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Calling a function breaks REPL in Juno -- ERROR: unlock from wrong thread #531

Closed vlandau closed 4 years ago

vlandau commented 4 years ago

Details

Steps to reproduce

  1. Run the following code from the code editor window: 
    
using GeoArrays

function read_raster(path) a = GeoArrays.read(path) a end

read_raster("test/input/some_raster.asc")

2. Type `2+2` in the REPL then press enter
3. REPL hangs, press CTRL-C to terminate and get the stacktrace

julia> 2+2 ^CERROR: InterruptException: Stacktrace: [1] poptaskref(::Base.InvasiveLinkedListSynchronized{Task}) at ./task.jl:702 [2] wait() at ./task.jl:709 [3] wait(::Base.GenericCondition{Base.Threads.SpinLock}) at ./condition.jl:106 [4] lock(::ReentrantLock) at ./lock.jl:80 [5] evalrepl(::Module, ::String) at /root/.julia/packages/Atom/cYxbS/src/repl.jl:221 [6] top-level scope at /root/.julia/packages/Atom/cYxbS/src/repl.jl:272 [7] eval(::Module, ::Any) at ./boot.jl:331 [8] eval_user_input(::Any, ::REPL.REPLBackend) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/REPL/src/REPL.jl:86 [9] macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/REPL/src/REPL.jl:118 [inlined] [10] (::REPL.var"#26#27"{REPL.REPLBackend})() at ./task.jl:358 ERROR: unlock from wrong thread Stacktrace: [1] error(::String) at ./error.jl:33 [2] unlock(::ReentrantLock) at ./lock.jl:101 [3] evalrepl(::Module, ::String) at /root/.julia/packages/Atom/cYxbS/src/repl.jl:251 [4] top-level scope at /root/.julia/packages/Atom/cYxbS/src/repl.jl:272


Here is [a link](https://github.com/Circuitscape/Omniscape.jl/blob/master/test/input/temperature.asc) the the .asc file I'm trying to read.

### Other Info
neither this:

using GeoArrays

function read_raster(path) a = GeoArrays.read(path) a.A end

read_raster("test/input/temperature.asc")

nor this

using GeoArrays a = GeoArrays.read(path)


cause the same error.

May be related to #501 

Here is [a link](https://discourse.julialang.org/t/calling-a-function-breaks-repl-in-juno-error-unlock-from-wrong-thread/36165/4) to a post detailing this issue on the Julia Discourse
pfitzseb commented 4 years ago

I can't reproduce any hangs with that file. Can you upload your manifest so I can use your exact environment?

vlandau commented 4 years ago

Below is a copy of the Manifest. It does appear that there are some issues with package versions? Not sure if these are the cause of the REPL issues... I'm getting lots messages about failure to precompile after using GeoArrays. Thanks!

# This file is machine-generated - editing it directly is not advised

[[AlgebraicMultigrid]]
deps = ["Compat", "IterativeSolvers", "Random"]
git-tree-sha1 = "a26560b0f8cb9104d96715c32f7c272504631ea9"
uuid = "2169fc97-5a83-5252-b627-83903c6c433c"
version = "0.2.2"

[[ArchGDAL]]
deps = ["DataStreams", "Dates", "GDAL", "GeoInterface"]
git-tree-sha1 = "16f2d6af2e0760de065881202cdc197975535fff"
uuid = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
version = "0.3.1"

[[ArnoldiMethod]]
deps = ["DelimitedFiles", "LinearAlgebra", "Random", "SparseArrays", "StaticArrays", "Test"]
git-tree-sha1 = "2b6845cea546604fb4dca4e31414a6a59d39ddcd"
uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
version = "0.0.4"

[[Arpack]]
deps = ["Arpack_jll", "Libdl", "LinearAlgebra"]
git-tree-sha1 = "2ff92b71ba1747c5fdd541f8fc87736d82f40ec9"
uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
version = "0.4.0"

[[Arpack_jll]]
deps = ["Libdl", "OpenBLAS_jll", "Pkg"]
git-tree-sha1 = "68a90a692ddc0eb72d69a6993ca26e2a923bf195"
uuid = "68821587-b530-5797-8361-c406ea357684"
version = "3.5.0+2"

[[ArrayInterface]]
deps = ["LinearAlgebra", "Requires", "SparseArrays"]
git-tree-sha1 = "8683deff18ed6cd123e2b4d4147d2dc21f19391b"
uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
version = "2.6.1"

