[med-svn] [ball] 01/01: Rework patches for sid
Danny Edel
dannyedel-guest at moszumanska.debian.org
Tue May 10 15:17:24 UTC 2016
This is an automated email from the git hooks/post-receive script.
dannyedel-guest pushed a commit to branch fix-debian-bug-777791
in repository ball.
commit 2d32f6aede2be0a8a7a88a0aee3f15a62f3aafb8
Author: Danny Edel <mail at danny-edel.de>
Date: Sun Apr 10 11:57:18 2016 +0200
Rework patches for sid
This fixes FTBFS. Also, enable tests in d/rules.
---
debian/patches/0001-missingSigned.patch | 32 ------
.../adjust-PoseClustering_Test-boost-1.58.patch | 13 +++
.../disable-assign-positions-from-template.patch | 10 ++
.../fix-FingerprintSimilarityClustering.patch | 54 +++++++++++
debian/patches/fix-PoseClustering_Test.patch | 17 ++++
...pilation-of-BinaryFingerprintMethods_test.patch | 81 ++++++++++++++++
.../fix-poseClustering-with-boost-1.60.patch | 108 +++++++++++++++++++++
debian/patches/fix-string-gcc5.patch | 73 ++++++++++++++
debian/patches/gcc5.diff | 18 ----
debian/patches/series | 9 +-
debian/rules | 12 ++-
11 files changed, 373 insertions(+), 54 deletions(-)
diff --git a/debian/patches/0001-missingSigned.patch b/debian/patches/0001-missingSigned.patch
deleted file mode 100644
index 6801495..0000000
--- a/debian/patches/0001-missingSigned.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From: Andreas Hildebrandt <ahildebr at uni-mainz.de>
-Date: Tue, 14 Aug 2012 17:14:31 +0200
-Subject: missingSigned
-
-===================================================================
----
- include/BALL/DATATYPE/hashGrid.h | 2 +-
- source/DATATYPE/hashGrid.C | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
---- a/include/BALL/DATATYPE/hashGrid.h
-+++ b/include/BALL/DATATYPE/hashGrid.h
-@@ -37,7 +37,7 @@ namespace BALL
- {
- namespace __private
- {
-- extern const char BALL_EXPORT neighbour_table_[27][3];
-+ extern const signed char BALL_EXPORT neighbour_table_[27][3];
- }
-
- template <typename Item> class HashGrid3;
---- a/source/DATATYPE/hashGrid.C
-+++ b/source/DATATYPE/hashGrid.C
-@@ -9,7 +9,7 @@ namespace BALL
- {
- namespace __private
- {
-- const char neighbour_table_[27][3] =
-+ const signed char neighbour_table_[27][3] =
- {
- { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 },
- { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 },
diff --git a/debian/patches/adjust-PoseClustering_Test-boost-1.58.patch b/debian/patches/adjust-PoseClustering_Test-boost-1.58.patch
new file mode 100644
index 0000000..d4cd089
--- /dev/null
+++ b/debian/patches/adjust-PoseClustering_Test-boost-1.58.patch
@@ -0,0 +1,13 @@
+Subject: Adjust boost::archive for boost-1.58 version
+Author: Danny Edel <debian at danny-edel.de>
+
+The archive format of boost-1.58 (currently in sid) and the
+version 1.60, which the upstream patch is for, only differs
+in the "version" field.
+
+Delete this patch once 1.60 is in sid.
