Run of fresh-snapshots for salmon

Try this locally (using the lintian-brush package):

debcheckout salmon
cd salmon
new-upstream --snapshot
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Processing: salmon
Total 1850 (delta 856), reused 1850 (delta 856)

/usr/lib/python3/dist-packages/debian/copyright.py:652: UserWarning: Fixing Format URL
  warnings.warn('Fixing Format URL')
Using upstream branch https://github.com/COMBINE-lab/salmon (guessed)
Total 11396 (delta 2), reused 0 (delta 0), pack-reused 11390
Using version string 0.14.0+git20190607.b1edd52.
No upstream upstream-revision format specified, trying git:b1edd52
No upstream upstream-revision format specified, trying git:b1edd52
Exporting upstream branch revision b'git-v1:b1edd526e1e8cdad6f01daaba2f9dc3f2abf19f4' to create the tarball
Total 11396 (delta 2), reused 0 (delta 0), pack-reused 11390
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v0.4.1 does not point to a valid object
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v0.10.1 does not point to a valid object
v0.12.0 does not point to a valid object
v0.11.1 does not point to a valid object
before-no-fmd does not point to a valid object
All changes applied successfully.
v0.4.2 does not point to a valid object
v0.11.0 does not point to a valid object
v0.5.0 does not point to a valid object
v0.7.0-pre does not point to a valid object
v0.5.1 does not point to a valid object
v0.9.0 does not point to a valid object
v0.10.2 does not point to a valid object
v0.7.2 does not point to a valid object
v0.11.3 does not point to a valid object
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v0.8.0 does not point to a valid object
v0.3.2 does not point to a valid object
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v0.10.0 does not point to a valid object
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v0.6.0 does not point to a valid object
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Committing to: /home/janitor/tmp/tmpq1sxxbve/salmon/
modified CMakeLists.txt
modified README.md
added cmake/Modules/FindCereal.cmake
added cmake/Modules/FindTBB.cmake
added cmake/Modules/Findlibdivsufsort.cmake
added cmake/Modules/Findlibgff.cmake
added cmake/Modules/Findlibstadenio.cmake
modified current_version.txt
modified debian/changelog
modified doc/source/alevin.rst
modified doc/source/conf.py
modified doc/source/library_type.rst
modified doc/source/salmon.rst
modified docker/Dockerfile
modified docker/build_test.sh
added include/AlevinHash.hpp
modified include/AlevinOpts.hpp
modified include/AlevinUtils.hpp
modified include/AlignmentGroup.hpp
modified include/AlignmentLibrary.hpp
modified include/BAMQueue.tpp
added include/BAMUtils.hpp
modified include/BarcodeGroup.hpp
modified include/CollapsedCellOptimizer.hpp
modified include/DedupUMI.hpp
modified include/EquivalenceClassBuilder.hpp
modified include/GZipWriter.hpp
modified include/Graph.hpp
added include/MappingStatistics.hpp
modified include/ReadExperiment.hpp
modified include/SalmonConfig.hpp
modified include/SalmonDefaults.hpp
modified include/SalmonIndex.hpp
modified include/SalmonOpts.hpp
modified include/SalmonUtils.hpp
modified include/Sampler.hpp
modified include/Transcript.hpp
modified include/WhiteList.hpp
added include/eigen3
added include/eigen3/Eigen
added include/eigen3/Eigen/Cholesky
added include/eigen3/Eigen/CholmodSupport
added include/eigen3/Eigen/Core
added include/eigen3/Eigen/Dense
added include/eigen3/Eigen/Eigen
added include/eigen3/Eigen/Eigenvalues
added include/eigen3/Eigen/Geometry
added include/eigen3/Eigen/Householder
added include/eigen3/Eigen/IterativeLinearSolvers
added include/eigen3/Eigen/Jacobi
added include/eigen3/Eigen/LU
added include/eigen3/Eigen/MetisSupport
added include/eigen3/Eigen/OrderingMethods
added include/eigen3/Eigen/PaStiXSupport
added include/eigen3/Eigen/PardisoSupport
added include/eigen3/Eigen/QR
added include/eigen3/Eigen/QtAlignedMalloc
added include/eigen3/Eigen/SPQRSupport
added include/eigen3/Eigen/SVD