[[AverageShiftedHistograms]]
deps = ["LinearAlgebra", "RecipesBase", "Statistics", "StatsBase", "UnicodePlots"]
git-tree-sha1 = "23b1a174f1ab4435bd32d6d99c49ec9316a4d233"
uuid = "77b51b56-6f8f-5c3a-9cb4-d71f9594ea6e"
version = "0.8.2"

[[Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[CEnum]]
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uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
version = "0.2.0"

[[CSV]]
deps = ["CategoricalArrays", "DataFrames", "Dates", "FilePathsBase", "Mmap", "Parsers", "PooledArrays", "Tables", "Unicode", "WeakRefStrings"]
git-tree-sha1 = "fe9b828d5e7b55431d75d6d180ef843d69dea048"
uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
version = "0.5.23"

[[Calculus]]
deps = ["LinearAlgebra"]
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uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
version = "0.5.1"

[[CategoricalArrays]]
deps = ["Compat", "DataAPI", "Future", "JSON", "Missings", "Printf", "Reexport", "Statistics", "Unicode"]
git-tree-sha1 = "23d7324164c89638c18f6d7f90d972fa9c4fa9fb"
uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
version = "0.7.7"

[[Circuitscape]]
deps = ["AlgebraicMultigrid", "Dates", "DelimitedFiles", "Distributed", "GZip", "IterativeSolvers", "LightGraphs", "LinearAlgebra", "Logging", "REPL", "SharedArrays", "SimpleWeightedGraphs", "SparseArrays", "Test"]
git-tree-sha1 = "e5b13ea5bd41d97ef988c6535929ce04d3e3d49d"
uuid = "2b7a1792-8151-5239-925d-e2b8fdfa3201"
version = "5.5.5"

[[ColorTypes]]
deps = ["FixedPointNumbers", "Random"]
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uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
version = "0.8.1"

[[CommonSubexpressions]]
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version = "0.2.0"

[[Compat]]
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git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "2.2.0"

[[CompilerSupportLibraries_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "067567a322fe466c5ec8d01413eee7127bd11699"
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "0.3.1+0"

[[CoordinateTransformations]]
deps = ["LinearAlgebra", "Rotations", "StaticArrays"]
git-tree-sha1 = "71333ea3f841bca6c1aa2863f11758eb9b37bfbc"
uuid = "150eb455-5306-5404-9cee-2592286d6298"
version = "0.5.1"

[[Crayons]]
git-tree-sha1 = "cb7a62895da739fe5bb43f1a26d4292baf4b3dc0"
uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
version = "4.0.1"

[[DataAPI]]
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version = "1.1.0"

[[DataFrames]]
deps = ["CategoricalArrays", "Compat", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "StatsBase", "TableTraits", "Tables", "Unicode"]
git-tree-sha1 = "7c0f86a01be0f77cc7f3f9096ed875f1217487e1"
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[[DataStreams]]
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[[DataStructures]]
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[[DataValueInterfaces]]
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version = "1.0.0"

[[Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[DelimitedFiles]]
deps = ["Mmap"]
uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"

[[DiffEqDiffTools]]
deps = ["LinearAlgebra", "SparseArrays", "StaticArrays"]
git-tree-sha1 = "b992345a39b4d9681342ae795a8dacc100730182"
uuid = "01453d9d-ee7c-5054-8395-0335cb756afa"
version = "0.14.0"

[[DiffResults]]
deps = ["StaticArrays"]
git-tree-sha1 = "da24935df8e0c6cf28de340b958f6aac88eaa0cc"
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version = "1.0.2"

[[DiffRules]]
deps = ["NaNMath", "Random", "SpecialFunctions"]
git-tree-sha1 = "eb0c34204c8410888844ada5359ac8b96292cfd1"
uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
version = "1.0.1"

[[Distances]]
deps = ["LinearAlgebra", "Statistics"]
git-tree-sha1 = "23717536c81b63e250f682b0e0933769eecd1411"
uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
version = "0.8.2"

[[Distributed]]
deps = ["Random", "Serialization", "Sockets"]
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"

[[Distributions]]
deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
git-tree-sha1 = "e063d0b5d27180b98edacd2b1cb90ecfbc171385"
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version = "0.21.12"

[[FilePathsBase]]
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[[FillArrays]]
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[[FiniteDiff]]
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[[FixedPointNumbers]]
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uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
version = "0.7.1"

[[ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
git-tree-sha1 = "88b082d492be6b63f967b6c96b352e25ced1a34c"
uuid = "f6369f11-7733-5829-9624-2563aa707210"
version = "0.10.9"

[[Future]]
deps = ["Random"]
uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"