+--- a/source/TEST/data/PoseClustering_wardtree.dat
++++ b/source/TEST/data/PoseClustering_wardtree.dat
+@@ -1 +1 @@
+-22 serialization::archive 13 0 0 15 14 0 0 1 0 0 1 0.000000000e+00 1 0 1 1 0.000000000e+00 1 0 2 1 0.000000000e+00 1 0 3 1 0.000000000e+00 1 0 4 1 0.000000000e+00 1 0 5 1 0.000000000e+00 1 0 6 1 0.000000000e+00 1 0 7 1 0.000000000e+00 0 0 2 2.930124538e-05 0 0 3 1.017511487e+00 0 0 4 2.349177122e+00 0 0 2 9.453108311e-01 0 0 2 1.095688367e-05 0 0 4 5.062472916e+01 0 0 8 5.839497375e+01 8 1 0 0 8 0 9 3 9 8 10 2 10 9 11 7 11 6 12 4 12 5 13 12 13 11 14 13 14 10 14
++22 serialization::archive 12 0 0 15 14 0 0 1 0 0 1 0.000000000e+00 1 0 1 1 0.000000000e+00 1 0 2 1 0.000000000e+00 1 0 3 1 0.000000000e+00 1 0 4 1 0.000000000e+00 1 0 5 1 0.000000000e+00 1 0 6 1 0.000000000e+00 1 0 7 1 0.000000000e+00 0 0 2 2.930124538e-05 0 0 3 1.017511487e+00 0 0 4 2.349177122e+00 0 0 2 9.453108311e-01 0 0 2 1.095688367e-05 0 0 4 5.062472916e+01 0 0 8 5.839497375e+01 8 1 0 0 8 0 9 3 9 8 10 2 10 9 11 7 11 6 12 4 12 5 13 12 13 11 14 13 14 10 14
diff --git a/debian/patches/disable-assign-positions-from-template.patch b/debian/patches/disable-assign-positions-from-template.patch
new file mode 100644
index 0000000..262e61a
--- /dev/null
+++ b/debian/patches/disable-assign-positions-from-template.patch
@@ -0,0 +1,10 @@
+--- a/source/APPLICATIONS/UTILITIES/BALLUtilities.cmake
++++ b/source/APPLICATIONS/UTILITIES/BALLUtilities.cmake
+@@ -8,7 +8,6 @@
+ assign_charges_from_rules
+ assign_radii_from_rules
+ assign_typenames_from_rules
+- assign_positions_from_template
+ atomtyper
+ calculate_RMSD
+ clip_protein_around_ligand
diff --git a/debian/patches/fix-FingerprintSimilarityClustering.patch b/debian/patches/fix-FingerprintSimilarityClustering.patch
new file mode 100644
index 0000000..1350aca
--- /dev/null
+++ b/debian/patches/fix-FingerprintSimilarityClustering.patch
@@ -0,0 +1,54 @@
+From 8ff1d1ba6b1963a9fa839ce28fb2a54139920648 Mon Sep 17 00:00:00 2001
+From: Daniel Stoeckel <dstoeckel at bioinf.uni-sb.de>
+Date: Thu, 2 Apr 2015 21:37:21 +0200
+Subject: [PATCH] FingerPrintSim: Fix build under clang 3.6
+
+Explicitly use boost::unordered_map, as both
+ using namespace std;
+and
+ using namespace boost;
+is present.
+---
+ source/APPLICATIONS/TOOLS/FingerprintSimilarityClustering.C | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/source/APPLICATIONS/TOOLS/FingerprintSimilarityClustering.C b/source/APPLICATIONS/TOOLS/FingerprintSimilarityClustering.C
+index 05bcd01..114fc68 100644
+--- a/source/APPLICATIONS/TOOLS/FingerprintSimilarityClustering.C
++++ b/source/APPLICATIONS/TOOLS/FingerprintSimilarityClustering.C
+@@ -233,7 +233,7 @@ void uniqueFingerprintsFilter(vector<vector<unsigned short> >& mol_features, con
+ }
+
+
+-void readMoleculeIdentifiers(unordered_map<unsigned int, set<String> >& mol_identifiers)
++void readMoleculeIdentifiers(boost::unordered_map<unsigned int, set<String> >& mol_identifiers)
+ {
+ File in("FFC_1_fingerprint_duplicates.txt", File::MODE_IN);
+
+@@ -275,7 +275,7 @@ void writeConnectedComponents(const vector<unsigned int>& m_indices,
+ out << "# CMPD_IDS: Comma separated list of original compound id(s) which map onto this SRC_NODE_ID." << endl;
+ out << "SRC_NODE_ID DST_NODE_INDEX TANIMOTO_SIM CMPD_IDS" << endl;
+
+- unordered_map<unsigned int, set<String> > mol_identifiers;
