[med-svn] [ray] branch master updated (28f1527 -> de847b5)
Andreas Tille
tille at debian.org
Thu Sep 25 15:09:22 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ray.
from 28f1527 Move debian/upstream to debian/upstream/metadata
new c3a06a2 Fix build problem on mips architectures
new 01b721d Imported Upstream version 2.3.1
new 359fae5 Merge tag 'upstream/2.3.1'
new 872b49f New upstream version
new 2e39a34 cme fix dpkg-control (including shortened synopsis)
new 3bd09d0 d/copyright: make sure all files are included in copyright statement and chose more strict license (GPL-3) for the missing files
new fbd1c08 add separate section for debian/*
new de847b5 Upload to unstable
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Documentation/RELEASE_PROCEDURE.txt | 7 +-
Documentation/Releases.txt | 1 +
MANUAL_PAGE.txt | 21 +-
Makefile | 6 +-
README.md | 3 +
RayPlatform/Makefile | 4 +-
RayPlatform/README.md | 3 +
RayPlatform/RayPlatform/actors/Actor.cpp | 1 +
RayPlatform/RayPlatform/actors/Playground.cpp | 26 ++
RayPlatform/RayPlatform/actors/Playground.h | 7 +
.../RayPlatform/communication/BufferedData.cpp | 14 +-
RayPlatform/RayPlatform/communication/Message.cpp | 333 ++++++++++++--
RayPlatform/RayPlatform/communication/Message.h | 105 +++--
.../RayPlatform/communication/MessageQueue.cpp | 12 +-
.../RayPlatform/communication/MessageRouter.cpp | 107 +++--
.../RayPlatform/communication/MessagesHandler.cpp | 207 ++++++---
.../RayPlatform/communication/MessagesHandler.h | 6 +-
.../communication/VirtualCommunicator.cpp | 50 +--
RayPlatform/RayPlatform/core/ComputeCore.cpp | 485 ++++++++++++++++-----
RayPlatform/RayPlatform/core/ComputeCore.h | 13 +-
RayPlatform/RayPlatform/core/OperatingSystem.cpp | 4 +-
RayPlatform/RayPlatform/core/RankProcess.h | 10 +-
RayPlatform/RayPlatform/cryptography/crypto.cpp | 4 +-
RayPlatform/RayPlatform/files/FileReader.cpp | 4 +
RayPlatform/RayPlatform/files/FileReader.h | 1 +
.../RayPlatform/handlers/MasterModeExecutor.cpp | 4 +-
.../RayPlatform/handlers/MessageTagExecutor.cpp | 4 +-
.../RayPlatform/handlers/SlaveModeExecutor.cpp | 4 +-
.../memory/ChunkAllocatorWithDefragmentation.cpp | 6 +-
.../RayPlatform/memory/DefragmentationGroup.cpp | 36 +-
.../RayPlatform/memory/DefragmentationLane.cpp | 8 +-
RayPlatform/RayPlatform/memory/DirtyBuffer.h | 3 +
RayPlatform/RayPlatform/memory/MyAllocator.cpp | 12 +-
.../RayPlatform/memory/ReusableMemoryStore.cpp | 14 +-
RayPlatform/RayPlatform/memory/RingAllocator.cpp | 60 ++-
RayPlatform/RayPlatform/memory/RingAllocator.h | 1 +
RayPlatform/RayPlatform/memory/allocator.cpp | 2 +-
RayPlatform/RayPlatform/profiling/TickLogger.cpp | 12 +-
.../routing/GraphImplementationDeBruijn.cpp | 2 +-
.../routing/GraphImplementationExperimental.cpp | 2 +-
.../routing/GraphImplementationGroup.cpp | 2 +-
.../routing/GraphImplementationKautz.cpp | 2 +-
.../routing/GraphImplementationRandom.cpp | 2 +-
RayPlatform/RayPlatform/routing/Polytope.cpp | 18 +-
RayPlatform/RayPlatform/routing/Torus.cpp | 24 +-
RayPlatform/RayPlatform/scheduling/SwitchMan.cpp | 24 +-
RayPlatform/RayPlatform/scheduling/TaskCreator.cpp | 4 +-
.../RayPlatform/scheduling/VirtualProcessor.cpp | 14 +-
RayPlatform/RayPlatform/structures/MyHashTable.h | 52 +--
.../RayPlatform/structures/MyHashTableGroup.h | 28 +-
.../RayPlatform/structures/MyHashTableIterator.h | 4 +-
RayPlatform/RayPlatform/structures/MyStack.h | 2 +-
.../RayPlatform/structures/SplayTreeIterator.h | 2 +-
