALLMacros.cmake
-+++ b/cmake/BALLMacros.cmake
-@@ -6,16 +6,22 @@
- ### minor modifications (marked with ## BALL ###)
- ###
- MACRO(QT4_WRAP_UI_BALL outfiles )
-- QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN})
-+ # since 2.8.12 qt4_extract_options has an additional argument
-+ # copied fix from OpenMS
-+ IF(${CMAKE_VERSION} VERSION_LESS "2.8.12")
-+ QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN})
-+ ELSE()
-+ QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN})
-+ ENDIF()
-
-- ### BALL ###
-+ ### BALL ###
- # create output directory (will not exist for out-of-source builds)
- FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/)
-
- FOREACH (it ${ui_files})
- GET_FILENAME_COMPONENT(outfile ${it} NAME_WE)
- GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE)
-- ### BALL ###
-+ ### BALL ###
- SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h)
- ADD_CUSTOM_COMMAND(OUTPUT ${outfile}
- COMMAND ${QT_UIC_EXECUTABLE}
diff --git a/debian/patches/HelpSipAmbiguity.patch b/debian/patches/HelpSipAmbiguity.patch
deleted file mode 100644
index 9869b18..0000000
--- a/debian/patches/HelpSipAmbiguity.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: ball/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
-===================================================================
---- ball.orig/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
-+++ ball/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
-@@ -26,7 +26,7 @@
- ModularWidget(const ModularWidget&) throw();
- ~ModularWidget() throw();
-
-- virtual void destroy() throw();
-+ //virtual void destroy() throw(); // Steffen
- virtual void clear() throw();
-
- static void registerWidget(ModularWidget*) throw(NullPointer);
diff --git a/debian/patches/gcc5.diff b/debian/patches/gcc5.diff
index d2ad78f..b3eabe6 100644
--- a/debian/patches/gcc5.diff
+++ b/debian/patches/gcc5.diff
@@ -2,6 +2,7 @@ Author: Matthias Klose <doko at debian.org>
Last-Update: Thu, 09 Jul 2015 12:17:06 +0200
Bug-Debian: https://bugs.debian.org/755225
Description: Fix some build errors with GCC 5 and clang++
+ (Most hunks of original patch taken over in upstream version 1.4.3~beta1
--- a/include/BALL/DATATYPE/string.h
+++ b/include/BALL/DATATYPE/string.h
@@ -15,60 +16,3 @@ Description: Fix some build errors with GCC 5 and clang++
/** \defgroup String String
An improved version of STL string.
-@@ -998,7 +1001,7 @@ namespace BALL
-
- ///
- BALL_EXPORT
-- friend std::istream& getline(std::istream& s, String& string, char delimiter = '\n');
-+ friend std::istream& getline(std::istream& s, String& string, char delimiter);
-
- //@}
-
---- a/source/FORMAT/molFileFactory.C
-+++ b/source/FORMAT/molFileFactory.C
-@@ -39,7 +39,7 @@ namespace BALL
- try
- {
- string s;
-- ok = std::getline(in,s);
-+ if (std::getline(in,s)) ok = true;
- }
- catch (const boost::iostreams::gzip_error& e)
- {
---- a/source/STRUCTURE/binaryFingerprintMethods.C
-+++ b/source/STRUCTURE/binaryFingerprintMethods.C
-@@ -10,7 +10,7 @@
- #include <BALL/SYSTEM/timer.h>
-
- #include <boost/foreach.hpp>
--
-+#include <boost/unordered_map.hpp>
-
- using namespace std;
- using namespace boost;
-@@ -1584,13 +1584,13 @@ bool BinaryFingerprintMethods::connected
- {
-
- // STEP 1: Get connected components and member indices
-- unordered_map<unsigned int, unordered_map<unsigned int, unsigned int> > ccs_tmp;
-- unordered_map<unsigned int, unordered_map<unsigned int, unsigned int> >::iterator ccs_iter;
-+ boost::unordered_map<unsigned int, boost::unordered_map<unsigned int, unsigned int> > ccs_tmp;
-+ boost::unordered_map<unsigned int, boost::unordered_map<unsigned int, unsigned int> >::iterator ccs_iter;
- BOOST_FOREACH(Vertex current_vertex, vertices(sim_graph))
- {
- if (ccs_tmp.find(ds->find_set(current_vertex)) == ccs_tmp.end())
- {
-- ccs_tmp[ds->find_set(current_vertex)] = unordered_map<unsigned int, unsigned int>();
-+ ccs_tmp[ds->find_set(current_vertex)] = boost::unordered_map<unsigned int, unsigned int>();
- }
-
- // ccs_tmp[ds->find_set(current_vertex)][current_vertex] = ccs_tmp[ds->find_set(current_vertex)].size();
-@@ -1608,7 +1608,7 @@ bool BinaryFingerprintMethods::connected
- }
-
- // STEP 3: Write information in return data structures
-- unordered_map<unsigned int, unsigned int>::iterator cc_iter;
-+ boost::unordered_map<unsigned int, unsigned int>::iterator cc_iter;
- for (size_iter=cc_sizes.begin(); size_iter!=cc_sizes.end(); ++size_iter)
- {
- ccs.push_back(vector<unsigned int>(size_iter->first, 0));
diff --git a/debian/patches/link_against_x11.patch b/debian/patches/link_against_x11.patch
index d0e3dc9..bf1da3a 100644
--- a/debian/patches/link_against_x11.patch
+++ b/debian/patches/link_against_x11.patch
@@ -5,9 +5,9 @@ Author: Lisandro Damián Nicanor Pérez Meyer <lisandro at debian.org>
Forwarded: no
Last-Update: 2015-06-05.
