Package: adun.app / 0.81-13

Metadata

Package Version Patches format
adun.app 0.81-13 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
05_no plugin script.patch | (download)

GNUmakefile.postamble | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 this patch is specific to debian.


15_link properly.patch | (download)

Kernel/AdunKernel/GNUmakefile | 2 1 + 1 - 0 !
Kernel/Base/GNUmakefile.preamble | 3 2 + 1 - 0 !
Kernel/GNUmakefile | 2 1 + 1 - 0 !
MolTalk/GNUmakefile.preamble | 2 1 + 1 - 0 !
UL/AdunServer/GNUmakefile | 2 1 + 1 - 0 !
UL/AdunServer/GNUmakefile.preamble | 4 1 + 3 - 0 !
UL/GNUmakefile | 2 1 + 1 - 0 !
UL/ULFramework/GNUmakefile | 2 1 + 1 - 0 !
UL/XMLLib/GNUmakefile.preamble | 3 2 + 1 - 0 !
9 files changed, 11 insertions(+), 11 deletions(-)

---
20_paths.patch | (download)

UL/AdunServer/main.m | 2 1 + 1 - 0 !
UL/ViewController.m | 5 2 + 3 - 0 !
2 files changed, 3 insertions(+), 4 deletions(-)

 this patch contains x-terminal-emulator, which is specific to debian.
 Adjust some essential paths.


fix implicit pointer.patch | (download)

Kernel/AdunKernel/Framework/AdunCellListHandler.m | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 aduncelllisthandler.m was missing a include for the function
 AdCreateError, resulting in a forced-FTBFS on 64 bit archs. See
 http://wiki.debian.org/ImplicitPointerConversions for more information.
gcc warnings.patch | (download)