added include/eigen3/Eigen/Sparse
added include/eigen3/Eigen/SparseCholesky
added include/eigen3/Eigen/SparseCore
added include/eigen3/Eigen/SparseLU
added include/eigen3/Eigen/SparseQR
added include/eigen3/Eigen/StdDeque
added include/eigen3/Eigen/StdList
added include/eigen3/Eigen/StdVector
added include/eigen3/Eigen/SuperLUSupport
added include/eigen3/Eigen/UmfPackSupport
added include/eigen3/Eigen/src
added include/eigen3/Eigen/src/Cholesky
added include/eigen3/Eigen/src/Cholesky/LDLT.h
added include/eigen3/Eigen/src/Cholesky/LLT.h
added include/eigen3/Eigen/src/Cholesky/LLT_LAPACKE.h
added include/eigen3/Eigen/src/CholmodSupport
added include/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h
added include/eigen3/Eigen/src/Core
added include/eigen3/Eigen/src/Core/Array.h
added include/eigen3/Eigen/src/Core/ArrayBase.h
added include/eigen3/Eigen/src/Core/ArrayWrapper.h
added include/eigen3/Eigen/src/Core/Assign.h
added include/eigen3/Eigen/src/Core/AssignEvaluator.h
added include/eigen3/Eigen/src/Core/Assign_MKL.h
added include/eigen3/Eigen/src/Core/BandMatrix.h
added include/eigen3/Eigen/src/Core/Block.h
added include/eigen3/Eigen/src/Core/BooleanRedux.h
added include/eigen3/Eigen/src/Core/CommaInitializer.h
added include/eigen3/Eigen/src/Core/ConditionEstimator.h
added include/eigen3/Eigen/src/Core/CoreEvaluators.h
added include/eigen3/Eigen/src/Core/CoreIterators.h
added include/eigen3/Eigen/src/Core/CwiseBinaryOp.h
added include/eigen3/Eigen/src/Core/CwiseNullaryOp.h
added include/eigen3/Eigen/src/Core/CwiseTernaryOp.h
added include/eigen3/Eigen/src/Core/CwiseUnaryOp.h
added include/eigen3/Eigen/src/Core/CwiseUnaryView.h
added include/eigen3/Eigen/src/Core/DenseBase.h
added include/eigen3/Eigen/src/Core/DenseCoeffsBase.h
added include/eigen3/Eigen/src/Core/DenseStorage.h
added include/eigen3/Eigen/src/Core/Diagonal.h
added include/eigen3/Eigen/src/Core/DiagonalMatrix.h
added include/eigen3/Eigen/src/Core/DiagonalProduct.h
added include/eigen3/Eigen/src/Core/Dot.h
added include/eigen3/Eigen/src/Core/EigenBase.h
added include/eigen3/Eigen/src/Core/ForceAlignedAccess.h
added include/eigen3/Eigen/src/Core/Fuzzy.h
added include/eigen3/Eigen/src/Core/GeneralProduct.h
added include/eigen3/Eigen/src/Core/GenericPacketMath.h
added include/eigen3/Eigen/src/Core/GlobalFunctions.h
added include/eigen3/Eigen/src/Core/IO.h
added include/eigen3/Eigen/src/Core/Inverse.h
added include/eigen3/Eigen/src/Core/Map.h
added include/eigen3/Eigen/src/Core/MapBase.h
added include/eigen3/Eigen/src/Core/MathFunctions.h
added include/eigen3/Eigen/src/Core/MathFunctionsImpl.h
added include/eigen3/Eigen/src/Core/Matrix.h
added include/eigen3/Eigen/src/Core/MatrixBase.h
added include/eigen3/Eigen/src/Core/NestByValue.h
added include/eigen3/Eigen/src/Core/NoAlias.h
added include/eigen3/Eigen/src/Core/NumTraits.h
added include/eigen3/Eigen/src/Core/PermutationMatrix.h
added include/eigen3/Eigen/src/Core/PlainObjectBase.h
added include/eigen3/Eigen/src/Core/Product.h
added include/eigen3/Eigen/src/Core/ProductEvaluators.h
added include/eigen3/Eigen/src/Core/Random.h
added include/eigen3/Eigen/src/Core/Redux.h
added include/eigen3/Eigen/src/Core/Ref.h
added include/eigen3/Eigen/src/Core/Replicate.h
added include/eigen3/Eigen/src/Core/ReturnByValue.h
added include/eigen3/Eigen/src/Core/Reverse.h
added include/eigen3/Eigen/src/Core/Select.h
added include/eigen3/Eigen/src/Core/SelfAdjointView.h
added include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h
added include/eigen3/Eigen/src/Core/Solve.h
added include/eigen3/Eigen/src/Core/SolveTriangular.h
added include/eigen3/Eigen/src/Core/SolverBase.h
added include/eigen3/Eigen/src/Core/StableNorm.h
added include/eigen3/Eigen/src/Core/Stride.h
added include/eigen3/Eigen/src/Core/Swap.h
added include/eigen3/Eigen/src/Core/Transpose.h
added include/eigen3/Eigen/src/Core/Transpositions.h
added include/eigen3/Eigen/src/Core/TriangularMatrix.h
added include/eigen3/Eigen/src/Core/VectorBlock.h
added include/eigen3/Eigen/src/Core/VectorwiseOp.h