++ boost::unordered_map<unsigned int, set<String> > mol_identifiers;
+ readMoleculeIdentifiers(mol_identifiers);
+
+ String cids;
+@@ -321,7 +321,7 @@ void writeConnectedComponents(const vector<unsigned int>& m_indices,
+ out << "# CMPD_IDS: Comma separated list of original compound id(s) which map onto this SRC_NODE_ID." << endl;
+ out << "SRC_NODE_INDEX DST_NODE_INDEX TANIMOTO_SIM CMPD_IDS" << endl;
+
+- unordered_map<unsigned int, set<String> > mol_identifiers;
++ boost::unordered_map<unsigned int, set<String> > mol_identifiers;
+ readMoleculeIdentifiers(mol_identifiers);
+
+ set<String>::iterator it;
+@@ -888,7 +888,7 @@ $ FingerprintSimilarityClustering -t target.sdf -fp_tag FPRINT -f 1 -id_tag NAME
+ Log.level(10) << "++ STEP 5: Remap fingerprint duplicates" << endl;
+
+
+- unordered_map<unsigned int, set<String> > identifiers;
++ boost::unordered_map<unsigned int, set<String> > identifiers;
+ readMoleculeIdentifiers(identifiers);
+
+ // Store final cluster information
diff --git a/debian/patches/fix-PoseClustering_Test.patch b/debian/patches/fix-PoseClustering_Test.patch
new file mode 100644
index 0000000..bc6e323
--- /dev/null
+++ b/debian/patches/fix-PoseClustering_Test.patch
@@ -0,0 +1,17 @@
+From 7bb01662db40ede50ae5472cc54cc3324aa99778 Mon Sep 17 00:00:00 2001
+From: Oliver Kohlbacher <oliver.kohlbacher at uni-tuebingen.de>
+Date: Fri, 11 Dec 2015 12:09:13 +0100
+Subject: [PATCH] Fixed PoseClustering test to account for changes in boost
+ serialization of floating point numbers.
+
+---
+ source/TEST/data/PoseClustering_wardtree.dat | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/source/TEST/data/PoseClustering_wardtree.dat b/source/TEST/data/PoseClustering_wardtree.dat
+index bac5592..064a09e 100644
+--- a/source/TEST/data/PoseClustering_wardtree.dat
++++ b/source/TEST/data/PoseClustering_wardtree.dat
+@@ -1 +1 @@
+-22 serialization::archive 10 0 0 15 14 0 0 1 0 0 1 0 1 0 1 1 0 1 0 2 1 0 1 0 3 1 0 1 0 4 1 0 1 0 5 1 0 1 0 6 1 0 1 0 7 1 0 0 0 2 2.9301245e-05 0 0 3 1.0175115 0 0 4 2.3491771 0 0 2 0.94531083 0 0 2 1.0956884e-05 0 0 4 50.624729 0 0 8 58.394974 8 1 0 0 8 0 9 3 9 8 10 2 10 9 11 7 11 6 12 4 12 5 13 12 13 11 14 13 14 10 14
++22 serialization::archive 13 0 0 15 14 0 0 1 0 0 1 0.000000000e+00 1 0 1 1 0.000000000e+00 1 0 2 1 0.000000000e+00 1 0 3 1 0.000000000e+00 1 0 4 1 0.000000000e+00 1 0 5 1 0.000000000e+00 1 0 6 1 0.000000000e+00 1 0 7 1 0.000000000e+00 0 0 2 2.930124538e-05 0 0 3 1.017511487e+00 0 0 4 2.349177122e+00 0 0 2 9.453108311e-01 0 0 2 1.095688367e-05 0 0 4 5.062472916e+01 0 0 8 5.839497375e+01 8 1 0 0 8 0 9 3 9 8 10 2 10 9 11 7 11 6 12 4 12 5 13 12 13 11 14 13 14 10 14
diff --git a/debian/patches/fix-compilation-of-BinaryFingerprintMethods_test.patch b/debian/patches/fix-compilation-of-BinaryFingerprintMethods_test.patch
new file mode 100644
index 0000000..0a2ee38
--- /dev/null
+++ b/debian/patches/fix-compilation-of-BinaryFingerprintMethods_test.patch
@@ -0,0 +1,81 @@
+From 3170b38ae1adac22c66a2b56df2456623be8ff58 Mon Sep 17 00:00:00 2001
+From: Daniel Stoeckel <dstoeckel at bioinf.uni-sb.de>
+Date: Fri, 1 May 2015 16:16:18 +0200
+Subject: [PATCH] Fix compilation of BinaryFingerprintMethods_test under gcc
+ 4.9/clang 3.6
+
+Use boost::unordered_map to disambiguate between std:: and boost::
+versions. Hopefully we will be able to rely on std:: in the not to distant
+future.
