Closed dlfivefifty closed 6 years ago
ChrisRackauckas
commented
6 years ago That's fresh? it shouldn't be required on DiffEq in v0.6.3 at all. I am not sure if I can test it out right now since I don't want to uninstall everything while at JuliaCon.
ChrisRackauckas
commented
6 years ago Can I get the Pkg.status()?
dlfivefifty
commented
6 years ago julia> Pkg.status()
10 required packages:
- Atom 0.6.16
- BenchmarkTools 0.3.2
- CLArrays 0.1.3+ master
- DifferentialEquations 2.3.0
- DistributedArrays 0.4.0
- IJulia 1.9.1
- Juno 0.4.1
- PkgDev 0.2.1
- Plots 0.17.4
- RandomMatrices 0.4.0
194 additional packages:
- ASTInterpreter2 0.1.1
- AbstractFFTs 0.3.2
- Adapt 0.2.0
- AlgebraicDiffEq 0.1.0
- AlmostBandedMatrices 0.0.0- master (unregistered)
- ApproxFun 0.8.1+ master
- AssetRegistry 0.0.2
- AxisAlgorithms 0.3.0
- AxisArrays 0.2.1
- BandedMatrices 0.5.0+ master
- BinDeps 0.8.8
- BinaryProvider 0.3.3
- Blink 0.7.0
- BlockArrays 0.4.0+ master
- BlockBandedMatrices 0.1.0+ master
- CLBLAS 1.2.0- master
- CLFFT 0.5.2
- Calculus 0.4.0
- CatIndices 0.1.0
- ChunkedArrays 0.1.1
- CodeTools 0.5.1
- ColorTypes 0.6.7
- ColorVectorSpace 0.5.2
- Colors 0.8.2
- Combinatorics 0.6.0
- CommonSubexpressions 0.1.0
- Compat 1.0.0
- ComplexPhasePortrait 0.0.0- master (unregistered)
- ComputationalResources 0.2.0
- Conda 1.0.0
- Contour 0.4.0
- CoordinateTransformations 0.5.0
- CustomUnitRanges 0.1.0
- DSP 0.5.0
- DataStructures 0.8.4
- DebuggerFramework 0.1.2
- DelayDiffEq 3.6.0
- DiffBase 0.3.2
- DiffEqBase 3.13.3
- DiffEqBiological 2.3.2
- DiffEqCallbacks 1.1.1
- DiffEqDevTools 1.0.2
- DiffEqDiffTools 0.4.1
- DiffEqFinancial 1.0.1
- DiffEqJump 4.5.1
- DiffEqMonteCarlo 0.10.1
- DiffEqNoiseProcess 1.0.2
- DiffEqOperators 1.3.0
- DiffEqPDEBase 0.4.0
- DiffEqParamEstim 1.1.2
- DiffEqSensitivity 1.2.0
- DiffEqUncertainty 0.1.0
- DiffResults 0.0.3
- DiffRules 0.0.6
- DimensionalPlotRecipes 0.0.2
- Distances 0.6.0
- Distributions 0.15.0
- DocSeeker 0.1.0
- Domains 0.0.0- dl/approxfun (unregistered)
- DualNumbers 0.4.0
- EllipsisNotation 0.3.0
- FFTViews 0.1.0
- FFTW 0.0.4
- FastGaussQuadrature 0.3.1 master
- FastTransforms 0.4.0+ master
- FileIO 0.9.1
- FillArrays 0.1.0 master
- FiniteElementDiffEq 0.5.0
- FixedPointNumbers 0.4.6
- ForwardDiff 0.7.5
- FunctionWrappers 0.1.0
- FunctionalCollections 0.3.2
- GPUArrays 0.2.4+ master
- GR 0.31.0
- GSL 0.3.6
- GenericSVD 0.1.0
- Graphics 0.3.0
- Hiccup 0.1.1
- HierarchicalMatrices 0.1.2 master
- Homebrew 0.6.4
- HttpCommon 0.4.0
- HttpParser 0.4.0
- HttpServer 0.3.1
- IdentityRanges 0.1.0
- ImageAxes 0.4.0
- ImageCore 0.6.0
- ImageDistances 0.0.2
- ImageFiltering 0.3.0
- ImageMetadata 0.4.1
- ImageMorphology 0.0.2
- ImageTransformations 0.4.2
- Images 0.14.0
- IndirectArrays 0.4.2