added include/eigen3/Eigen/src/Core/Visitor.h
added include/eigen3/Eigen/src/Core/arch
added include/eigen3/Eigen/src/Core/arch/AVX
added include/eigen3/Eigen/src/Core/arch/AVX/Complex.h
added include/eigen3/Eigen/src/Core/arch/AVX/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/AVX/PacketMath.h
added include/eigen3/Eigen/src/Core/arch/AVX/TypeCasting.h
added include/eigen3/Eigen/src/Core/arch/AVX512
added include/eigen3/Eigen/src/Core/arch/AVX512/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/AVX512/PacketMath.h
added include/eigen3/Eigen/src/Core/arch/AltiVec
added include/eigen3/Eigen/src/Core/arch/AltiVec/Complex.h
added include/eigen3/Eigen/src/Core/arch/AltiVec/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/AltiVec/PacketMath.h
added include/eigen3/Eigen/src/Core/arch/CUDA
added include/eigen3/Eigen/src/Core/arch/CUDA/Complex.h
added include/eigen3/Eigen/src/Core/arch/CUDA/Half.h
added include/eigen3/Eigen/src/Core/arch/CUDA/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/CUDA/PacketMath.h
added include/eigen3/Eigen/src/Core/arch/CUDA/PacketMathHalf.h
added include/eigen3/Eigen/src/Core/arch/CUDA/TypeCasting.h
added include/eigen3/Eigen/src/Core/arch/Default
added include/eigen3/Eigen/src/Core/arch/Default/Settings.h
added include/eigen3/Eigen/src/Core/arch/NEON
added include/eigen3/Eigen/src/Core/arch/NEON/Complex.h
added include/eigen3/Eigen/src/Core/arch/NEON/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h
added include/eigen3/Eigen/src/Core/arch/SSE
added include/eigen3/Eigen/src/Core/arch/SSE/Complex.h
added include/eigen3/Eigen/src/Core/arch/SSE/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h
added include/eigen3/Eigen/src/Core/arch/SSE/TypeCasting.h
added include/eigen3/Eigen/src/Core/arch/ZVector
added include/eigen3/Eigen/src/Core/arch/ZVector/Complex.h
added include/eigen3/Eigen/src/Core/arch/ZVector/MathFunctions.h
added include/eigen3/Eigen/src/Core/arch/ZVector/PacketMath.h
added include/eigen3/Eigen/src/Core/functors
added include/eigen3/Eigen/src/Core/functors/AssignmentFunctors.h
added include/eigen3/Eigen/src/Core/functors/BinaryFunctors.h
added include/eigen3/Eigen/src/Core/functors/NullaryFunctors.h
added include/eigen3/Eigen/src/Core/functors/StlFunctors.h
added include/eigen3/Eigen/src/Core/functors/TernaryFunctors.h
added include/eigen3/Eigen/src/Core/functors/UnaryFunctors.h
added include/eigen3/Eigen/src/Core/products
added include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h
added include/eigen3/Eigen/src/Core/products/GeneralMatrixMatrix.h
added include/eigen3/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
added include/eigen3/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h
added include/eigen3/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h
added include/eigen3/Eigen/src/Core/products/GeneralMatrixVector.h
added include/eigen3/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h
added include/eigen3/Eigen/src/Core/products/Parallelizer.h
added include/eigen3/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
added include/eigen3/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h
added include/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector.h
added include/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
added include/eigen3/Eigen/src/Core/products/SelfadjointProduct.h
added include/eigen3/Eigen/src/Core/products/SelfadjointRank2Update.h
added include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h
added include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h
added include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h
added include/eigen3/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
added include/eigen3/Eigen/src/Core/products/TriangularSolverMatrix.h
added include/eigen3/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
added include/eigen3/Eigen/src/Core/products/TriangularSolverVector.h
added include/eigen3/Eigen/src/Core/util
added include/eigen3/Eigen/src/Core/util/BlasUtil.h