Kernel/AdunKernel/CoreAdditions/AdunController.m | 1 0 + 1 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunFileSystemSimulationStorage.m | 6 2 + 4 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunIOManager.m | 11 3 + 8 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunSimulationData.m | 6 2 + 4 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunTemplateProcessor.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunTrajectory.m | 13 3 + 10 - 0 !
Kernel/AdunKernel/Framework/AdFrameworkFunctions.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdGBSWTermBornRadiiMethods.m | 9 3 + 6 - 0 !
Kernel/AdunKernel/Framework/AdGBSWTermIntegrationMethods.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/Framework/AdIndexSetConversions.m | 3 2 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunBerendsenThermostat.m | 4 1 + 3 - 0 !
Kernel/AdunKernel/Framework/AdunCellListHandler.m | 3 1 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunCharmmForceField.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunConfigurationGenerator.m | 6 6 + 0 - 0 !
Kernel/AdunKernel/Framework/AdunContainerDataSource.m | 9 3 + 6 - 0 !
Kernel/AdunKernel/Framework/AdunDataMatrix.m | 50 26 + 24 - 0 !
Kernel/AdunKernel/Framework/AdunDataSource.m | 28 13 + 15 - 0 !
Kernel/AdunKernel/Framework/AdunElementSelection.m | 10 3 + 7 - 0 !
Kernel/AdunKernel/Framework/AdunForceField.m | 9 9 + 0 - 0 !
Kernel/AdunKernel/Framework/AdunForceFieldCollection.m | 3 1 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunHarmonicConstraintTerm.m | 13 8 + 5 - 0 !
Kernel/AdunKernel/Framework/AdunLangevinThermostat.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunLinkedList.m | 10 4 + 6 - 0 !
Kernel/AdunKernel/Framework/AdunMinimiser.m | 5 2 + 3 - 0 !
Kernel/AdunKernel/Framework/AdunModelObject.m | 26 0 + 26 - 0 !
Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m | 24 11 + 13 - 0 !
Kernel/AdunKernel/Framework/AdunMultithreadedNonbondedTerm.m | 14 3 + 11 - 0 !
Kernel/AdunKernel/Framework/AdunNonbondedTerm.m | 13 13 + 0 - 0 !
Kernel/AdunKernel/Framework/AdunSCAAS.m | 4 1 + 3 - 0 !
Kernel/AdunKernel/Framework/AdunSimpleListHandler.m | 12 6 + 6 - 0 !
Kernel/AdunKernel/Framework/AdunSimulator.m | 7 2 + 5 - 0 !
Kernel/AdunKernel/Framework/AdunSmoothedGBTerm.m | 8 2 + 6 - 0 !
Kernel/AdunKernel/Headers/AdunKernel/AdunFileSystemSimulationStorage.h | 2 1 + 1 - 0 !
Kernel/AdunKernel/Headers/AdunKernel/AdunModelObject.h | 16 0 + 16 - 0 !
Kernel/Base/AdFourierTorsion.c | 7 1 + 6 - 0 !
Kernel/Base/AdGeneralizedBornFunctions.c | 4 2 + 2 - 0 !
Kernel/Base/AdHarmonicImproperTorsion.c | 4 1 + 3 - 0 !
Kernel/Base/AdLinkedList.c | 6 3 + 3 - 0 !
Kernel/Base/AdLinkedList.h | 4 2 + 2 - 0 !
Kernel/Base/AdMatrix.c | 2 1 + 1 - 0 !
Kernel/Base/AdQuadratureFunctions.c | 8 4 + 4 - 0 !
Kernel/Base/AdQuaternion.c | 6 3 + 3 - 0 !
Kernel/Base/AdVolumeFunctions.c | 18 7 + 11 - 0 !
Kernel/Base/AdVolumeFunctions.h | 2 1 + 1 - 0 !
Kernel/main.m | 1 0 + 1 - 0 !
MolTalk/MTChain.m | 8 1 + 7 - 0 !
MolTalk/MTPDBParser.m | 16 7 + 9 - 0 !
MolTalk/MTPairwiseSequenceAlignment.m | 4 2 + 2 - 0 !
MolTalk/MTPairwiseStrxAlignment.m | 10 1 + 9 - 0 !
MolTalk/MTResidue.m | 1 1 + 0 - 0 !
MolTalk/MTStructure.m | 2 0 + 2 - 0 !
MolTalk/privateMTStructure.m | 34 16 + 18 - 0 !
UL/AdunServer/AdServer.m | 5 1 + 4 - 0 !
UL/AdunServer/main.m | 3 1 + 2 - 0 !
UL/ULAnalyser.m | 33 12 + 21 - 0 !
UL/ULAnalyserDataSetView.m | 15 6 + 9 - 0 !
UL/ULAnalyserGnuplotExtensions.m | 17 7 + 10 - 0 !
UL/ULAnalyserPluginExtensions.m | 14 8 + 6 - 0 !
UL/ULDatabaseBrowser.m | 28 13 + 15 - 0 !
UL/ULDatabaseBrowserDataDisplay.m | 2 1 + 1 - 0 !
UL/ULExportController.m | 31 10 + 21 - 0 !
UL/ULExportPanel.m | 2 1 + 1 - 0 !
UL/ULFramework/PDBConfigurationBuilder.m | 48 21 + 27 - 0 !
UL/ULFramework/ULAnalysisManager.m | 8 4 + 4 - 0 !
UL/ULFramework/ULConfigurationBuilder.m | 4 0 + 4 - 0 !
UL/ULFramework/ULDatabaseIndex.h | 2 1 + 1 - 0 !
UL/ULFramework/ULDatabaseIndex.m | 12 6 + 6 - 0 !
UL/ULFramework/ULFileSystemDatabaseBackend.m | 10 5 + 5 - 0 !
UL/ULFramework/ULIOManager.m | 4 1 + 3 - 0 !
UL/ULFramework/ULInteractionsBuilder.m | 4 2 + 2 - 0 !
UL/ULFramework/ULMerger.m | 7 3 + 4 - 0 !
UL/ULFramework/ULProcess.m | 13 3 + 10 - 0 !
UL/ULFramework/ULProcessManager.m | 8 4 + 4 - 0 !
UL/ULFramework/ULServerManager.m | 14 6 + 8 - 0 !
UL/ULFramework/ULSimpleMergerDelegate.m | 8 4 + 4 - 0 !
UL/ULFramework/ULSystem.m | 6 3 + 3 - 0 !
UL/ULFramework/ULSystemBuilder.m | 1 0 + 1 - 0 !
UL/ULFramework/ULTemplate.m | 4 1 + 3 - 0 !
UL/ULOutlineViewDelegate.m | 116 59 + 57 - 0 !
UL/ULPasteboard.h | 2 1 + 1 - 0 !
UL/ULPasteboard.m | 4 2 + 2 - 0 !
UL/ULPreferences.m | 6 3 + 3 - 0 !
UL/ULProgressPanel.m | 6 3 + 3 - 0 !
UL/ULPropertiesPanel.m | 3 1 + 2 - 0 !
UL/ULSimulationCreator.m | 11 6 + 5 - 0 !
UL/ULStatusTable.m | 9 4 + 5 - 0 !
UL/ULSystemViewController.h | 5 4 + 1 - 0 !
UL/ULSystemViewController.m | 14 3 + 11 - 0 !
UL/ULTemplateViewController.h | 2 1 + 1 - 0 !
UL/ULTemplateViewController.m | 17 7 + 10 - 0 !
UL/ULViewControllerSimulationCommands.m | 5 0 + 5 - 0 !
UL/XMLLib/XMLNode.m | 2 1 + 1 - 0 !
92 files changed, 410 insertions(+), 571 deletions(-)