- InfiniteArrays 0.0.0- master (unregistered)
- Interpolations 0.7.3
- IntervalSets 0.2.0+ dl/open
- IterTools 0.2.1
- IterativeSolvers 0.6.0
- IteratorInterfaceExtensions 0.0.2
- JSExpr 0.2.1
- JSON 0.17.2
- LNR 0.0.2
- Lazy 0.12.1
- LazyArrays 0.0.0- master (unregistered)
- LearnBase 0.1.6
- LineSearches 3.2.5
- LinearAlgebra 0.0.0- master (unregistered)
- LinearMaps 1.0.4
- LossFunctions 0.2.0
- LowRankApprox 0.1.3+ master
- LsqFit 0.3.0
- MacroTools 0.4.2
- MappedArrays 0.0.7
- Matcha 0.1.1
- MbedTLS 0.5.12
- Measures 0.2.0
- Media 0.3.0
- Missings 0.2.10
- MuladdMacro 0.0.2
- MultiScaleArrays 0.7.1
- MultivariateOrthogonalPolynomials 0.0.0- master (unregistered)
- Mustache 0.3.3
- Mux 0.3.1
- NLSolversBase 4.4.1
- NLsolve 1.0.1
- NaNMath 0.3.1
- NamedTuples 4.0.2
- Nullables 0.0.6
- Observables 0.1.2
- OffsetArrays 0.6.0
- OpenCL 0.7.0
- Optim 0.14.1
- OptimBase 1.0.0
- OrdinaryDiffEq 3.21.0
- OscillatoryIntegrals 0.0.0- master (unregistered)
- PDMats 0.8.0
- PaddedViews 0.3.0
- ParameterizedFunctions 3.1.0
- Parameters 0.9.1
- PenaltyFunctions 0.0.2
- Pidfile 1.0.0
- PlotThemes 0.2.0
- PlotUtils 0.4.4
- PoissonRandom 0.0.1
- Polynomials 0.4.0
- PositiveFactorizations 0.1.0
- Primes 0.3.0
- ProgressMeter 0.5.6
- QuadGK 0.3.0
- RandomNumbers 0.1.1
- RangeArrays 0.2.0
- RatFun 0.0.0- master (unregistered)
- Ratios 0.2.0
- RecipesBase 0.3.1
- RecursiveArrayTools 0.15.0
- Reexport 0.1.0
- Requires 0.4.4
- ResettableStacks 0.3.1
- RiemannHilbert 0.0.0- master (unregistered)
- Rmath 0.4.0
- Roots 0.6.0
- Rotations 0.7.2
- SHA 0.5.7
- SIUnits 0.1.0
- SO 0.0.0- master (unregistered)
- ShowItLikeYouBuildIt 0.2.0
- Showoff 0.2.0
- SimpleTraits 0.6.0
- SingularIntegralEquations 0.3.2+ development
- SortingAlgorithms 0.2.1
- SpecialFunctions 0.6.0
- SpectralMeasures 0.0.0- master (unregistered)
- StaticArrays 0.7.2
- StatsBase 0.23.1
- StatsFuns 0.6.1
- SteadyStateDiffEq 0.4.0
- StochasticDiffEq 4.4.5
- StringDistances 0.2.1
- Sugar 0.4.5
- Sundials 1.6.0
- SymEngine 0.4.1
- TableTraits 0.2.0
- TexExtensions 0.1.0
- TiledIteration 0.1.0
- ToeplitzMatrices 0.4.1 master
- Tokenize 0.4.2
- Transpiler 0.4.6+ sd/funcprototypes
- URIParser 0.3.1
- VectorizedRoutines 0.0.2
- VersionParsing 1.1.1
- WebIO 0.2.5
- WebSockets 0.5.0
- WoodburyMatrices 0.3.0
- ZMQ 0.6.3I have no idea why you have DifferentialEquations.jl 2.3.0, but you should have 4.5.0 in a fresh install. This doesn't look like a fresh install though: there's a bunch of other pinned packages. I don't know if that actually caused something to downgrade or if it's just a v0.6 resolver bug.
dlfivefifty
commented
6 years ago Ah, "fresh" was not the right word: "fresh" as in I didn't have DifferentialEquations.jl and then called Pkg.add("DifferentialEquations").