added include/eigen3/Eigen/src/Core/util/Constants.h
added include/eigen3/Eigen/src/Core/util/DisableStupidWarnings.h
added include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h
added include/eigen3/Eigen/src/Core/util/MKL_support.h
added include/eigen3/Eigen/src/Core/util/Macros.h
added include/eigen3/Eigen/src/Core/util/Memory.h
added include/eigen3/Eigen/src/Core/util/Meta.h
added include/eigen3/Eigen/src/Core/util/NonMPL2.h
added include/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h
added include/eigen3/Eigen/src/Core/util/StaticAssert.h
added include/eigen3/Eigen/src/Core/util/XprHelper.h
added include/eigen3/Eigen/src/Eigenvalues
added include/eigen3/Eigen/src/Eigenvalues/ComplexEigenSolver.h
added include/eigen3/Eigen/src/Eigenvalues/ComplexSchur.h
added include/eigen3/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h
added include/eigen3/Eigen/src/Eigenvalues/EigenSolver.h
added include/eigen3/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
added include/eigen3/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
added include/eigen3/Eigen/src/Eigenvalues/HessenbergDecomposition.h
added include/eigen3/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
added include/eigen3/Eigen/src/Eigenvalues/RealQZ.h
added include/eigen3/Eigen/src/Eigenvalues/RealSchur.h
added include/eigen3/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h
added include/eigen3/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
added include/eigen3/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h
added include/eigen3/Eigen/src/Eigenvalues/Tridiagonalization.h
added include/eigen3/Eigen/src/Geometry
added include/eigen3/Eigen/src/Geometry/AlignedBox.h
added include/eigen3/Eigen/src/Geometry/AngleAxis.h
added include/eigen3/Eigen/src/Geometry/EulerAngles.h
added include/eigen3/Eigen/src/Geometry/Homogeneous.h
added include/eigen3/Eigen/src/Geometry/Hyperplane.h
added include/eigen3/Eigen/src/Geometry/OrthoMethods.h
added include/eigen3/Eigen/src/Geometry/ParametrizedLine.h
added include/eigen3/Eigen/src/Geometry/Quaternion.h
added include/eigen3/Eigen/src/Geometry/Rotation2D.h
added include/eigen3/Eigen/src/Geometry/RotationBase.h
added include/eigen3/Eigen/src/Geometry/Scaling.h
added include/eigen3/Eigen/src/Geometry/Transform.h
added include/eigen3/Eigen/src/Geometry/Translation.h
added include/eigen3/Eigen/src/Geometry/Umeyama.h
added include/eigen3/Eigen/src/Geometry/arch
added include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h
added include/eigen3/Eigen/src/Householder
added include/eigen3/Eigen/src/Householder/BlockHouseholder.h
added include/eigen3/Eigen/src/Householder/Householder.h
added include/eigen3/Eigen/src/Householder/HouseholderSequence.h
added include/eigen3/Eigen/src/IterativeLinearSolvers
added include/eigen3/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h
added include/eigen3/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h
added include/eigen3/Eigen/src/Jacobi
added include/eigen3/Eigen/src/Jacobi/Jacobi.h
added include/eigen3/Eigen/src/LU
added include/eigen3/Eigen/src/LU/Determinant.h
added include/eigen3/Eigen/src/LU/FullPivLU.h
added include/eigen3/Eigen/src/LU/InverseImpl.h
added include/eigen3/Eigen/src/LU/PartialPivLU.h
added include/eigen3/Eigen/src/LU/PartialPivLU_LAPACKE.h
added include/eigen3/Eigen/src/LU/arch
added include/eigen3/Eigen/src/LU/arch/Inverse_SSE.h
added include/eigen3/Eigen/src/MetisSupport
added include/eigen3/Eigen/src/MetisSupport/MetisSupport.h
added include/eigen3/Eigen/src/OrderingMethods
added include/eigen3/Eigen/src/OrderingMethods/Amd.h
added include/eigen3/Eigen/src/OrderingMethods/Eigen_Colamd.h
added include/eigen3/Eigen/src/OrderingMethods/Ordering.h
added include/eigen3/Eigen/src/PaStiXSupport
added include/eigen3/Eigen/src/PaStiXSupport/PaStiXSupport.h
added include/eigen3/Eigen/src/PardisoSupport
added include/eigen3/Eigen/src/PardisoSupport/PardisoSupport.h
added include/eigen3/Eigen/src/QR
added include/eigen3/Eigen/src/QR/ColPivHouseholderQR.h
