Gallium.jl
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Can not precompile Gallium
I'm relatively new to Julia and wanted to try out Gallium.jl
When I tried I get this error:
I tried to build, remove/add, and checkout the package. But I still get the same error. Help! Plz?
I am working on a Mac with macOS Sierra. Julia version 0.5.0. Gallium version 0.0.4
Pkg.free("DWARF") might help. (Independent but also recommended, you might want to upgrade to 0.5.2.)
Unfortunately, Pkg.free("DWARF") didnt work. Also how do I upgrade without deleting my current julia and reinstall it. Will I have to reinstall all of my packages?
If you built from source it should be git pull && make. You should make sure you're on the release-0.5 branch. If you downloaded a binary you should just download a fresher one, deleting the old one. You won't need to reinstall all your packages, though the first time you use it you will have to recompile.
Unfortunately, Pkg.free("DWARF") didnt work.
What does "didn't work" mean? Did it give an error message, or did it just not solve the problem? For more help you'll probably need to post the results of Pkg.status().
Sorry, I meant that it did not fix the problem
I then kept getting the same error.
I ran Pkg.status() and this was the result
julia>Pkg.status() 69 required packages:
- Atom 0.5.10
- Bio 0.4.7
- BioMedQuery 0.2.2
- Blink 0.5.2
- CUDArt 0.3.1
- Clp 0.3.1
- Compat 0.26.0
- Conda 0.5.3
- Cxx 0.1.1
- DecisionTree 0.6.0
- DifferentialEquations 2.2.1
- Distributions 0.13.0
- Documenter 0.11.1
- Escher 0.3.3
- Evolutionary 0.1.2
- EvolvingGraphs 0.1.0
- Flux 0.1.1
- Gadfly 0.6.2
- Gallium 0.0.4+ master
- GraphLayout 0.3.1
- GraphPlot 0.1.0
- Homebrew 0.5.7
- HttpParser 0.2.0
- IJulia 1.5.0
- Interact 0.4.5
- JuMP 0.17.1
- JuliaWebAPI 0.2.1
- LightGraphs 0.7.7
- LightGraphsExtras 0.1.0
- Lint 0.5.2
- Logging 0.3.1
- MAT 0.3.2
- MXNet 0.2.3
- MatrixDepot 0.5.6
- MatrixNetworks 0.1.0
- Mosek 0.6.1
- Mux 0.2.3
- MySQL 0.1.0
- NetworkViz 0.0.2
- ODBC 0.5.2
- ODE 0.6.0
- OpenGene 0.1.10
- ParallelAccelerator 0.2.2
- PhyloNetworks 0.5.0
- PlotRecipes 0.2.0
- Plotly 0.1.1
- PlotlyJS 0.6.2
- Plots 0.11.3
- Primes 0.1.3
- ProfileView 0.2.1
- PyCall 1.12.0
- PyPlot 2.3.2
- QuantEcon 0.10.1
- RDatasets 0.2.0
- RecipesBase 0.1.0
- Requests 0.4.1
- SQLite 0.4.5
- ScikitLearn 0.3.0
- StatPlots 0.3.0
- StatsBase 0.16.0
- Sundials 0.12.0
- TensorFlow 0.6.1
- ThreeJS 0.3.0
- TikzGraphs 0.5.0
- Twitter 0.3.0
- TypeCheck 0.0.3
- WAV 0.8.5
- Wallace 0.0.1
- Winston 0.13.0 188 additional packages:
- ASTInterpreter 0.0.4+ master
- AbstractTrees 0.1.0 master
- AlgebraicDiffEq 0.1.0
- ArgParse 0.5.0
- AutoHashEquals 0.1.1
- AxisAlgorithms 0.1.6
- BGZFStreams 0.1.3
- BaseTestNext 0.2.2
- BinDeps 0.6.0
- Blosc 0.2.1
- BlossomV 0.3.0
- BufferedStreams 0.3.3
- COFF 0.0.2+ master
- CRC 1.2.0
