DifferentialEquations Pkg won't be added

package

#6

Yeap, I always do Pkg.update() before adding any package. But sometimes I feel (not convince) that updating Github repositories is not promptly applied to Julia METADATA. I’ll try again tomorrow :slight_smile:


#7

Alright. Let me know if you have any issues. It should all be fixed, but if it’s not then you’re a good test case :slight_smile:.


#8

Hi Chris,

To jump in here if that’s ok, this morning Pkg.add(“DifferentialEquations”) indeed installed again. Is below list, e.g. DifferentialEquations.jl v"1.5.0", correct on Julia v"0.5.1"? This is after a (daily) Pkg.update().

Regards,
Rob

julia> Pkg.add(“DifferentialEquations”)
INFO: Updating cache of DiffEqPDEBase…
INFO: Updating cache of LearnBase…
INFO: Updating cache of ParameterizedFunctions…
INFO: Updating cache of Sundials…
INFO: Updating cache of SymEngine…
INFO: Installing AlgebraicDiffEq v0.1.0
INFO: Installing ChunkedArrays v0.1.1
INFO: Downgrading DiffEqBase: v0.15.0 => v0.6.0
INFO: Installing DiffEqDevTools v0.6.0
INFO: Installing DiffEqPDEBase v0.1.0
INFO: Installing DiffEqParamEstim v0.1.0
INFO: Installing DiffEqSensitivity v0.0.4
INFO: Installing DifferentialEquations v1.5.0
INFO: Installing EllipsisNotation v0.0.2
INFO: Installing FiniteElementDiffEq v0.2.1
INFO: Installing GenericSVD v0.0.2
INFO: Installing InplaceOps v0.1.0
INFO: Installing LearnBase v0.1.5
INFO: Installing LossFunctions v0.0.3
INFO: Downgrading ODE: v0.4.0 => v0.3.0
INFO: Installing OrdinaryDiffEq v1.0.2
INFO: Installing ParameterizedFunctions v1.2.0
INFO: Installing ResettableStacks v0.1.0
INFO: Installing StochasticDiffEq v0.5.0
INFO: Installing StokesDiffEq v0.1.0
INFO: Installing Sundials v0.9.0
INFO: Installing SymEngine v0.1.5
INFO: Installing VectorizedRoutines v0.0.2
INFO: Building Rmath
INFO: Building Sundials
INFO: Building Conda
INFO: Building SymEngine
INFO: Package database updated

This is on:

julia> versioninfo()
Julia Version 0.5.1
Commit 6445c82 (2017-03-05 13:25 UTC)
Platform Info:
OS: macOS (x86_64-apple-darwin13.4.0)
CPU: Intel® Core™ i5-6267U CPU @ 2.90GHz
WORD_SIZE: 64
BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
LAPACK: libopenblas64_
LIBM: libopenlibm
LLVM: libLLVM-3.7.1 (ORCJIT, broadwell)


#9

Hmm, I just wiped .julia and install gave DifferentialEquations v1.10.1 with DiffEqBase v0.15.0. For some reason it’s giving you a really old version. Would you mind posting your Pkg.status() so I can investigate this a bit? During this update I think we ran into a package resolver bug in Pkg, and we’re still not quite sure why the downgrading is happening in some cases.

Note that if you have LSODA.jl installed, you will get downgraded. That’s the only case I currently know of, and it hasn’t updated yet because that’s related to this other Discourse question:

But hopefully that will get worked out soon a new version can be tagged there. For now, if you have LSODA.jl, remove it (it doesn’t come standard with DifferentialEquations, so it’s only there if you intentionally installed it)


#10

Thanks Chris,

Attached the (long) list. LSODA.jl is not installed.

I’m quite ok to wipe .julia v"0.5" to try what you did (last time I tried that was late December). I’ll hold off for now until you have had time if to scan this list and maybe would like me to try something.