I'll try later with an actual fresh install.
dlfivefifty
commented
6 years ago Though I guess the actual issue is a missing upper bound somewhere in METADATA: DifferentialEquations.jl v2.3 should work.
ChrisRackauckas
commented
6 years ago No, if I put the upper bound then all of METADATA breaks, so it can't be there. Upper bounds isn't friendly to the Pkg2 resolver.
ChrisRackauckas
commented
6 years ago Closing this as specific to the master branches chosen there. A clean build should work though, and sometimes the Pkg2 resolver breaks but that's an upstream issue. v0.7/v1.0 shouldn't have any issues though given the new environments setup.
pjgorski
commented
6 years ago Hi, my issue is similar to the above, so I put my post here.
Everything had worked fine until today I made few updates: updated Atom.jl, added one package ("MAT"), clicked Pkg.update(). Currently I am on Julia 0.6.4.
From now on, the code fails on 'using DifferentialEquations'. Part of error message:
INFO: Precompiling module DifferentialEquations. WARNING: Module DataStructures with uuid 174515684151649 is missing from the cache. This may mean module DataStructures does not support precompilation but is imported by a module that does. ERROR: LoadError: Declaring precompile(false) is not allowed in files that are being precompiled. (...) while loading /home/pgorski/.julia/v0.6/DiffEqNoiseProcess/src/DiffEqNoiseProcess.jl, in expression starting on line 5 ERROR: LoadError: Failed to precompile DiffEqNoiseProcess to /home/pgorski/.julia/lib/v0.6/DiffEqNoiseProcess.ji. (...) while loading /home/pgorski/.julia/v0.6/DifferentialEquations/src/DifferentialEquations.jl, in expression starting on line 9 ERROR: LoadError: Failed to precompile DifferentialEquations to /home/pgorski/.julia/lib/v0.6/DifferentialEquations.ji.
DifferentialEquations also fails tests:
julia> Pkg.test("DifferentialEquations") INFO: Computing test dependencies for DifferentialEquations... INFO: Cloning cache of DiffEqProblemLibrary from https://github.com/JuliaDiffEq/DiffEqProblemLibrary.jl.git INFO: Installing DiffEqProblemLibrary v2.5.0 INFO: Building DiffEqBase (...) INFO: Building SpecialFunctions INFO: Building SymEngine Info: Found a valid dl path libgmp.so while looking for libmpfr (...) Info: /home/pgorski/.julia/v0.6/SymEngine/deps/symengine-0.3/lib/libmpfr.so matches our search criteria of libmpfr Info: Found a valid dl path libgmp.so while looking for libgmp Info: /home/pgorski/.julia/v0.6/SymEngine/deps/symengine-0.3/lib/libgmp.so matches our search criteria of libgmp Info: Found a valid dl path libgmp.so while looking for libsymengine (...) Info: /home/pgorski/.julia/v0.6/SymEngine/deps/symengine-0.3/lib/libsymengine.so matches our search criteria of libsymengine Info: Found a valid dl path libgmp.so while looking for libmpc (...) Info: /home/pgorski/.julia/v0.6/SymEngine/deps/symengine-0.3/lib/libmpc.so matches our search criteria of libmpc INFO: Building RandomNumbers g++ -shared -fPIC -O3 -maes aesni.cpp ars.cpp -o librandom123.so INFO: Testing DifferentialEquations Starting tests Test Summary: | Pass Total Default Discrete Algorithm | 1 1 3.804607 seconds (2.22 M allocations: 123.514 MiB, 1.32% gc time) Test Summary: | Pass Total Default ODE Algorithm | 21 21 217.452485 seconds (147.65 M allocations: 13.034 GiB, 1.62% gc time) Test Summary: | Pass Total Default Steady State Algorithm | 1 1 13.981563 seconds (12.35 M allocations: 580.785 MiB, 1.85% gc time) Default SDE Algorithm: Test Failed Expression: typeof(sol.alg) <: EM Stacktrace: [1] include_from_node1(::String) at ./loading.jl:576 [2] include(::String) at ./sysimg.jl:14 [3] macro expansion at /home/pgorski/.julia/v0.6/DifferentialEquations/test/runtests.jl:8 [inlined] [4] macro expansion at ./test.jl:860 [inlined] [5] macro expansion at ./util.jl:237 [inlined] [6] anonymous at ./
:? Default SDE Algorithm: Test Failed Expression: typeof(sol.alg) <: EulerHeun Stacktrace: [1] include_from_node1(::String) at ./loading.jl:576 [2] include(::String) at ./sysimg.jl:14 [3] macro expansion at /home/pgorski/.julia/v0.6/DifferentialEquations/test/runtests.jl:8 [inlined] [4] macro expansion at ./test.jl:860 [inlined] [5] macro expansion at ./util.jl:237 [inlined] [6] anonymous at ./ :? Test Summary: | Pass Fail Total Default SDE Algorithm | 6 2 8 ERROR: LoadError: Some tests did not pass: 6 passed, 2 failed, 0 errored, 0 broken. while loading /home/pgorski/.julia/v0.6/DifferentialEquations/test/runtests.jl, in expression starting on line 8 =====================================================================================[ ERROR: DifferentialEquations ]====================================================================================== failed process: Process(
/home/pgorski/julia-9d11f62bcb/bin/julia -Cgeneric -J/home/pgorski/julia-9d11f62bcb/lib/julia/sys.so --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes /home/pgorski/.julia/v0.6/DifferentialEquations/test/runtests.jl, ProcessExited(1)) [1] (...)
Part of Pkg.status():
julia> Pkg.status() 5 required packages:
- Atom 0.6.16
- BenchmarkTools 0.3.2
- DifferentialEquations 4.5.0
- MAT 0.4.0
- Plots 0.17.4 127 additional packages: (...)
- DataStructures 0.8.4
- DebuggerFramework 0.1.2
- DelayDiffEq 3.6.0
- DiffBase 0.3.2
- DiffEqBase 3.13.3
- DiffEqBiological 2.3.2
- DiffEqCallbacks 1.1.1
- DiffEqDevTools 1.0.2
- DiffEqDiffTools 0.4.1
- DiffEqFinancial 1.0.1
- DiffEqJump 4.5.1
- DiffEqMonteCarlo 0.10.1
- DiffEqNoiseProcess 1.0.2
- DiffEqOperators 1.3.0
- DiffEqPDEBase 0.4.0
- DiffEqParamEstim 1.1.2
- DiffEqPhysics 1.0.0
- DiffEqSensitivity 1.2.0
- DiffEqUncertainty 0.1.0
- DiffResults 0.0.3
- DiffRules 0.0.7 (...)
- GR 0.32.3
- GenericSVD 0.1.0 (...)
- NLSolversBase 4.4.1
- NLsolve 1.0.1
- NaNMath 0.3.2
- NamedTuples 4.0.2
- Nullables 0.0.7
- Observables 0.1.2
- Optim 0.14.1
- OptimBase 1.0.0
- OrdinaryDiffEq 3.21.0
- PDMats 0.8.0 (...)
- StaticArrays 0.7.2
- StatsBase 0.23.1
- StatsFuns 0.6.1
- SteadyStateDiffEq 0.4.0
- StochasticDiffEq 4.4.5
- StringDistances 0.2.1
- Sundials 1.6.0
- SymEngine 0.4.2 (...)
ChrisRackauckas
commented
6 years ago Those are two different things. The first just requires that you start Julia: it cannot recompile files which are still in use. The second part is that SymEngine didn't build properly on your system. Re-run Pkg.build("SymEngine") and if it fails then you might want to report to SymEngine.jl, though they are probably on master now.
pjgorski
commented
6 years ago Thanks! (Before posting I have restarted Julia. )
After running Pkg.build("SymEngine") and restarting ones again, everything works fine.
I just did a fresh `Pkg.add("DifferentialEquations") in 0.6.3 and get the following: