include/BALL/DATATYPE/hashGrid.h | 2 1 + 1 - 0 !
source/DATATYPE/hashGrid.C | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 missingsigned

===================================================================

source/TEST/BinaryFingerprintMethods_test.C | 22 11 + 11 - 0 !
1 file changed, 11 insertions(+), 11 deletions(-)

 [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.

cmake/BALLConfigStdStringFeatures.cmake | 12 12 + 0 - 0 !
cmake/config.h.in | 1 1 + 0 - 0 !
include/BALL/DATATYPE/string.h | 2 1 + 1 - 0 !
include/BALL/DATATYPE/string.iC | 2 1 + 1 - 0 !
4 files changed, 15 insertions(+), 2 deletions(-)

 [patch] fix: string failed to compile with newer gcc versions

include/BALL/DOCKING/COMMON/poseClustering.h | 9 9 + 0 - 0 !
source/DOCKING/COMMON/poseClustering.C | 64 64 + 0 - 0 !
2 files changed, 73 insertions(+)

 [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.

doc/TUTORIAL/macros.tex | 5 3 + 2 - 0 !
1 file changed, 3 insertions(+), 2 deletions(-)

 the style psboxit is missing - use fbox as replacement

CMakeLists.txt | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 link against libx11
 Something has changed since Jessie and now we need to explicitely link
 against X11.

cmake/FindSIP.cmake | 28 1 + 27 - 0 !
cmake/FindSIP.py | 3 3 + 0 - 0 !
2 files changed, 4 insertions(+), 27 deletions(-)

 fix sip library detection
 The old algorithm used hard-coded library names and thus could not
 detect our multi-arched name.
 .
 Instead of that, just import sip from Python script and use the
 __file__ property to find the library.

source/APPLICATIONS/UTILITIES/BALLUtilities.cmake | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 drop assign_positions_from_template from build process

source/APPLICATIONS/TOOLS/FingerprintSimilarityClustering.C | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 explicitly use boost::unordered_map, as both
    using namespace std;
and
    using namespace boost;
is present.

source/PYTHON/EXTENSIONS/VIEW/box.sip | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 [patch] fix python bindings for box

source/TEST/Socket_test.C | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 [patch] increased sleeping time in socket_test

The test quite often failed in build slaves because startup time was too short.