 adapt to the new gnustep api and fix few gcc warnings.
 Fixes the following warnings, most of them due to changes of
 data types in recent gnustep-base.  NSNotFound is 64-bit as of
 -base/1.24, so use the right data type when comparing.
 .
 comparison is always true/false due to limited range of data type
 passing argument N of 'foo' from incompatible pointer type
 array subscript is above array bounds
 comparison between pointer and integer
 comparison between signed and unsigned integer expressions
 overflow in implicit constant conversion
 'foo' is used uninitialized in this function
 ‘foo’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 assignment makes integer from pointer without a cast
 unused parameter ‘foo’ [-Wunused-parameter]
 unused variable ‘foo’ [-Wunused-variable]
 variable ‘foo’ set but not used [-Wunused-but-set-variable]
 statement with no effect [-Wunused-value]
 suggest parentheses around assignment used as truth value [-Wparentheses]
 missing braces around initializer [-Wmissing-braces]
 control reaches end of non-void function [-Wreturn-type]
 no return statement in function returning non-void [-Wreturn-type]
 ' ' flag used with ‘%u’ gnu_printf format [-Wformat=]
 output truncated before the last format character [-Wformat-truncation=]
 ‘receiver’ may not respond to ‘-message’
 multiple methods named ‘-foo’ found
 operation on ‘foo’ may be undefined [-Wsequence-point]
enable scripting extension.patch | (download)

UL/Extensions/ULApplicationScripting/GNUmakefile | 5 2 + 3 - 0 !
UL/Extensions/ULApplicationScripting/GNUmakefile.preamble | 7 5 + 2 - 0 !
UL/Extensions/ULApplicationScripting/ULScriptManager.m | 14 6 + 8 - 0 !
UL/GNUmakefile | 1 1 + 0 - 0 !
UL/ViewController.m | 88 37 + 51 - 0 !
5 files changed, 51 insertions(+), 64 deletions(-)

 enable the scripting extension.
 Also fixes some problems with building and loading and a bunch of
 trivial compiler warnings.
enable sql extension.patch | (download)

UL/Extensions/ULSQLDatabaseBackend/GNUmakefile | 3 1 + 2 - 0 !
UL/Extensions/ULSQLDatabaseBackend/GNUmakefile.preamble | 7 5 + 2 - 0 !
UL/Extensions/ULSQLDatabaseBackend/ULSQLDatabaseBackend.h | 2 0 + 2 - 0 !
UL/Extensions/ULSQLDatabaseBackend/ULSQLDatabaseBackend.m | 14 6 + 8 - 0 !
UL/GNUmakefile | 3 2 + 1 - 0 !
UL/ULFramework/ULDatabaseInterface.m | 56 30 + 26 - 0 !
6 files changed, 44 insertions(+), 41 deletions(-)

 enable the sql backend extension.
 Fix some trivial compiler warnings in the process.
invalid observer.patch | (download)