Regards,
Rob

           _

_ _ ()_ | A fresh approach to technical computing
() | () () | Documentation: http://docs.julialang.org
_ _ | | __ _ | Type “?help” for help.
| | | | | | |/ ` | |
| | |
| | | | (
| | | Version 0.5.1 (2017-03-05 13:25 UTC)
/ |_|||_’_| | Official http://julialang.org/ release
|__/ | x86_64-apple-darwin13.4.0

julia> Pkg.status()
53 required packages:

  • ApproxFun 0.6.0
  • Atom 0.5.10
  • BenchmarkTools 0.0.7
  • CSV 0.1.4
  • Cairo 0.3.0
  • Cbc 0.3.1
  • Clp 0.3.0
  • Combinatorics 0.4.0
  • DataFrames 0.9.0
  • DataTables 0.0.2
  • Dierckx 0.2.0
  • DifferentialEquations 1.5.0
  • Documenter 0.9.2
  • Escher 0.3.3
  • Espresso 0.1.0+ master
  • GLM 0.7.0
  • GR 0.19.0
  • Gadfly 0.6.0
  • GraphViz 0.1.0
  • Graphs 0.7.1+ master
  • HDF5 0.8.0
  • Homebrew 0.5.6
  • HyperDualNumbers 1.0.0
  • IJulia 1.4.1
  • Interact 0.4.3
  • Interpolations 0.4.0
  • Ipopt 0.2.6
  • IterativeSolvers 0.2.2
  • Jags 1.0.2+ master
  • JuMP 0.16.2
  • JuliaFEM 0.2.1
  • Lint 0.5.0
  • LsqFit 0.2.0
  • Luxor 0.8.3
  • Mamba 0.10.0
  • NLsolve 0.9.1
  • ODE 0.3.0
  • Permutations 0.0.1
  • PkgDev 0.1.3
  • Plots 0.10.3+ master
  • PyPlot 2.3.1
  • Query 0.3.2+ master
  • RCall 0.7.2
  • Roots 0.3.0
  • Stan 1.0.2+ master
  • StaticArrays 0.3.0
  • Switch 0.0.1
  • Symata 0.2.0+ master
  • TaylorSeries 0.4.0
  • TypedTables 0.1.2
  • Unitful 0.2.2+ master
  • Unums 0.2.1
  • WriteVTK 0.5.1
    162 additional packages:
  • ASTInterpreter 0.0.4
  • AbstractTrees 0.0.4
  • AlgebraicDiffEq 0.1.0
  • ArgParse 0.4.0
  • AxisAlgorithms 0.1.6
  • AxisArrays 0.1.2
  • BHAA 0.0.0- master (unregistered)
  • BHAAnalysis 0.0.0- master (unregistered)
  • BHACases 0.0.0- master (unregistered)
  • BHAPlotRecipes 0.0.0- master (unregistered)
  • BandedMatrices 0.2.2
  • BinDeps 0.4.7
  • Blink 0.5.1
  • Blosc 0.2.0
  • BoreHoleAssemblyAnalysis 0.0.0- master (unregistered)
  • BufferedStreams 0.3.2
  • COFF 0.0.2
  • CRC 1.2.0
  • Calculus 0.2.2
  • CategoricalArrays 0.1.3
  • ChunkedArrays 0.1.1
  • ClassicalLaminateTheory 0.0.0- master (unregistered)
  • CodeTools 0.4.3
  • Codecs 0.3.0
  • ColorTypes 0.4.0
  • Colors 0.7.3
  • Compat 0.23.0
  • Compose 0.5.0
  • Conda 0.5.3
  • Contour 0.2.0
  • DWARF 0.1.0
  • DataArrays 0.3.12
  • DataStreams 0.1.3
  • DataStructures 0.5.3
  • Dates 0.4.4
  • DiffBase 0.1.0
  • DiffEqBase 0.6.0
  • DiffEqDevTools 0.6.0
  • DiffEqPDEBase 0.1.0
  • DiffEqParamEstim 0.1.0
  • DiffEqSensitivity 0.0.4
  • Distances 0.4.1
  • Distributions 0.12.3
  • DocStringExtensions 0.3.2
  • DualNumbers 0.3.0
  • EDxMIT15053 0.0.0- master (unregistered)
  • EDxMIT201 0.0.0- master (unregistered)