.../RayPlatform/structures/StaticVector.cpp | 4 +-
code/CoverageGatherer/CoverageDistribution.cpp | 2 +-
code/CoverageGatherer/CoverageGatherer.cpp | 14 +-
code/EdgePurger/EdgePurger.cpp | 6 +-
code/FusionData/FusionData.cpp | 24 +-
code/FusionTaskCreator/FusionWorker.cpp | 4 +-
code/GeneOntology/GeneOntology.cpp | 47 +-
code/GeneOntology/KeyEncoder.cpp | 14 +-
code/GenomeNeighbourhood/GenomeNeighbourhood.cpp | 28 +-
code/JoinerTaskCreator/JoinerWorker.cpp | 16 +-
code/KmerAcademyBuilder/BloomFilter.cpp | 22 +-
code/KmerAcademyBuilder/Kmer.h | 2 +-
code/KmerAcademyBuilder/KmerAcademyBuilder.cpp | 10 +-
code/Library/Library.cpp | 12 +-
code/Library/LibraryWorker.cpp | 10 +-
code/MachineHelper/MachineHelper.cpp | 19 +-
code/MessageProcessor/MessageProcessor.cpp | 114 ++---
code/Mock/Mock.cpp | 4 +-
code/Mock/Parameters.cpp | 56 ++-
code/Mock/common_functions.cpp | 4 +-
code/Mock/common_functions.h | 2 +-
code/NetworkTest/NetworkTest.cpp | 4 +-
code/Partitioner/Partitioner.cpp | 4 +-
code/Scaffolder/Scaffolder.cpp | 38 +-
code/Scaffolder/ScaffoldingAlgorithm.cpp | 10 +-
code/Scaffolder/ScaffoldingEdge.cpp | 4 +-
code/Searcher/ColorSet.cpp | 71 +--
code/Searcher/ColorSet.h | 5 +-
code/Searcher/DistributionWriter.cpp | 2 +-
code/Searcher/QualityCaller.cpp | 2 +-
code/Searcher/SearchDirectory.cpp | 56 +--
code/Searcher/Searcher.cpp | 152 +++----
code/Searcher/VirtualKmerColor.cpp | 10 +-
code/SeedExtender/BubbleTool.cpp | 10 +-
code/SeedExtender/DepthFirstSearchData.cpp | 14 +-
code/SeedExtender/Direction.cpp | 2 +-
code/SeedExtender/ReadFetcher.cpp | 16 +-
code/SeedExtender/SeedExtender.cpp | 74 ++--
code/SeedExtender/VertexMessenger.cpp | 6 +-
code/SeedingData/PathHandle.cpp | 21 +-
code/SeedingData/PathHandle.h | 15 +-
code/SeedingData/SeedWorker.cpp | 4 +-
code/SeedingData/SeedingData.cpp | 31 +-
code/SequencesIndexer/IndexerWorker.cpp | 12 +-
code/SequencesIndexer/SequencesIndexer.cpp | 12 +-
code/SequencesLoader/ArrayOfReads.cpp | 26 +-
code/SequencesLoader/BzReader.cpp | 2 +-
code/SequencesLoader/FastqGzLoader.cpp | 14 +-
code/SequencesLoader/Loader.cpp | 8 +-
code/SequencesLoader/Read.cpp | 2 +-
code/SequencesLoader/SequenceFileDetector.cpp | 10 +
code/SequencesLoader/SequencesLoader.cpp | 26 +-
.../SpuriousSeedAnnihilator/AnnihilationWorker.cpp | 6 +-
code/SpuriousSeedAnnihilator/AttributeFetcher.cpp | 2 +-
code/SpuriousSeedAnnihilator/GraphExplorer.cpp | 6 +-
.../SeedFilteringWorkflow.cpp | 4 +-
.../SeedMergingWorkflow.cpp | 4 +-
.../SpuriousSeedAnnihilator.cpp | 16 +-
code/Surveyor/CoalescenceManager.cpp | 33 +-
code/Surveyor/GenomeGraphReader.cpp | 51 ++-
code/Surveyor/GenomeGraphReader.h | 3 +
code/Surveyor/MatrixOwner.cpp | 47 +-
code/Surveyor/MatrixOwner.h | 4 +
code/Surveyor/Mother.cpp | 130 ++++--
code/Surveyor/Mother.h | 6 +-
code/Surveyor/StoreKeeper.cpp | 179 +++++++-
code/Surveyor/StoreKeeper.h | 2 +
code/TaxonomyViewer/TaxonomyViewer.cpp | 52 ++-
code/VerticesExtractor/GridTable.cpp | 34 +-
code/VerticesExtractor/GridTableIterator.cpp | 2 +-
code/VerticesExtractor/Vertex.cpp | 16 +-
code/VerticesExtractor/VerticesExtractor.cpp | 10 +-
code/application_core/Machine.cpp | 2 +-
code/application_core/Machine.h | 2 +-
debian/changelog | 20 +
debian/control | 11 +-
debian/copyright | 40 +-
debian/patches/mips.patch | 18 +
debian/patches/series | 1 +
132 files changed, 2407 insertions(+), 1153 deletions(-)
create mode 100644 debian/patches/mips.patch
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