UL/ULSystemViewController.m | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 fix segmentation fault when loading a molecule file.
 A premature -relase message invalidates the observer and causes
 NSInvalidArgumentException when attempting to post the notification.
 With older gnustep-base this lead to frozen UI, with 1.25 UL crashes.
Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/adun.app/+bug/914750
spelling errors.patch | (download)

Kernel/AdunKernel/CoreAdditions/AdunCore.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunFileSystemSimulationStorage.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunIOManager.m | 12 6 + 6 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunSimulationData.m | 6 3 + 3 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunTemplateProcessor.m | 8 4 + 4 - 0 !
Kernel/AdunKernel/CoreAdditions/AdunTrajectory.m | 6 3 + 3 - 0 !
Kernel/AdunKernel/CoreAdditions/Commands/AdEndSimulationCommand.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunAmberForceField.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunCharmmForceField.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunConfigurationGenerator.m | 6 3 + 3 - 0 !
Kernel/AdunKernel/Framework/AdunDataMatrix.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunDynamics.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunEnzymixForceField.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunGRFNonbondedTerm.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunMatrixStructureCoder.m | 4 2 + 2 - 0 !
Kernel/AdunKernel/Framework/AdunMinimiser.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunMolecularMechanicsForceField.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunPureNonbondedTerm.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunShiftedNonbondedTerm.m | 2 1 + 1 - 0 !
Kernel/AdunKernel/Framework/AdunSmoothedGBTerm.m | 2 1 + 1 - 0 !
Kernel/Base/AdHarmonicBond.c | 2 1 + 1 - 0 !
Kernel/Base/AdHarmonicImproperTorsion.c | 2 1 + 1 - 0 !
Kernel/main.m | 6 3 + 3 - 0 !
UL/AdunServer/AdServer.m | 6 3 + 3 - 0 !
UL/Extensions/ULApplicationScripting/ULScriptManager.m | 2 1 + 1 - 0 !
UL/ULAnalyserGnuplotExtensions.m | 2 1 + 1 - 0 !
UL/ULFramework/PDBConfigurationBuilder.m | 8 4 + 4 - 0 !
UL/ULFramework/ULAnalysisManager.m | 8 4 + 4 - 0 !
UL/ULFramework/ULFileSystemDatabaseBackend.m | 4 2 + 2 - 0 !
UL/ULFramework/ULIOManager.m | 2 1 + 1 - 0 !
UL/ULFramework/ULInteractionsBuilder.m | 2 1 + 1 - 0 !
UL/ULFramework/ULMerger.m | 2 1 + 1 - 0 !
UL/ULFramework/ULProcess.m | 4 2 + 2 - 0 !
UL/ULFramework/ULServerManager.m | 4 2 + 2 - 0 !
UL/ULFramework/ULSystemController.m | 2 1 + 1 - 0 !
UL/ULProgressPanel.m | 4 2 + 2 - 0 !
UL/ULSystemViewController.m | 4 2 + 2 - 0 !
UL/ViewController.m | 2 1 + 1 - 0 !
38 files changed, 72 insertions(+), 72 deletions(-)

 fix some spelling errors.
check return value.patch | (download)

Kernel/AdunKernel/CoreAdditions/AdunIOManager.m | 20 12 + 8 - 0 !
MolTalk/MTFileStream.m | 3 2 + 1 - 0 !
UL/AdunServer/AdServer.m | 3 2 + 1 - 0 !
UL/ViewController.m | 3 2 + 1 - 0 !
4 files changed, 18 insertions(+), 11 deletions(-)

 check the return value of `freopen' and `fread'.
ftbfs powerpcspe.patch | (download)

MolTalk/GNUmakefile.preamble | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 fix ftbfs on powerpcspe.
 Disable all platform-specific flags as they are wrong (imply a better
 machine/CPU compared to the lowest supported on a given arch).