  • EDxMath226 0.0.0- master (unregistered)
  • EEM 0.0.0- master (unregistered)
  • ELF 0.1.0
  • Einsum 0.1.0
  • EllipsisNotation 0.0.2
  • FactCheck 0.4.3
  • FastGaussQuadrature 0.2.1
  • FastTransforms 0.1.0
  • FileIO 0.3.1
  • FiniteElementDiffEq 0.2.1
  • FixedPointNumbers 0.3.6
  • FixedSizeArrays 0.2.5
  • Formatting 0.2.1
  • ForwardDiff 0.4.2
  • FunctionalCollections 0.3.2
  • GZip 0.3.0
  • Gallium 0.0.4
  • GenericSVD 0.0.2
  • Geomechanics 0.0.0- master (unregistered)
  • Graphics 0.2.0
  • Hexagons 0.1.0
  • Hiccup 0.1.1
  • HttpCommon 0.2.7
  • HttpParser 0.2.0
  • HttpServer 0.2.0
  • InplaceOps 0.1.0
  • IntervalSets 0.0.5
  • IterableTables 0.0.0- master (unregistered)
  • Iterators 0.3.0
  • JLD 0.6.10
  • JSON 0.9.0
  • JuliaParser 0.7.4
  • Juno 0.2.7
  • KernelDensity 0.3.2
  • LNR 0.0.2
  • LaTeXStrings 0.2.1
  • Lazy 0.11.6
  • LearnBase 0.1.5
  • LegacyStrings 0.2.1
  • Libz 0.2.4
  • LightXML 0.5.0
  • LineSearches 0.1.5
  • Loess 0.2.0
  • Logging 0.3.1
  • LossFunctions 0.0.3
  • MachO 0.0.4
  • MacroTools 0.3.6
  • Markdown 0.3.0
  • Matcha 0.0.1
  • MathProgBase 0.6.4
  • MbedTLS 0.4.5
  • Measures 0.1.0
  • Media 0.2.7
  • Memoize 0.1.0
  • Mustache 0.1.4
  • Mux 0.2.3
  • NMfE 0.0.0- master (unregistered)
  • NaNMath 0.2.4
  • NamedArrays 0.6.0
  • NamedTuples 2.1.0
  • Nettle 0.3.0
  • NullableArrays 0.1.0
  • ObjFileBase 0.0.4
  • Optim 0.7.8
  • OrdinaryDiffEq 1.0.2
  • PDMats 0.5.6
  • ParameterizedFunctions 1.2.0
  • Parameters 0.7.2
  • Patchwork 0.3.1
  • PlotThemes 0.1.1
  • PlotUtils 0.3.0
  • PolynomialFactors 0.0.4
  • Polynomials 0.1.5
  • PositiveFactorizations 0.0.4
  • Primes 0.1.3
  • PtFEM 0.0.0- master (unregistered)
  • PyCall 1.11.1
  • QuadGK 0.1.2
  • RangeArrays 0.1.2
  • Ranges 0.0.1
  • Ratios 0.0.4
  • Reactive 0.3.7
  • RecipesBase 0.1.0
  • RecursiveArrayTools 0.2.0
  • Reexport 0.0.3
  • Requires 0.3.0
  • ResettableStacks 0.1.0
  • ReverseDiffSparse 0.7.2
  • Rmath 0.1.6
  • RobGoedmansNotebooks 0.0.0- master (unregistered)
  • SHA 0.3.2
  • Showoff 0.1.1
  • SimpleTraits 0.4.0+ master
  • SortingAlgorithms 0.1.1
  • SpecialFunctions 0.1.1
  • StatsBase 0.13.1
  • StatsFuns 0.5.0
  • StochasticDiffEq 0.5.0
  • StokesDiffEq 0.1.0
  • StructIO 0.0.2
  • Sugar 0.1.0
  • Sundials 0.9.0
  • SymEngine 0.1.5
  • TerminalUI 0.0.2
  • TextWrap 0.2.0
  • ToeplitzMatrices 0.2.0
  • URIParser 0.1.8
  • UnitfulOFU 0.0.0- master (unregistered)
  • UnitfulPlots 0.0.0- master (unregistered)
  • VT100 0.1.0
  • VectorizedRoutines 0.0.2
  • WeakRefStrings 0.2.0
  • WebSockets 0.2.1
  • WoodburyMatrices 0.2.2
  • ZMQ 0.4.2