- CUDAdrv 0.4.0
- Cairo 0.3.0
- Calculus 0.2.2
- CategoricalArrays 0.1.4
- Cbc 0.3.2
- ChunkedArrays 0.1.1
- Clustering 0.8.0
- CodeTools 0.4.5
- Codecs 0.3.0
- ColorTypes 0.5.1
- Colors 0.7.3
- Combinatorics 0.4.0
- CompilerTools 0.2.1
- Compose 0.5.2
- ConfParser 0.0.9
- Contour 0.3.0
- CoupledFields 0.0.1
- DSP 0.2.0
- DWARF 0.1.0
- DataArrays 0.4.1
- DataFlow 0.1.0
- DataFrames 0.9.1
- DataStreams 0.1.3
- DataStructures 0.5.3
- Dates 0.4.4
- DecFP 0.3.0
- DelayDiffEq 0.4.0
- DevTools 0.0.0- master (unregistered)
- DiffBase 0.1.0
- DiffEqBase 1.9.0
- DiffEqBiological 0.2.0
- DiffEqCallbacks 0.1.1
- DiffEqDevTools 0.8.1
- DiffEqFinancial 0.2.0
- DiffEqJump 0.4.0
- DiffEqMonteCarlo 0.6.0
- DiffEqNoiseProcess 0.2.0
- DiffEqPDEBase 0.3.2
- DiffEqParamEstim 0.4.0
- DiffEqSensitivity 0.2.2
- DiffEqUncertainty 0.0.1
- DimensionalPlotRecipes 0.0.2
- Distances 0.4.1
- DocOpt 0.2.1
- DocStringExtensions 0.3.3
- DualNumbers 0.3.0
- ELF 0.1.0+ master
- EllipsisNotation 0.1.0
- EzXML 0.4.3
- FactCheck 0.4.3
- FileIO 0.3.1
- FiniteElementDiffEq 0.4.0
- FixedPointNumbers 0.3.8
- FixedSizeArrays 0.2.5
- Formatting 0.2.1
- ForwardDiff 0.4.2
- FunctionalCollections 0.3.2
- GLM 0.7.0
- GZip 0.3.0
- GenericSVD 0.0.2
- GeometryTypes 0.2.2
- Graphics 0.2.0
- Graphs 0.7.1
- Gtk 0.13.0
- GtkReactive 0.2.1
- Gumbo 0.3.0
- HDF5 0.8.1
- Hexagons 0.1.0
- Hiccup 0.1.1
- HttpCommon 0.2.7
- HttpServer 0.2.0
- IndexableBitVectors 0.1.2
- IniFile 0.3.1
- Interpolations 0.6.2
- IntervalSets 0.0.5
- IntervalTrees 0.1.0
- IterativeSolvers 0.3.1
- Iterators 0.3.1
- JLD 0.6.10
- JSON 0.12.0
- JuliaParser 0.7.4+ master
- Juno 0.2.7
- KernelDensity 0.3.2
- LNR 0.0.2
- LaTeXStrings 0.2.1
- Lazy 0.11.7
- LearnBase 0.1.5
- LegacyStrings 0.2.2
- Libz 0.2.4
- LightXML 0.5.0
- LineSearches 0.1.5
- LinearMaps 0.3.0
- Loess 0.2.0
- LossFunctions 0.0.3
- LsqFit 0.3.0
- MATLAB 0.5.1+ master
- MNIST 0.0.2
- MachO 0.0.4+ master
- MacroTools 0.3.6
- Markdown 0.3.0
- MathProgBase 0.6.4
- MbedTLS 0.4.5
- Measures 0.1.0
- Media 0.2.7
- MultiScaleArrays 0.3.0
- Mustache 0.1.4
- NLSolversBase 2.1.3
- NLopt 0.3.4
- NLsolve 0.9.1
- NaNMath 0.2.5
- NearestNeighbors 0.2.0
- Nettle 0.3.0
- NetworkLayout 0.0.1
- Networks 0.0.0- master (unregistered)
- NullableArrays 0.1.1
- OAuth 0.4.1
- ObjFileBase 0.0.4+ master
- Optim 0.7.8
- OptimBase 0.1.0
- OrdinaryDiffEq 2.4.0
- PDMats 0.7.0
- ParameterizedFunctions 2.1.0
- Parameters 0.7.2
- ParserCombinator 1.7.11
- Patchwork 0.4.0
- PlotThemes 0.1.4
- PlotUtils 0.4.1
- PolynomialFactors 0.0.6
- Polynomials 0.1.5
- PositiveFactorizations 0.0.4
- ProtoBuf 0.4.0
- QuadGK 0.1.2
- RData 0.1.0
- Ranges 0.0.1
- Ratios 0.1.0
- Reactive 0.5.2 master
- RecursiveArrayTools 0.8.0
- Reexport 0.0.3
- Requires 0.3.0
- ResettableStacks 0.1.0
- ReverseDiffSparse 0.7.3
- Rmath 0.1.6
- Roots 0.3.1
- RoundingIntegers 0.0.2