[[GDAL]]
deps = ["CEnum", "GDAL_jll", "PROJ_jll"]
git-tree-sha1 = "19f19ed857ef5551ec600935e209c2ceaace0f01"
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[[GDAL_jll]]
deps = ["GEOS_jll", "LibCURL_jll", "Libdl", "PROJ_jll", "Pkg", "SQLite_jll", "Zlib_jll"]
git-tree-sha1 = "b73c63b05036d90de4561bae34cf1462157020e9"
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[[GEOS_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "c846f97f9114974e4b49ed51a6060853e6b1dd39"
uuid = "d604d12d-fa86-5845-992e-78dc15976526"
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[[GZip]]
deps = ["Libdl"]
git-tree-sha1 = "039be665faf0b8ae36e089cd694233f5dee3f7d6"
uuid = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
version = "0.5.1"

[[GeoArrays]]
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git-tree-sha1 = "36d6006090fd63361c70abbb18485f3c255d0595"
uuid = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
version = "0.2.0"

[[GeoInterface]]
deps = ["RecipesBase"]
git-tree-sha1 = "37541e9ae0bd9dcdeb26f285d9a7f54cc881ab5e"
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[[GeoStatsBase]]
deps = ["AverageShiftedHistograms", "CSV", "DataFrames", "Distances", "Distributed", "Distributions", "LinearAlgebra", "MLJBase", "NearestNeighbors", "Optim", "Parameters", "Random", "RecipesBase", "StaticArrays", "Statistics", "StatsBase", "Tables"]
git-tree-sha1 = "e94a68e36ec1ddb7cbb6ad5aef8336df88b0dada"
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[[Inflate]]
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[[InteractiveUtils]]
deps = ["Markdown"]
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[[IterativeSolvers]]
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[[IteratorInterfaceExtensions]]
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[[JSON]]
deps = ["Dates", "Mmap", "Parsers", "Unicode"]
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[[LearnBase]]
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[[LibCURL_jll]]
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[[LibGit2]]
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[[LibSSH2_jll]]
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git-tree-sha1 = "2daf0a757293e5355904b96262fcc54cf45d8fd3"
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[[Libdl]]
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[[LightGraphs]]
deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
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[[LineSearches]]
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[[LinearAlgebra]]
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[[Logging]]
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[[LossFunctions]]
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version = "0.5.1"

[[MLJBase]]
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git-tree-sha1 = "af65194442b42ea18dccb796032996e2b42b3ad2"
uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
version = "0.7.5"

[[MacroTools]]
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[[Markdown]]
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uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[MbedTLS_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "066a4467008745eed36dad973ceb66405785a621"
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.16.0+1"

[[Missings]]
deps = ["DataAPI"]
git-tree-sha1 = "de0a5ce9e5289f27df672ffabef4d1e5861247d5"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "0.4.3"

[[Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"

[[NLSolversBase]]
deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
git-tree-sha1 = "7c4e66c47848562003250f28b579c584e55becc0"
uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
version = "7.6.1"

[[NaNMath]]
git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f"
uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
version = "0.3.3"

[[NearestNeighbors]]
deps = ["Distances", "StaticArrays"]
git-tree-sha1 = "8bc6180f328f3c0ea2663935db880d34c57d6eae"
uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
version = "0.4.4"

[[OpenBLAS_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "139adbff69e8149e68824994b68f06a61a5a2797"
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.7+8"

[[OpenSpecFun_jll]]
deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"]
git-tree-sha1 = "d51c416559217d974a1113522d5919235ae67a87"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.3+3"

[[Optim]]
deps = ["Calculus", "DiffEqDiffTools", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "Random", "SparseArrays", "StatsBase", "Test"]
git-tree-sha1 = "a626e09c1f7f019b8f3a30a8172c7b82d2f4810b"
uuid = "429524aa-4258-5aef-a3af-852621145aeb"
version = "0.18.1"

[[OrderedCollections]]
deps = ["Random", "Serialization", "Test"]
git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.1.0"

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pfitzseb commented 4 years ago

Oh, the "unlock from wrong thread" issue should be fixed with Atom.jl 0.12.10, in case you wanna give that a go.

I'll look into whether I can repro the issue with your Manifest.

vlandau commented 4 years ago

I'll try that now and post back here ASAP. Thanks so much!

vlandau commented 4 years ago

Looks to be working after that update! Thanks for the help.

The other errors/warnings I was geting have to do with conflicts in the function names of packages that were in the environment. Should be able to fix that by using import instead of using on my end.

vlandau commented 4 years ago

Fixed by JunoLab/Atom.jl/pull/300