---- ball-1.4.2+20140406.orig/CMakeLists.txt
-+++ ball-1.4.2+20140406/CMakeLists.txt
-@@ -550,7 +550,7 @@ TARGET_LINK_LIBRARIES(BALL ${BALL_DEP_LI
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -622,7 +622,7 @@ TARGET_LINK_LIBRARIES(BALL ${BALL_DEP_LI
${QT_QTCORE_LIBRARY}
${QT_QTSQL_LIBRARY}
${QT_QTNETWORK_LIBRARY}
diff --git a/debian/patches/more-gcc5_issues.patch b/debian/patches/more-gcc5_issues.patch
deleted file mode 100644
index e797e25..0000000
--- a/debian/patches/more-gcc5_issues.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-From: Andreas Hildebrandt <andreas.hildebrandt at uni-mainz.de>
-Date: Fri, 4 Apr 2014 14:34:42 +0200
-Bug-Debian: https://bugs.debian.org/777791
-Origin: upstream, cherry picked from
- https://github.com/BALL-Project/ball/commit/6700400576521250cbe4f8d201391168eb80e0df.patch
-Subject: Use c++11 on Clang.
- The patch was changed for source/FORMAT/molFileFactory.C
-
---- a/cmake/BALLCompilerSpecific.cmake
-+++ b/cmake/BALLCompilerSpecific.cmake
-@@ -178,4 +178,7 @@ ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQU
- CXX_COMPILER_VERSION_MINOR ${CXX_COMPILER_VERSION})
-
- SET(CXX_COMPILER_VERSION "${CXX_COMPILER_VERSION_MAJOR}.${CXX_COMPILER_VERSION_MINOR}")
-+
-+ ## Clang should use c++-11 - mode
-+ ADD_BALL_DEFINITIONS("-std=c++11")
- ENDIF()
---- a/source/PYTHON/EXTENSIONS/BALL/file.sip
-+++ b/source/PYTHON/EXTENSIONS/BALL/file.sip
-@@ -22,14 +22,14 @@ class File
- #include <BALL/SYSTEM/file.h>
- using namespace BALL;
-
--/*
-- const File::OpenMode BALL_File__IN = File::MODE_IN;
-- const File::OpenMode BALL_File__OUT = File::MODE_OUT;
-- const File::OpenMode BALL_File__APP = File::MODE_APP;
-- const File::OpenMode BALL_File__BINARY = File::MODE_BINARY;
-- const File::OpenMode BALL_File__ATE = File::MODE_ATE;
-- const File::OpenMode BALL_File__TRUNC = File::MODE_TRUNC;
--*/
-+ /*
-+ const File::OpenMode MODE_IN = std::ios::in;
-+ const File::OpenMode MODE_OUT = std::ios::out;
-+ const File::OpenMode MODE_APP = std::ios::app;
-+ const File::OpenMode MODE_BINARY = std::ios::binary;
-+ const File::OpenMode MODE_ATE = std::ios::ate;
-+ const File::OpenMode MODE_TRUNC = std::ios::trunc;
-+ */
-
- %End
- public:
-@@ -44,7 +44,8 @@ class File
- };
-
-
-- enum {
-+ /*
-+ unsigned enum {
- MODE_IN,
- MODE_OUT,
- MODE_APP,
-@@ -52,6 +53,7 @@ class File
- MODE_ATE,
- MODE_TRUNC
- };
-+ */
-
-
- File();
---- a/source/FORMAT/molFileFactory.C
-+++ b/source/FORMAT/molFileFactory.C
-@@ -39,7 +39,7 @@ namespace BALL
- try
- {
- string s;
-- if (std::getline(in,s)) ok = true;
-+ if (bool(std::getline(in,s))) ok = true;
- }
- catch (const boost::iostreams::gzip_error& e)
- {
diff --git a/debian/patches/nopsboxit.patch b/debian/patches/nopsboxit.patch
index 06cea8a..e048d34 100644
--- a/debian/patches/nopsboxit.patch
+++ b/debian/patches/nopsboxit.patch
@@ -1,7 +1,5 @@
-Index: ball/doc/TUTORIAL/macros.tex
-===================================================================
---- ball.orig/doc/TUTORIAL/macros.tex
-+++ ball/doc/TUTORIAL/macros.tex
+--- a/doc/TUTORIAL/macros.tex
++++ b/doc/TUTORIAL/macros.tex
@@ -11,8 +11,9 @@
\usepackage{times}
% use postscript fonts
diff --git a/debian/patches/series b/debian/patches/series
index ff239f4..79b5a78 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,13 +1,5 @@
0001-missingSigned.patch
-#0008-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
-#0009-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
-#0010-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch
-0101-cmake-syntax.patch
-0102-fix-boost-compatibility-issue.patch
-0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
nopsboxit.patch
-HelpSipAmbiguity.patch
link_against_x11.patch
findsip.patch
gcc5.diff
-more-gcc5_issues.patch
--
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