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JunoLab / Atom.jl

Julia Client for Atom
MIT License
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Atom.jl fails to load after update #30

Closed mkborregaard closed 8 years ago

mkborregaard commented 8 years ago

Hi, after Pkg.update() and using Atom gives

julia> using Atom
INFO: Precompiling module Atom...
ERROR: LoadError: LoadError: ArgumentError: AbstractTrees not found in path
 in compilecache at loading.jl:377
 in require at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 [inlined code] from none:2
 in anonymous at no file:0
 in process_options at /usr/local/lib/julia/sys.dylib
 in _start at /usr/local/lib/julia/sys.dylib
while loading /Users/michael/.julia/v0.4/JuliaParser/src/token.jl, in expression starting on line 4
while loading /Users/michael/.julia/v0.4/JuliaParser/src/JuliaParser.jl, in expression starting on line 7
ERROR: LoadError: LoadError: LoadError: Failed to precompile JuliaParser to /Users/michael/.julia/lib/v0.4/JuliaParser.ji
 in error at /usr/local/lib/julia/sys.dylib
 in compilecache at loading.jl:384
 in require at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 [inlined code] from none:2
 in anonymous at no file:0
 in process_options at /usr/local/lib/julia/sys.dylib
 in _start at /usr/local/lib/julia/sys.dylib
while loading /Users/michael/.julia/v0.4/CodeTools/src/parse/scope.jl, in expression starting on line 6
while loading /Users/michael/.julia/v0.4/CodeTools/src/parse/parse.jl, in expression starting on line 1
while loading /Users/michael/.julia/v0.4/CodeTools/src/CodeTools.jl, in expression starting on line 10
ERROR: LoadError: LoadError: Failed to precompile CodeTools to /Users/michael/.julia/lib/v0.4/CodeTools.ji
 in error at /usr/local/lib/julia/sys.dylib
 in compilecache at loading.jl:384
 in require at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 in include at /usr/local/lib/julia/sys.dylib
 in include_from_node1 at /usr/local/lib/julia/sys.dylib
 [inlined code] from none:2
 in anonymous at no file:0
 in process_options at /usr/local/lib/julia/sys.dylib
 in _start at /usr/local/lib/julia/sys.dylib
while loading /Users/michael/.julia/v0.4/Atom/src/eval.jl, in expression starting on line 1
while loading /Users/michael/.julia/v0.4/Atom/src/Atom.jl, in expression starting on line 9
ERROR: Failed to precompile Atom to /Users/michael/.julia/lib/v0.4/Atom.ji
 in error at /usr/local/lib/julia/sys.dylib
 in compilecache at loading.jl:384
 in compilecache at loading.jl:373
 in require at loading.jl:250
 [inlined code] from /Users/michael/.julia/v0.4/Requires/src/require.jl:11
 in require at /Users/michael/.julia/v0.4/Requires/src/hook.jl:17

I have tried Pkg.checkout("Atom") but that gives:

julia> Pkg.checkout("Atom")
INFO: Checking out Atom master...
INFO: Pulling Atom latest master...
WARNING: julia is fixed at 0.4.4-pre+2 conflicting with requirement for JuliaParser: [0.5.0-,∞)
ERROR: AbstractTrees can't be installed because it has no versions that support 0.4.4-pre+2 of julia. You may need to update METADATA by running `Pkg.update()`
 in error at error.jl:22
 in resolve at /usr/local/lib/julia/sys.dylib
 in resolve at pkg/entry.jl:404
 in anonymous at pkg/entry.jl:198
 in transact at pkg/git.jl:97
 in _checkout at pkg/entry.jl:190
 in checkout at pkg/entry.jl:205
 in anonymous at pkg/dir.jl:31
 in cd at file.jl:22
 in cd at pkg/dir.jl:31
 in checkout at pkg.jl:37
sglyon commented 8 years ago

Can you report Pkg.status()?

