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 <[email protected]> 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 <[email protected]> -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 <[email protected]> + +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> -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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ball.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