- SHA 0.3.3
- ScikitLearnBase 0.3.0
- ShowItLikeYouBuildIt 0.0.1
- Showoff 0.1.1
- SimpleTraits 0.5.0
- SortingAlgorithms 0.1.1
- SpecialFunctions 0.1.1
- StaticArrays 0.3.1
- StatsFuns 0.5.0
- SteadyStateDiffEq 0.1.0
- StochasticDiffEq 2.2.1
- StructIO 0.0.2+ master
- SugarBLAS 0.0.3
- SymEngine 0.2.0
- TerminalUI 0.0.2+ master
- TextWrap 0.2.0
- TikzPictures 0.4.0
- Tk 0.5.2
- Tokenize 0.1.8
- URIParser 0.1.8
- UnicodePlots 0.2.3
- VT100 0.1.0 master
- VectorizedRoutines 0.0.2
- WeakRefStrings 0.2.0
- WebSockets 0.2.3
- WoodburyMatrices 0.2.2
- XMLconvert 0.1.0
- YAML 0.2.1
- ZMQ 0.4.3
- ZipFile 0.4.0
You may want to Pkg.free all the packages that Gallium uses (including Gallium itself, which I see you have checked out on master). The issue is likely that there may be a partial migration towards 0.6 support, and from Gallium's perspective 0.6 is a totally different beast from 0.5. If you stick with tagged packages you have greater odds of having it work.
Doing Pkg.free did the trick! It works now. (On an aside: Do you recommend upgrading to v0.6?)
Gallium doesn't work on 0.6 yet AFAIK. Otherwise, yes, 0.6 is very nice. We're on release candidates now, but it seems that the official release could come in a matter of days.
i end up in a similar error (struct not defined) on a linux box and v0.5.2 julia, and unfortunately
julia> Pkg.free("Gallium")
INFO: Freeing Gallium
WARNING: julia is fixed at 0.5.2 conflicting with requirement for Cxx: [0.6.0,∞)
INFO: No packages to install, update or remove
Is this issue currently being worked on? The package still fails on ASTInterpreter.
Its been figured out
On Thu, Aug 10, 2017 at 3:55 PM, Andrey Shedko [email protected] wrote:
Is this issue currently being worked on?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Keno/Gallium.jl/issues/193#issuecomment-321656552, or mute the thread https://github.com/notifications/unsubscribe-auth/APb1LPFCn-olEHnPS2pynELVT8oMo4m7ks5sW2BIgaJpZM4N77Py .
Still fails as follows:
julia> using Gallium
WARNING: deprecated syntax "local declfile="", declline=0" at /home/rra/.julia/v0.6/Gallium/src/Gallium.jl:455.
Use "local declfile, declline = "", 0" instead.
WARNING: deprecated syntax "local dbgs=nothing, cu=nothing, sp=nothing" at /home/rra/.julia/v0.6/Gallium/src/Gallium.jl:466.
Use "local dbgs, cu, sp = nothing, nothing, nothing" instead.
WARNING: deprecated syntax "abstract LocationSource" at /home/rra/.julia/v0.6/Gallium/src/Gallium.jl:690.
Use "abstract type LocationSource end" instead.
INFO: Precompiling module Gallium.
WARNING: deprecated syntax "local declfile="", declline=0" at /home/rra/.julia/v0.6/Gallium/src/Gallium.jl:455.
Use "local declfile, declline = "", 0" instead.
WARNING: deprecated syntax "local dbgs=nothing, cu=nothing, sp=nothing" at /home/rra/.julia/v0.6/Gallium/src/Gallium.jl:466.