+---
+ source/TEST/BinaryFingerprintMethods_test.C | 22 +++++++++++-----------
+ 1 file changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/source/TEST/BinaryFingerprintMethods_test.C b/source/TEST/BinaryFingerprintMethods_test.C
+index 1f0bb53..e776f12 100644
+--- a/source/TEST/BinaryFingerprintMethods_test.C
++++ b/source/TEST/BinaryFingerprintMethods_test.C
+@@ -331,7 +331,7 @@ CHECK(cutoffSearch())
+
+ float sim;
+ String key;
+- unordered_map<string, float> results;
++ boost::unordered_map<string, float> results;
+ LineBasedFile lbf(BALL_TEST_DATA_PATH(BinaryFingerprintMethods_SimSearchResults.csv), File::MODE_IN);
+ while(lbf.readLine())
+ {
+@@ -347,8 +347,8 @@ CHECK(cutoffSearch())
+
+ float cutoff = 0.0;
+ String outfile_name = "_BALL_CUTOFF_SEARCH_TEST.tmp";
+- unordered_map<string, float>::iterator it;
+- unordered_map<string, float> results_subset;
++ boost::unordered_map<string, float>::iterator it;
++ boost::unordered_map<string, float> results_subset;
+
+ while (cutoff <= 1.0)
+ {
+@@ -391,9 +391,9 @@ CHECK(connectedComponents(store_nns=true))
+ unsigned int id, min_id, int_cutoff;
+ map<string, float> tmp_cc;
+ map<string, float>::iterator cc_it;
+- unordered_map<unsigned int, map<string, float> > ccs_results;
+- unordered_map<unsigned int, map<string, float> >::iterator ccs_it;
+- unordered_map<unsigned int, unordered_map<unsigned int, map<string, float> > > all_ccs;
++ boost::unordered_map<unsigned int, map<string, float> > ccs_results;
++ boost::unordered_map<unsigned int, map<string, float> >::iterator ccs_it;
++ boost::unordered_map<unsigned int, boost::unordered_map<unsigned int, map<string, float> > > all_ccs;
+
+ LineBasedFile lbf(BALL_TEST_DATA_PATH(BinaryFingerprintMethods_ConnectedComponents.csv), File::MODE_IN);
+ while(lbf.readLine())
+@@ -409,7 +409,7 @@ CHECK(connectedComponents(store_nns=true))
+ }
+
+ int_cutoff = lbf.getField(1).toUnsignedInt();
+- all_ccs[int_cutoff] = unordered_map<unsigned int, map<string, float> >();
++ all_ccs[int_cutoff] = boost::unordered_map<unsigned int, map<string, float> >();
+
+ continue;
+ }
+@@ -539,9 +539,9 @@ CHECK(connectedComponents(store_nns=false))
+ unsigned int id, int_cutoff;
+ map<string, float> tmp_cc;
+ map<string, float>::iterator cc_it;
+- unordered_map<unsigned int, map<string, float> > ccs_results;
+- unordered_map<unsigned int, map<string, float> >::iterator ccs_it;
+- unordered_map<unsigned int, unordered_map<unsigned int, map<string, float> > > all_ccs;
++ boost::unordered_map<unsigned int, map<string, float> > ccs_results;
++ boost::unordered_map<unsigned int, map<string, float> >::iterator ccs_it;
++ boost::unordered_map<unsigned int, boost::unordered_map<unsigned int, map<string, float> > > all_ccs;
+