added include/eigen3/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h
added include/eigen3/Eigen/src/QR/CompleteOrthogonalDecomposition.h
added include/eigen3/Eigen/src/QR/FullPivHouseholderQR.h
added include/eigen3/Eigen/src/QR/HouseholderQR.h
added include/eigen3/Eigen/src/QR/HouseholderQR_LAPACKE.h
added include/eigen3/Eigen/src/SPQRSupport
added include/eigen3/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
added include/eigen3/Eigen/src/SVD
added include/eigen3/Eigen/src/SVD/BDCSVD.h
added include/eigen3/Eigen/src/SVD/JacobiSVD.h
added include/eigen3/Eigen/src/SVD/JacobiSVD_LAPACKE.h
added include/eigen3/Eigen/src/SVD/SVDBase.h
added include/eigen3/Eigen/src/SVD/UpperBidiagonalization.h
added include/eigen3/Eigen/src/SparseCholesky
added include/eigen3/Eigen/src/SparseCholesky/SimplicialCholesky.h
added include/eigen3/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
added include/eigen3/Eigen/src/SparseCore
added include/eigen3/Eigen/src/SparseCore/AmbiVector.h
added include/eigen3/Eigen/src/SparseCore/CompressedStorage.h
added include/eigen3/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
added include/eigen3/Eigen/src/SparseCore/MappedSparseMatrix.h
added include/eigen3/Eigen/src/SparseCore/SparseAssign.h
added include/eigen3/Eigen/src/SparseCore/SparseBlock.h
added include/eigen3/Eigen/src/SparseCore/SparseColEtree.h
added include/eigen3/Eigen/src/SparseCore/SparseCompressedBase.h
added include/eigen3/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
added include/eigen3/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
added include/eigen3/Eigen/src/SparseCore/SparseDenseProduct.h
added include/eigen3/Eigen/src/SparseCore/SparseDiagonalProduct.h
added include/eigen3/Eigen/src/SparseCore/SparseDot.h
added include/eigen3/Eigen/src/SparseCore/SparseFuzzy.h
added include/eigen3/Eigen/src/SparseCore/SparseMap.h
added include/eigen3/Eigen/src/SparseCore/SparseMatrix.h
added include/eigen3/Eigen/src/SparseCore/SparseMatrixBase.h
added include/eigen3/Eigen/src/SparseCore/SparsePermutation.h
added include/eigen3/Eigen/src/SparseCore/SparseProduct.h
added include/eigen3/Eigen/src/SparseCore/SparseRedux.h
added include/eigen3/Eigen/src/SparseCore/SparseRef.h
added include/eigen3/Eigen/src/SparseCore/SparseSelfAdjointView.h
added include/eigen3/Eigen/src/SparseCore/SparseSolverBase.h
added include/eigen3/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
added include/eigen3/Eigen/src/SparseCore/SparseTranspose.h
added include/eigen3/Eigen/src/SparseCore/SparseTriangularView.h
added include/eigen3/Eigen/src/SparseCore/SparseUtil.h
added include/eigen3/Eigen/src/SparseCore/SparseVector.h
added include/eigen3/Eigen/src/SparseCore/SparseView.h
added include/eigen3/Eigen/src/SparseCore/TriangularSolver.h
added include/eigen3/Eigen/src/SparseLU
added include/eigen3/Eigen/src/SparseLU/SparseLU.h
added include/eigen3/Eigen/src/SparseLU/SparseLUImpl.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_Memory.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_Structs.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_Utils.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_column_bmod.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_column_dfs.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_panel_bmod.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_panel_dfs.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_pivotL.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_pruneL.h
added include/eigen3/Eigen/src/SparseLU/SparseLU_relax_snode.h
added include/eigen3/Eigen/src/SparseQR
added include/eigen3/Eigen/src/SparseQR/SparseQR.h
added include/eigen3/Eigen/src/StlSupport
added include/eigen3/Eigen/src/StlSupport/StdDeque.h
added include/eigen3/Eigen/src/StlSupport/StdList.h
added include/eigen3/Eigen/src/StlSupport/StdVector.h
added include/eigen3/Eigen/src/StlSupport/details.h
added include/eigen3/Eigen/src/SuperLUSupport
added include/eigen3/Eigen/src/SuperLUSupport/SuperLUSupport.h
added include/eigen3/Eigen/src/UmfPackSupport