Use "local dbgs, cu, sp = nothing, nothing, nothing" instead.
WARNING: deprecated syntax "abstract LocationSource" at /home/rra/.julia/v0.6/Gallium/src/Gallium.jl:690.
Use "abstract type LocationSource end" instead.
WARNING: deprecated syntax "abstract ReplacementLoc" at /home/rra/.julia/v0.6/ASTInterpreter/src/ASTInterpreter.jl:155.
Use "abstract type ReplacementLoc end" instead.
ERROR: LoadError: syntax: extra token ".¬" after end of expression
Stacktrace:
[1] include_from_node1(::String) at ./loading.jl:569
[2] include(::String) at ./sysimg.jl:14
[3] anonymous at ./<missing>:2
while loading /home/rra/.julia/v0.6/ASTInterpreter/src/ASTInterpreter.jl, in expression starting on line 914
ERROR: LoadError: Failed to precompile ASTInterpreter to /home/rra/.julia/lib/v0.6/ASTInterpreter.ji.
Stacktrace:
[1] compilecache(::String) at ./loading.jl:703
[2] _require(::Symbol) at ./loading.jl:456
[3] require(::Symbol) at ./loading.jl:398
[4] include_from_node1(::String) at ./loading.jl:569
[5] include(::String) at ./sysimg.jl:14
[6] anonymous at ./<missing>:2
while loading /home/rra/.julia/v0.6/Gallium/src/Gallium.jl, in expression starting on line 3
ERROR: Failed to precompile Gallium to /home/rra/.julia/lib/v0.6/Gallium.ji.
Stacktrace:
[1] compilecache(::String) at ./loading.jl:703
[2] _require(::Symbol) at ./loading.jl:490
[3] require(::Symbol) at ./loading.jl:398
^ Am having the same problem, can't precompile with the same error message
I also got an error when compiling Gallium (see in the attached file Gallium_error.txt). Could anyone please help me with this? Thanks in advance!
I also got some similar issues with Julia 0.7. I have updated the packages.
julia> using Gallium
[ Info: Precompiling Gallium [87a02803-f0ee-5d26-846e-298423f06ab0]
WARNING: importing deprecated binding Base.Nullable into DebuggerFramework.
ERROR: LoadError: ArgumentError: invalid type for argument val in method definition for print_var at /
usr/people/jingpeng/.julia/packages/DebuggerFramework/9yZZM/src/DebuggerFramework.jl:14
Stacktrace:
[1] top-level scope at none:0
[2] include at ./boot.jl:317 [inlined]
[3] include_relative(::Module, ::String) at ./loading.jl:1038
[4] include(::Module, ::String) at ./sysimg.jl:29
[5] top-level scope at none:2
[6] eval at ./boot.jl:319 [inlined]
[7] eval(::Expr) at ./client.jl:399
[8] top-level scope at ./none:3
in expression starting at /usr/people/jingpeng/.julia/packages/DebuggerFramework/9yZZM/src/DebuggerFra
mework.jl:13
ERROR: LoadError: Failed to precompile DebuggerFramework [67417a49-6d77-5db2-98c7-c13144130cd2] to /us
r/people/jingpeng/.julia/compiled/v0.7/DebuggerFramework/0bKxs.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] macro expansion at ./logging.jl:313 [inlined]
[3] compilecache(::Base.PkgId, ::String) at ./loading.jl:1185
[4] _require(::Base.PkgId) at ./logging.jl:311
[5] require(::Base.PkgId) at ./loading.jl:852
[6] macro expansion at ./logging.jl:311 [inlined]
[7] require(::Module, ::Symbol) at ./loading.jl:834
[8] include at ./boot.jl:317 [inlined]
[9] include_relative(::Module, ::String) at ./loading.jl:1038
[10] include(::Module, ::String) at ./sysimg.jl:29
[11] top-level scope at none:2
[12] eval at ./boot.jl:319 [inlined]
[13] eval(::Expr) at ./client.jl:399
[14] top-level scope at ./none:3
in expression starting at /usr/people/jingpeng/.julia/packages/ASTInterpreter2/b1fAq/src/ASTInterpret$
You may want to try Rebugger.jl for a 1.0 debugger.
@keno Should we archive Gallium.jl for now?