+ LineBasedFile lbf(BALL_TEST_DATA_PATH(BinaryFingerprintMethods_ConnectedComponents.csv), File::MODE_IN);
+ while(lbf.readLine())
+@@ -557,7 +557,7 @@ CHECK(connectedComponents(store_nns=false))
+ }
+
+ int_cutoff = lbf.getField(1).toUnsignedInt();
+- all_ccs[int_cutoff] = unordered_map<unsigned int, map<string, float> >();
++ all_ccs[int_cutoff] = boost::unordered_map<unsigned int, map<string, float> >();
+
+ continue;
+ }
diff --git a/debian/patches/fix-poseClustering-with-boost-1.60.patch b/debian/patches/fix-poseClustering-with-boost-1.60.patch
new file mode 100644
index 0000000..5613351
--- /dev/null
+++ b/debian/patches/fix-poseClustering-with-boost-1.60.patch
@@ -0,0 +1,108 @@
+From 029fd2b9a0365e5926bcb4e2c227533efb356423 Mon Sep 17 00:00:00 2001
+From: Daniel Stoeckel <dstoeckel at bioinf.uni-sb.de>
+Date: Thu, 18 Feb 2016 22:23:21 +0100
+Subject: [PATCH] Fix building PoseClustering with Boost versions >= 1.60
+
+A VertexProperty must be Copy Constructible, Assignable, and
+Default Constructible. Additionally in newer Boost versions also
+Move Constructible and Assignable are required.
+---
+ include/BALL/DOCKING/COMMON/poseClustering.h | 9 ++++
+ source/DOCKING/COMMON/poseClustering.C | 64 ++++++++++++++++++++++++++++
+ 2 files changed, 73 insertions(+)
+
+diff --git a/include/BALL/DOCKING/COMMON/poseClustering.h b/include/BALL/DOCKING/COMMON/poseClustering.h
+index 5ffce0b..9d1a7ca 100644
+--- a/include/BALL/DOCKING/COMMON/poseClustering.h
++++ b/include/BALL/DOCKING/COMMON/poseClustering.h
+@@ -218,6 +218,15 @@ namespace BALL
+ class BALL_EXPORT ClusterProperties
+ {
+ public:
++ ClusterProperties();
++ ClusterProperties(const ClusterProperties&);
++
++ ClusterProperties& operator=(const ClusterProperties&);
++
++#ifdef BALL_HAS_RVALUE_REFERENCES
++ ClusterProperties(ClusterProperties&&) noexcept;
++ ClusterProperties& operator=(ClusterProperties&&) noexcept;
++#endif
+ /** Serialization method
+ */
+ template <class Archive>
+diff --git a/source/DOCKING/COMMON/poseClustering.C b/source/DOCKING/COMMON/poseClustering.C
+index bb2ae7d..1c25888 100644
+--- a/source/DOCKING/COMMON/poseClustering.C
++++ b/source/DOCKING/COMMON/poseClustering.C
+@@ -1717,6 +1717,70 @@ std::cout << current_level << " " << num_poses << " " << percentage << std::endl
+ }
+ #endif
+
++ PoseClustering::ClusterProperties::ClusterProperties()
++ : size(0),
++ merged_at(0.0f)
++#ifdef POSECLUSTERING_DEBUG
++ , current_cluster_id(0.0f)
++#endif
++ {
++
++ }
++
++ PoseClustering::ClusterProperties::ClusterProperties(const PoseClustering::ClusterProperties& o)
++ : poses(o.poses),
++ size(o.size),
++ center(o.center),
++ merged_at(o.merged_at)
++#ifdef POSECLUSTERING_DEBUG
++ , current_cluster_id(o.current_cluster_id)
++#endif