include/BALL/COMMON/rtti.h | 4 2 + 2 - 0 !
include/BALL/CONCEPT/composite.h | 4 2 + 2 - 0 !
include/BALL/CONCEPT/object.iC | 4 2 + 2 - 0 !
include/BALL/KERNEL/predicate.h | 2 1 + 1 - 0 !
include/BALL/VIEW/MODELS/standardColorProcessor.h | 4 2 + 2 - 0 !
source/APPLICATIONS/BALLVIEW/demoTutorialDialog.C | 10 5 + 5 - 0 !
source/APPLICATIONS/BALLVIEW/mainframe.C | 2 1 + 1 - 0 !
source/CONCEPT/client.C | 2 1 + 1 - 0 !
source/CONCEPT/molecularInformation.C | 20 10 + 10 - 0 !
source/CONCEPT/moleculeObjectCreator.C | 6 3 + 3 - 0 !
source/FORMAT/MOL2File.C | 8 4 + 4 - 0 !
source/FORMAT/NMRStarFile.C | 8 4 + 4 - 0 !
source/KERNEL/PDBAtom.C | 6 3 + 3 - 0 !
source/KERNEL/atomContainer.C | 2 1 + 1 - 0 !
source/KERNEL/chain.C | 2 1 + 1 - 0 !
source/KERNEL/molecule.C | 2 1 + 1 - 0 !
source/KERNEL/residue.C | 6 3 + 3 - 0 !
source/KERNEL/secondaryStructure.C | 4 2 + 2 - 0 !
source/KERNEL/selector.C | 2 1 + 1 - 0 !
source/KERNEL/standardPredicates.C | 2 1 + 1 - 0 !
source/MOLMEC/AMBER/GAFFTypeProcessor.C | 2 1 + 1 - 0 !
source/NMR/EFShiftProcessor.C | 4 2 + 2 - 0 !
source/NMR/HBondShiftProcessor.C | 4 2 + 2 - 0 !
source/NMR/anisotropyShiftProcessor.C | 2 1 + 1 - 0 !
source/NMR/empiricalHSShiftProcessor.C | 4 2 + 2 - 0 !
source/NMR/haighMallionShiftProcessor.C | 2 1 + 1 - 0 !
source/NMR/johnsonBoveyShiftProcessor.C | 4 2 + 2 - 0 !
source/NMR/randomCoilShiftProcessor.C | 2 1 + 1 - 0 !
source/NMR/shiftModel1D.C | 4 2 + 2 - 0 !
source/NMR/shiftModel2D.C | 4 2 + 2 - 0 !
source/PYTHON/EXTENSIONS/BALLPyMacros.h | 4 2 + 2 - 0 !
source/STRUCTURE/HBondProcessor.C | 6 3 + 3 - 0 !
source/STRUCTURE/assignBondOrderProcessor.C | 6 3 + 3 - 0 !
source/STRUCTURE/bindingPocketProcessor.C | 6 3 + 3 - 0 !
source/STRUCTURE/defaultProcessors.C | 4 2 + 2 - 0 !
source/STRUCTURE/disulfidBondProcessor.C | 8 4 + 4 - 0 !
source/STRUCTURE/geometricProperties.C | 2 1 + 1 - 0 !
source/STRUCTURE/reconstructFragmentProcessor.C | 2 1 + 1 - 0 !
source/STRUCTURE/secondaryStructureProcessor.C | 4 2 + 2 - 0 !
source/STRUCTURE/sideChainPlacementProcessor.C | 12 6 + 6 - 0 !
source/STRUCTURE/structureMapper.C | 4 2 + 2 - 0 !
source/TEST/AddCartoonModel_test.C | 4 2 + 2 - 0 !
source/TEST/AtomContainer_test.C | 2 1 + 1 - 0 !
source/TEST/Atom_test.C | 4 2 + 2 - 0 !
source/TEST/Bond_test.C | 2 1 + 1 - 0 !
source/TEST/Chain_test.C | 2 1 + 1 - 0 !
source/TEST/Composite_test4.C | 4 2 + 2 - 0 !
source/TEST/Fragment_test.C | 2 1 + 1 - 0 !
source/TEST/Molecule_test.C | 2 1 + 1 - 0 !
source/TEST/NamedProperty_test.C | 20 10 + 10 - 0 !
source/TEST/NucleicAcid_test.C | 2 1 + 1 - 0 !
source/TEST/Nucleotide_test.C | 2 1 + 1 - 0 !
source/TEST/PDBAtom_test.C | 4 2 + 2 - 0 !
source/TEST/PersistenceManager_test.C | 2 1 + 1 - 0 !
source/TEST/Protein_test.C | 2 1 + 1 - 0 !
source/TEST/RTTI_test.C | 52 26 + 26 - 0 !
source/TEST/Residue_test.C | 2 1 + 1 - 0 !
source/TEST/SecondaryStructure_test.C | 2 1 + 1 - 0 !
source/TEST/System_test.C | 2 1 + 1 - 0 !
source/TEST/TextPersistenceManager_test.C | 2 1 + 1 - 0 !
source/TEST/Vector2_test.C | 4 2 + 2 - 0 !
source/TEST/XDRPersistenceManager_test.C | 12 6 + 6 - 0 !
source/TUTORIAL/bounding_box.C | 4 2 + 2 - 0 !
source/VIEW/DIALOGS/atomOverview.C | 4 2 + 2 - 0 !
source/VIEW/DIALOGS/bondProperties.C | 8 4 + 4 - 0 !
source/VIEW/DIALOGS/coloringSettingsDialog.C | 52 26 + 26 - 0 !
source/VIEW/DIALOGS/compositeProperties.C | 14 7 + 7 - 0 !