#11

For what it’s worth, my most recent bout of ‘unsatisfiable package requirements’ also limited me to DifferentialEquations v1.5.


#12

Not sure if it is true for others. But doing a clean reinstall of all my Julia packages, I find that I can’t have both the Juno stuff (Atom etc) and DifferentialEquations at the same time. But I can have just DiffEq stuff now if I don’t install Atom!


#13

Oops, thank you, that fixed it for me as well! (I just dir Pkg.rm(“Atom”) and all packages were upgraded)


#14

Do you guys have ImageMagick.jl installed? I can reproduce this by, in a fresh install:

  1. Adding DifferentialEquations
  2. Setting up Juno
  3. Adding Plots
  4. Adding ImageMagick

I’ll start trying to find out what’s up (or if it’s a Pkg resolver issue), but if we can narrow down the test case it would help.


#15

No, I haven’t, but I remember I had similar storms around Image.jl and co a couple of weeks ago so I removed them.

Below what Pkg.rm(“Atom”) did:

julia> Pkg.rm(“Atom”)
INFO: Updating cache of DelayDiffEq…
INFO: Updating cache of DiffEqCallbacks…
INFO: Updating cache of DiffEqDevTools…
INFO: Updating cache of DiffEqFinancial…
INFO: Updating cache of DiffEqJump…
INFO: Updating cache of DiffEqMonteCarlo…
INFO: Updating cache of DiffEqParamEstim…
INFO: Updating cache of DiffEqSensitivity…
INFO: Updating cache of DifferentialEquations…
INFO: Updating cache of FiniteElementDiffEq…
INFO: Updating cache of OrdinaryDiffEq…
INFO: Updating cache of StochasticDiffEq…
INFO: Installing DelayDiffEq v0.3.0
INFO: Upgrading DiffEqBase: v0.6.0 => v0.15.0
INFO: Installing DiffEqBiological v0.0.1
INFO: Installing DiffEqCallbacks v0.0.2
INFO: Upgrading DiffEqDevTools: v0.6.0 => v0.7.0
INFO: Installing DiffEqFinancial v0.1.0
INFO: Installing DiffEqJump v0.3.0
INFO: Installing DiffEqMonteCarlo v0.2.0
INFO: Upgrading DiffEqPDEBase: v0.1.0 => v0.2.0
INFO: Upgrading DiffEqParamEstim: v0.1.0 => v0.2.0
INFO: Upgrading DiffEqSensitivity: v0.0.4 => v0.1.0
INFO: Upgrading DifferentialEquations: v1.5.0 => v1.10.1
INFO: Upgrading FiniteElementDiffEq: v0.2.1 => v0.3.0
INFO: Installing MultiScaleArrays v0.1.0
INFO: Upgrading ODE: v0.3.0 => v0.4.0
INFO: Upgrading OrdinaryDiffEq: v1.0.2 => v1.8.0
INFO: Upgrading ParameterizedFunctions: v1.2.0 => v1.3.0
INFO: Upgrading StochasticDiffEq: v0.5.0 => v1.4.0
INFO: Upgrading Sundials: v0.9.0 => v0.10.0
INFO: Removing ASTInterpreter v0.0.4
INFO: Removing AbstractTrees v0.0.4
INFO: Removing Atom v0.5.10
INFO: Removing Blink v0.5.1
INFO: Removing COFF v0.0.2
INFO: Removing CRC v1.2.0
INFO: Removing CodeTools v0.4.3
INFO: Removing DWARF v0.1.0
INFO: Removing ELF v0.1.0
INFO: Removing Gallium v0.0.4
INFO: Removing JuliaParser v0.7.4
INFO: Removing LNR v0.0.2
INFO: Removing MachO v0.0.4
INFO: Removing Mustache v0.1.4
INFO: Removing ObjFileBase v0.0.4
INFO: Removing StructIO v0.0.2
INFO: Removing TerminalUI v0.0.2
INFO: Removing VT100 v0.1.0
INFO: Building Rmath
INFO: Building Sundials
INFO: Building Conda
INFO: Building SymEngine
INFO: Package database updated

julia> Pkg.installed(“ImageMagick”)


#16

I’m now playing around and getting from really wild results. Example, adding and removing Plots/ImageMagick a few times, now it will sometimes downgrade after removing a package.

Pkg.update()
INFO: Updating METADATA...
INFO: Computing changes...
INFO: No packages to install, update or remove

Pkg.rm("Plots")
INFO: Downgrading ForwardDiff: v0.4.2 => v0.2.5
INFO: Downgrading LsqFit: v0.2.0 => v0.1.0
INFO: Downgrading NLsolve: v0.9.1 => v0.8.0
INFO: Downgrading Optim: v0.7.8 => v0.6.1
INFO: Removing DiffBase v0.1.0
INFO: Removing FixedSizeArrays v0.2.5
INFO: Removing Measures v0.1.0
INFO: Removing PlotThemes v0.1.1
INFO: Removing PlotUtils v0.3.0
INFO: Removing Plots v0.10.3
INFO: Removing Showoff v0.1.1

We should bring @tkelman in on this, but that sounds like a resolver bug to me. I looked around and don’t see any package with a Juno.jl maximum version (only minimum versions), so I don’t see how that could downgrade things.