++ {
++ }
++
++ PoseClustering::ClusterProperties&
++ PoseClustering::ClusterProperties::operator=(const PoseClustering::ClusterProperties& o)
++ {
++ if(&o != this)
++ {
++ poses = o.poses;
++ size = o.size;
++ center = o.center;
++ merged_at = o.merged_at;
++#ifdef POSECLUSTERING_DEBUG
++ current_cluster_id = o.current_cluster_id;
++#endif
++ }
++
++ return *this;
++ }
++
++#ifdef BALL_HAS_RVALUE_REFERENCES
++ PoseClustering::ClusterProperties::ClusterProperties(ClusterProperties&& o) noexcept
++ : poses(std::move(o.poses)),
++ size(o.size),
++ center(std::move(o.center)),
++ merged_at(o.merged_at)
++#ifdef POSECLUSTERING_DEBUG
++ , current_cluster_id(o.current_cluster_id)
++#endif
++ {
++ }
++
++ PoseClustering::ClusterProperties&
++ PoseClustering::ClusterProperties::operator=(ClusterProperties&& o) noexcept
++ {
++ poses = std::move(o.poses);
++ size = o.size;
++ center = std::move(o.center);
++ merged_at = o.merged_at;
++#ifdef POSECLUSTERING_DEBUG
++ current_cluster_id = o.current_cluster_id;
++#endif
++ return *this;
++ }
++#endif
++
+ template <class Archive>
+ void PoseClustering::ClusterProperties::serialize(Archive& ar, const unsigned int /*version*/)
+ {
diff --git a/debian/patches/fix-string-gcc5.patch b/debian/patches/fix-string-gcc5.patch
new file mode 100644
index 0000000..8d68299
--- /dev/null
+++ b/debian/patches/fix-string-gcc5.patch
@@ -0,0 +1,73 @@
+From b3679aa7e996962623772daa5f9db2d4a7d0d581 Mon Sep 17 00:00:00 2001
+From: Thomas Kemmer <thomas at binaryden.de>
+Date: Fri, 11 Dec 2015 16:51:39 +0100
+Subject: [PATCH] Fix: String failed to compile with newer GCC versions
+
+---
+ cmake/BALLConfigStdStringFeatures.cmake | 12 ++++++++++++
+ cmake/config.h.in | 1 +
+ include/BALL/DATATYPE/string.h | 2 +-
+ include/BALL/DATATYPE/string.iC | 2 +-
+ 4 files changed, 15 insertions(+), 2 deletions(-)
+
+diff --git a/cmake/BALLConfigStdStringFeatures.cmake b/cmake/BALLConfigStdStringFeatures.cmake
+index 08b1207..12bfaf2 100644
+--- a/cmake/BALLConfigStdStringFeatures.cmake
++++ b/cmake/BALLConfigStdStringFeatures.cmake
+@@ -26,6 +26,18 @@ CHECK_CXX_SOURCE_COMPILES(
+ int main(int, char**)
+ {
+ std::string s;
++ std::string::const_iterator c_it = s.cbegin();
++ std::string::iterator result = s.insert(c_it, {'a', 'b'});
++
++ return 0;
++ }" BALL_HAS_STD_STRING_CONST_ITERATOR_INITLIST_INSERT
++)
++
++CHECK_CXX_SOURCE_COMPILES(
++ "#include <string>
++ int main(int, char**)
++ {
++ std::string s;
+ s.shrink_to_fit();
+
+ return 0;
+diff --git a/cmake/config.h.in b/cmake/config.h.in
+index 6742032..51768a7 100755
+--- a/cmake/config.h.in
++++ b/cmake/config.h.in
+@@ -229,6 +229,7 @@
+
+ // Defines whether the c++ std lib implementation supports const_iterators in insert, replace, ...