source/VIEW/DIALOGS/displayProperties.C | 12 6 + 6 - 0 !
source/VIEW/DIALOGS/exportGeometryDialog.C | 12 6 + 6 - 0 !
source/VIEW/DIALOGS/labelDialog.C | 2 1 + 1 - 0 !
source/VIEW/DIALOGS/lightSettings.C | 2 1 + 1 - 0 !
source/VIEW/DIALOGS/modelSettingsDialog.C | 30 15 + 15 - 0 !
source/VIEW/DIALOGS/modifyRepresentationDialog.C | 14 7 + 7 - 0 !
source/VIEW/DIALOGS/molecularFileDialog.C | 4 2 + 2 - 0 !
source/VIEW/DIALOGS/preferences.C | 2 1 + 1 - 0 !
source/VIEW/KERNEL/MODES/editMode.C | 10 5 + 5 - 0 !
source/VIEW/KERNEL/mainControl.C | 20 10 + 10 - 0 !
source/VIEW/KERNEL/modularWidget.C | 4 2 + 2 - 0 !
source/VIEW/KERNEL/preferencesEntry.C | 58 29 + 29 - 0 !
source/VIEW/KERNEL/representation.C | 10 5 + 5 - 0 !
source/VIEW/MODELS/HBondModel.C | 2 1 + 1 - 0 !
source/VIEW/MODELS/colorProcessor.C | 8 4 + 4 - 0 !
source/VIEW/MODELS/labelModel.C | 6 3 + 3 - 0 !
source/VIEW/MODELS/lineModel.C | 2 1 + 1 - 0 !
source/VIEW/MODELS/standardColorProcessor.C | 34 17 + 17 - 0 !
source/VIEW/MODELS/surfaceModel.C | 4 2 + 2 - 0 !
source/VIEW/MODELS/vanDerWaalsModel.C | 2 1 + 1 - 0 !
source/VIEW/RENDERING/RENDERERS/POVRenderer.C | 10 5 + 5 - 0 !
source/VIEW/RENDERING/RENDERERS/XML3DRenderer.C | 8 4 + 4 - 0 !
source/VIEW/RENDERING/RENDERERS/renderer.C | 28 14 + 14 - 0 !
source/VIEW/RENDERING/RENDERERS/rtfactRenderer.C | 16 8 + 8 - 0 !
source/VIEW/RENDERING/RENDERERS/tilingRenderer.C | 2 1 + 1 - 0 !
source/VIEW/RENDERING/renderSetup.C | 26 13 + 13 - 0 !
source/VIEW/WIDGETS/datasetControl.C | 2 1 + 1 - 0 !
source/VIEW/WIDGETS/dockingController.C | 4 2 + 2 - 0 !
source/VIEW/WIDGETS/genericControl.C | 2 1 + 1 - 0 !
source/VIEW/WIDGETS/geometricControl.C | 10 5 + 5 - 0 !
source/VIEW/WIDGETS/helpViewer.C | 6 3 + 3 - 0 !
source/VIEW/WIDGETS/molecularControl.C | 50 25 + 25 - 0 !
source/VIEW/WIDGETS/molecularStructure.C | 18 9 + 9 - 0 !
source/VIEW/WIDGETS/scene.C | 30 15 + 15 - 0 !
source/VIEW/WIDGETS/testFramework.C | 10 5 + 5 - 0 !
102 files changed, 431 insertions(+), 431 deletions(-)

 [patch] modified rtti function iskindof to take a pointer argument.

On OSX 10.10 and later tests failed because a reference to
a deleted object was handed over to isKindOf. Taking the pointer
of that object led to a segmentation fault.
To prevent passing references to deleted objects, the reference
argument to be checked is replaced by the pointer of that object directly.

source/TEST/PoseClustering_test.C | 51 45 + 6 - 0 !
1 file changed, 45 insertions(+), 6 deletions(-)

 poseclustering_test: replace file comparision with deserialisation

source/TEST/XDRPersistenceManager_test.C | 16 15 + 1 - 0 !
1 file changed, 15 insertions(+), 1 deletion(-)

 [patch] fix xdrpersistencemanager_test

The test serialised a default constructed Bond, which was subsequently
deserialised. However, this means the Bond was serialised in an invalid
state which could trigger crashes upon deserialisation.

To fix the broken test just add two Atoms to the Bond.

Probably we should also make sure, that no objects in an invalid state
can be serialised...

source/TEST/cmake/BALLTestExecutables.cmake | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 the amberff_test fails unreproducibly, so we disabled it
temporarily to resolve FTBFS.
.
The problem is known upstream, see
https://github.com/BALL-Project/ball/issues/584