Is there an easy way to query what set of version requirements caused the downgrades?


#17

I believe it is a resolver bug, I have never been able to find an actual version compatibility conflict, and I’ve been getting these errors basically every time I try and update for weeks.


#18

Well if it is, for better or worse, at least it sounds like we have a reproducible example.


#19

Maybe More Pkg trouble: "unsatisfiable package requirements detected" from a few days ago is related?


#20

Does this issue also occur on 0.6? @carlobaldassi contributed several PRs improving the resolver. I don’t know if those have been backported yet.


#21

I tried Pkg.update() and Pkg.add("DifferentialEquations") under the fresh condition, and finally managed to add the package! However, under this condition I couldn’t add Atom. I agree with @crbinz.


#22

One was backported to 0.5.1, the other was not. One of the cases where the metadata sanity check failed yesterday would happen on 0.5.1 but not 0.5.0, which seems to have been a situation where the resolver got worse from one of the recent changes.


#23

I’ll tag LSODA.jl soon. That’s the only package without a release to satisfy DiffEqBase 0.15.0. It’s not required by DifferentialEquations.jl, but I wonder if by its mere existence that’s what’s causing the downgrade. This “other package exists” being the problem would make sense with the METADATA sanity check issues we had.


#24

LSODA.jl got tagged and I cannot recreate the problem anymore. Can someone else who was noting this give it a try?

If no one can re-create this anymore, then it’s definitely because the package resolver was being pulled back by LSODA, even if you didn’t have it installed.


#25

Pkg.add(“Atom”) still downgrades quite a few packages, maybe forced by the downgrading of DiffEqBase?


julia> Pkg.add(“Atom”)
INFO: Installing ASTInterpreter v0.0.4
INFO: Installing AbstractTrees v0.0.4
INFO: Installing Atom v0.5.10
INFO: Installing Blink v0.5.1
INFO: Installing COFF v0.0.2
INFO: Installing CRC v1.2.0
INFO: Installing CodeTools v0.4.3
INFO: Installing DWARF v0.1.0
INFO: Downgrading DiffEqBase: v0.15.0 => v0.6.0
INFO: Downgrading DiffEqDevTools: v0.7.0 => v0.6.0
INFO: Downgrading DiffEqPDEBase: v0.2.0 => v0.1.0
INFO: Downgrading DiffEqParamEstim: v0.2.0 => v0.1.0
INFO: Downgrading DiffEqSensitivity: v0.1.0 => v0.0.4
INFO: Downgrading DifferentialEquations: v1.10.1 => v1.5.0
INFO: Installing ELF v0.1.0
INFO: Downgrading FiniteElementDiffEq: v0.3.0 => v0.2.1
INFO: Installing Gallium v0.0.4
INFO: Installing JuliaParser v0.7.4
INFO: Installing LNR v0.0.2
INFO: Installing MachO v0.0.4
INFO: Installing Mustache v0.1.4
INFO: Downgrading ODE: v0.4.0 => v0.3.0
INFO: Installing ObjFileBase v0.0.4
INFO: Downgrading OrdinaryDiffEq: v1.8.0 => v1.0.2
INFO: Downgrading ParameterizedFunctions: v1.3.0 => v1.2.0
INFO: Downgrading StochasticDiffEq: v1.4.0 => v0.5.0
INFO: Installing StructIO v0.0.2
INFO: Downgrading Sundials: v0.10.0 => v0.9.0
INFO: Installing TerminalUI v0.0.2
INFO: Installing VT100 v0.1.0
INFO: Removing DelayDiffEq v0.3.0
INFO: Removing DiffEqBiological v0.0.1
INFO: Removing DiffEqCallbacks v0.0.2
INFO: Removing DiffEqFinancial v0.1.0
INFO: Removing DiffEqJump v0.3.0
INFO: Removing DiffEqMonteCarlo v0.2.0
INFO: Removing MultiScaleArrays v0.1.0
INFO: Building HttpParser
INFO: Building Homebrew