added include/eigen3/Eigen/src/UmfPackSupport/UmfPackSupport.h
added include/eigen3/Eigen/src/misc
added include/eigen3/Eigen/src/misc/Image.h
added include/eigen3/Eigen/src/misc/Kernel.h
added include/eigen3/Eigen/src/misc/RealSvd2x2.h
added include/eigen3/Eigen/src/misc/blas.h
added include/eigen3/Eigen/src/misc/lapack.h
added include/eigen3/Eigen/src/misc/lapacke.h
added include/eigen3/Eigen/src/misc/lapacke_mangling.h
added include/eigen3/Eigen/src/plugins
added include/eigen3/Eigen/src/plugins/ArrayCwiseBinaryOps.h
added include/eigen3/Eigen/src/plugins/ArrayCwiseUnaryOps.h
added include/eigen3/Eigen/src/plugins/BlockMethods.h
added include/eigen3/Eigen/src/plugins/CommonCwiseBinaryOps.h
added include/eigen3/Eigen/src/plugins/CommonCwiseUnaryOps.h
added include/eigen3/Eigen/src/plugins/MatrixCwiseBinaryOps.h
added include/eigen3/Eigen/src/plugins/MatrixCwiseUnaryOps.h
added include/eigen3/signature_of_eigen3_matrix_library
added include/eigen3/unsupported
added include/eigen3/unsupported/Eigen
added include/eigen3/unsupported/Eigen/AdolcForward
added include/eigen3/unsupported/Eigen/AlignedVector3
added include/eigen3/unsupported/Eigen/ArpackSupport
added include/eigen3/unsupported/Eigen/AutoDiff
added include/eigen3/unsupported/Eigen/BVH
added include/eigen3/unsupported/Eigen/CXX11
added include/eigen3/unsupported/Eigen/CXX11/Tensor
added include/eigen3/unsupported/Eigen/CXX11/TensorSymmetry
added include/eigen3/unsupported/Eigen/CXX11/ThreadPool
added include/eigen3/unsupported/Eigen/CXX11/src
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h
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added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h
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added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h
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added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorSycl.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorSyclConvertToDeviceExpression.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExprConstructor.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractAccessor.h
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added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorSyclLeafCount.h
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added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h
added include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h
added include/eigen3/unsupported/Eigen/CXX11/src/TensorSymmetry
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added include/eigen3/unsupported/Eigen/CXX11/src/TensorSymmetry/util
added include/eigen3/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h
added include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool
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added include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h
added include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h
added include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/SimpleThreadPool.h
added include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h
added include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h
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added include/eigen3/unsupported/Eigen/CXX11/src/util
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added include/eigen3/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h
added include/eigen3/unsupported/Eigen/CXX11/src/util/EmulateArray.h
added include/eigen3/unsupported/Eigen/CXX11/src/util/EmulateCXX11Meta.h
added include/eigen3/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h
added include/eigen3/unsupported/Eigen/EulerAngles
added include/eigen3/unsupported/Eigen/FFT
added include/eigen3/unsupported/Eigen/IterativeSolvers
added include/eigen3/unsupported/Eigen/KroneckerProduct
added include/eigen3/unsupported/Eigen/LevenbergMarquardt
added include/eigen3/unsupported/Eigen/MPRealSupport
added include/eigen3/unsupported/Eigen/MatrixFunctions
added include/eigen3/unsupported/Eigen/MoreVectorization
added include/eigen3/unsupported/Eigen/NonLinearOptimization
added include/eigen3/unsupported/Eigen/NumericalDiff
added include/eigen3/unsupported/Eigen/OpenGLSupport
added include/eigen3/unsupported/Eigen/Polynomials
added include/eigen3/unsupported/Eigen/Skyline
added include/eigen3/unsupported/Eigen/SparseExtra
added include/eigen3/unsupported/Eigen/SpecialFunctions
added include/eigen3/unsupported/Eigen/Splines
added include/eigen3/unsupported/Eigen/src
added include/eigen3/unsupported/Eigen/src/AutoDiff
added include/eigen3/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h
added include/eigen3/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h
added include/eigen3/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h
added include/eigen3/unsupported/Eigen/src/BVH
added include/eigen3/unsupported/Eigen/src/BVH/BVAlgorithms.h
added include/eigen3/unsupported/Eigen/src/BVH/KdBVH.h
added include/eigen3/unsupported/Eigen/src/Eigenvalues
added include/eigen3/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h
added include/eigen3/unsupported/Eigen/src/EulerAngles
added include/eigen3/unsupported/Eigen/src/EulerAngles/EulerAngles.h
added include/eigen3/unsupported/Eigen/src/EulerAngles/EulerSystem.h
added include/eigen3/unsupported/Eigen/src/FFT
added include/eigen3/unsupported/Eigen/src/FFT/ei_fftw_impl.h
added include/eigen3/unsupported/Eigen/src/FFT/ei_kissfft_impl.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/DGMRES.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/GMRES.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/IterationController.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/MINRES.h
added include/eigen3/unsupported/Eigen/src/IterativeSolvers/Scaling.h
added include/eigen3/unsupported/Eigen/src/KroneckerProduct
added include/eigen3/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h
added include/eigen3/unsupported/Eigen/src/LevenbergMarquardt
added include/eigen3/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h
added include/eigen3/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h
added include/eigen3/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h
added include/eigen3/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h
added include/eigen3/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h
added include/eigen3/unsupported/Eigen/src/MatrixFunctions
added include/eigen3/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h
added include/eigen3/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h
added include/eigen3/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h
added include/eigen3/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h
added include/eigen3/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h
added include/eigen3/unsupported/Eigen/src/MatrixFunctions/StemFunction.h
added include/eigen3/unsupported/Eigen/src/MoreVectorization
added include/eigen3/unsupported/Eigen/src/MoreVectorization/MathFunctions.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/chkder.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/covar.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/dogleg.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/lmpar.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/r1updt.h
added include/eigen3/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h
added include/eigen3/unsupported/Eigen/src/NumericalDiff
added include/eigen3/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h
added include/eigen3/unsupported/Eigen/src/Polynomials
added include/eigen3/unsupported/Eigen/src/Polynomials/Companion.h
added include/eigen3/unsupported/Eigen/src/Polynomials/PolynomialSolver.h
added include/eigen3/unsupported/Eigen/src/Polynomials/PolynomialUtils.h
added include/eigen3/unsupported/Eigen/src/Skyline
added include/eigen3/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h
added include/eigen3/unsupported/Eigen/src/Skyline/SkylineMatrix.h