+ #cmakedefine BALL_HAS_STD_STRING_CONST_ITERATOR_FUNCTIONS
++#cmakedefine BALL_HAS_STD_STRING_CONST_ITERATOR_INITLIST_INSERT
+
+ // Defines whether the c++ std lib implementation supports shrink_to_fit in string
+ #cmakedefine BALL_HAS_STD_STRING_SHRINK_TO_FIT
+diff --git a/include/BALL/DATATYPE/string.h b/include/BALL/DATATYPE/string.h
+index c6a8618..51135e6 100644
+--- a/include/BALL/DATATYPE/string.h
++++ b/include/BALL/DATATYPE/string.h
+@@ -1219,7 +1219,7 @@ namespace BALL
+ ///
+ template <class InputIterator>
+ iterator insert(iterator p, InputIterator first, InputIterator last);
+-#if defined(BALL_HAS_INITIALIZER_LISTS) && defined(BALL_HAS_STD_STRING_CONST_ITERATOR_FUNCTIONS)
++#if defined(BALL_HAS_INITIALIZER_LISTS) && defined(BALL_HAS_STD_STRING_CONST_ITERATOR_INITLIST_INSERT)
+ ///
+ String& insert(const_iterator p, std::initializer_list<char> li);
+ #endif
+diff --git a/include/BALL/DATATYPE/string.iC b/include/BALL/DATATYPE/string.iC
+index 954d15b..f0e9b3c 100644
+--- a/include/BALL/DATATYPE/string.iC
++++ b/include/BALL/DATATYPE/string.iC
+@@ -1372,7 +1372,7 @@ String::iterator String::insert(iterator p, InputIterator first, InputIterator l
+ return str_.insert(p, first, last);
+ }
+
+-#if defined(BALL_HAS_INITIALIZER_LISTS) && defined(BALL_HAS_STD_STRING_CONST_ITERATOR_FUNCTIONS)
++#if defined(BALL_HAS_INITIALIZER_LISTS) && defined(BALL_HAS_STD_STRING_CONST_ITERATOR_INITLIST_INSERT)
+ BALL_INLINE
+ String& String::insert(const_iterator p, std::initializer_list<char> li)
+ {
diff --git a/debian/patches/gcc5.diff b/debian/patches/gcc5.diff
deleted file mode 100644
index b3eabe6..0000000
--- a/debian/patches/gcc5.diff
+++ /dev/null
@@ -1,18 +0,0 @@
-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
-@@ -47,6 +47,9 @@ namespace BALL
- {
- // forward declaration
- class Substring;
-+ class String;
-+ BALL_EXPORT
-+ std::istream& getline(std::istream& s, String& string, char delimiter = '\n');
-
- /** \defgroup String String
- An improved version of STL string.
diff --git a/debian/patches/series b/debian/patches/series
index 79b5a78..0a5cff1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,10 @@
-0001-missingSigned.patch
+fix-compilation-of-BinaryFingerprintMethods_test.patch
+fix-string-gcc5.patch
+fix-poseClustering-with-boost-1.60.patch
nopsboxit.patch
link_against_x11.patch
findsip.patch
-gcc5.diff
+fix-PoseClustering_Test.patch
+adjust-PoseClustering_Test-boost-1.58.patch
+disable-assign-positions-from-template.patch
+fix-FingerprintSimilarityClustering.patch
diff --git a/debian/rules b/debian/rules
index da751c8..9753f4a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,13 +17,21 @@ PYTHON_VERSION=2.6
PYTHON_SITE_PATH=$(shell python -c "import distutils.sysconfig; print distutils.sysconfig.get_python_lib(0,0)[4:];")
%:
- dh $@ --buildsystem=cmake
+ dh $@ --buildsystem=cmake --builddirectory=build
override_dh_auto_configure:
mkdir -p build
cd build && LDFLAGS="$(LDFLAGS)" CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" \
cmake .. -DCMAKE_SOURCE_DIR=$(CURDIR) -DCMAKE_INSTALL_PREFIX=./usr -DBALL_PATH=/usr -DBALL_DATA_PATH=/usr/share/BALL-$(SOVERSION)/data
+# Set BALL_DATA_PATH so that test scripts find it
+export BALL_DATA_PATH=$(CURDIR)/data
+# Make sure HOME exists (for Directory_test)
+export HOME=/tmp
+
+# Disable test for arch-indep builds
+override_dh_auto_test-indep:
+
override_dh_auto_build-arch:
## Fix upstream issue of missing UI files
uic-qt4 source/VIEW/DIALOGS/assignBondOrderConfigurationDialog.ui > include/BALL/VIEW/UIC/ui_assignBondOrderConfigurationDialog.h
@@ -37,7 +45,7 @@ override_dh_auto_build-arch:
## Somehow the code
## ADD_BALL_UIFILES("VIEW/DIALOGS" "${UI_LIST}")
## needs to be called before the build code below can be started
- make -C build BALL VIEW BALLView install
+ make -C build BALL VIEW BALLView build_tests install
override_dh_auto_build-indep:
make -C build doc doc_tutorial install
--
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