added include/eigen3/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h
added include/eigen3/unsupported/Eigen/src/Skyline/SkylineProduct.h
added include/eigen3/unsupported/Eigen/src/Skyline/SkylineStorage.h
added include/eigen3/unsupported/Eigen/src/Skyline/SkylineUtil.h
added include/eigen3/unsupported/Eigen/src/SparseExtra
added include/eigen3/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h
added include/eigen3/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h
added include/eigen3/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h
added include/eigen3/unsupported/Eigen/src/SparseExtra/MarketIO.h
added include/eigen3/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
added include/eigen3/unsupported/Eigen/src/SparseExtra/RandomSetter.h
added include/eigen3/unsupported/Eigen/src/SpecialFunctions
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/arch
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/arch/CUDA
added include/eigen3/unsupported/Eigen/src/SpecialFunctions/arch/CUDA/CudaSpecialFunctions.h
added include/eigen3/unsupported/Eigen/src/Splines
added include/eigen3/unsupported/Eigen/src/Splines/Spline.h
added include/eigen3/unsupported/Eigen/src/Splines/SplineFitting.h
added include/eigen3/unsupported/Eigen/src/Splines/SplineFwd.h
added include/kseq.h
deleted include/ksw2pp
deleted include/ksw2pp/KSW2Aligner.hpp
deleted include/ksw2pp/kalloc.h
deleted include/ksw2pp/ksw2.h
deleted include/metro
deleted include/metro/metrohash.h
deleted include/metro/metrohash128.h
deleted include/metro/metrohash128crc.h
deleted include/metro/metrohash64.h
deleted include/metro/platform.h
deleted include/metro/testvector.h
added include/posix.h
deleted include/tsl
deleted include/tsl/array_growth_policy.h
deleted include/tsl/array_hash.h
deleted include/tsl/array_map.h
deleted include/tsl/array_set.h
deleted include/tsl/bhopscotch_map.h
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deleted include/tsl/hopscotch_growth_policy.h
deleted include/tsl/hopscotch_hash.h
deleted include/tsl/hopscotch_map.h
deleted include/tsl/hopscotch_set.h
deleted include/tsl/robin_growth_policy.h
deleted include/tsl/robin_hash.h
deleted include/tsl/robin_map.h
deleted include/tsl/robin_set.h
added scripts/cpld.bash
modified scripts/fetchRapMap.sh
modified src/Alevin.cpp
added src/AlevinHash.cpp
modified src/AlevinUtils.cpp
modified src/AlignmentModel.cpp
added src/BAMUtils.cpp
modified src/BuildSalmonIndex.cpp
modified src/CMakeLists.txt
modified src/CollapsedCellOptimizer.cpp
modified src/CollapsedEMOptimizer.cpp
modified src/CollapsedGibbsSampler.cpp
modified src/DedupUMI.cpp
modified src/FastxParser.cpp
modified src/GZipWriter.cpp
modified src/Graph.cpp
modified src/ProgramOptionsGenerator.cpp
modified src/Salmon.cpp
modified src/SalmonAlevin.cpp
modified src/SalmonQuantMerge.cpp
modified src/SalmonQuantify.cpp
modified src/SalmonQuantifyAlignments.cpp
modified src/SalmonUtils.cpp
modified src/WhiteList.cpp
deleted src/ksw2pp
deleted src/ksw2pp/KSW2Aligner.cpp
deleted src/ksw2pp/kalloc.c
deleted src/ksw2pp/ksw2_dispatch.c
deleted src/ksw2pp/ksw2_extd.c
deleted src/ksw2pp/ksw2_extd2_sse.c
deleted src/ksw2pp/ksw2_extf2_sse.c
deleted src/ksw2pp/ksw2_exts2_sse.c
deleted src/ksw2pp/ksw2_extz.c
deleted src/ksw2pp/ksw2_extz2_sse.c
deleted src/ksw2pp/ksw2_gg.c
deleted src/ksw2pp/ksw2_gg2.c
deleted src/ksw2pp/ksw2_gg2_sse.c
deleted src/metro
deleted src/metro/metrohash128.cpp
deleted src/metro/metrohash128crc.cpp
deleted src/metro/metrohash64.cpp
added src/posix.cc
modified tests/alevin_test_data.tar.gz
modified tests/basic_alevin_test.sh
Committed revision 90.
Worker failed: An error (1) occurred refreshing quilt patches: None

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patching file CMakeLists.txt
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patching file src/CMakeLists.txt
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Patch debian/patches/use_debian_packaged_libs.patch does not apply (enforce with -f)

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