Within the last week the master branch of JuliaParser.jl moved to no longer support anything on the 0.4 julia release cycle (i.e. it is a 0.5dev only package now).

mkborregaard commented 8 years ago

Sure, here goes:

julia> Pkg.status()
47 required packages:
 - Atom                          0.4.1              master
 - Bio                           0.1.0+             phyloplot
 - Blink                         0.3.4+             master
 - Bootstrap                     0.3.3
 - Cairo                         0.2.31
 - CodeTools                     0.3.0+             master
 - Color                         0.2.11
 - ColorBrewer                   0.3.0
 - Colors                        0.6.3
 - Compose                       0.4.2
 - DataFrames                    0.7.0
 - DataFramesMeta                0.1.1
 - DataStructures                0.4.3
 - Dates                         0.4.4
 - Distributions                 0.8.10
 - EcologicalNetwork             1.0.1
 - FactCheck                     0.4.2
 - FunctionalData                0.1.0
 - GLM                           0.5.0
 - GLPlot                        0.0.5
 - Gadfly                        0.4.2
 - GeoInterface                  0.0.1
 - Geodesy                       0.0.1
 - GreatCircle                   0.0.1
 - IJulia                        1.1.8
 - ImageView                     0.1.19
 - Images                        0.5.3
 - JLD                           0.5.9
 - Lint                          0.2.3
 - MAT                           0.2.14
 - MixedModels                   0.4.5
 - NamedArrays                   0.4.6
 - OpenStreetMap                 0.8.2
 - Pandas                        0.2.0
 - Phylogenetics                 0.0.2
 - Plotly                        0.0.3+             master
 - PlotlyJS                      0.1.4
 - Plots                         0.5.3+             master
 - QuartzImageIO                 0.1.2
 - RCall                         0.4.0
 - RDatasets                     0.1.2
 - Roots                         0.1.26             master
 - SFML                          0.1.0
 - Shapefile                     0.0.3
 - Stats                         0.1.0
 - TestImages                    0.1.0
 - Yeppp                         0.0.10
90 additional packages:
 - ArrayViews                    0.6.4
 - BinDeps                       0.3.21
 - Blosc                         0.1.4
 - BufferedStreams               0.0.3
 - Calculus                      0.1.14
 - Codecs                        0.1.5
 - ColorTypes                    0.2.1
 - ColorVectorSpace              0.1.1
 - Compat                        0.7.13
 - Conda                         0.1.9
 - Contour                       0.1.0
 - DataArrays                    0.2.20
 - Distances                     0.3.0
 - Docile                        0.5.23
 - DualNumbers                   0.2.2
 - FileIO                        0.0.4
 - FixedPointNumbers             0.1.2
 - FixedSizeArrays               0.0.10
 - ForwardDiff                   0.1.6
 - GLAbstraction                 0.0.10
 - GLFW                          1.1.2
 - GLText                        0.0.4
 - GLWindow                      0.1.0
 - GMT                           0.0.0-             master (unregistered)
 - GZip                          0.2.18
 - GeometryTypes                 0.1.3
 - Graphics                      0.1.3
 - Graphs                        0.6.0
 - Grid                          0.4.0
 - HDF5                          0.5.8
 - Hexagons                      0.0.4
 - Hiccup                        0.0.2
 - Homebrew                      0.2.0
 - HttpCommon                    0.2.4
 - HttpParser                    0.1.1
 - HttpServer                    0.1.5
 - ImmutableArrays               0.0.11
 - IniFile                       0.2.5
 - IntervalTrees                 0.0.5
 - Iterators                     0.1.9
 - JSON                          0.5.0
 - JuliaParser                   0.7.1+             master
 - KernelDensity                 0.1.2
 - LNR                           0.0.2
 - LaTeXStrings                  0.1.6
 - Lazy                          0.10.1
 - Lexicon                       0.1.18
 - LibExpat                      0.1.2
 - Libz                          0.0.2
 - LightXML                      0.2.1
 - Loess                         0.0.6
 - Logging                       0.2.0
 - MacroTools                    0.3.0+             master
 - MathProgBase                  0.4.3
 - MbedTLS                       0.2.1
 - Measures                      0.0.2
 - Media                         0.1.2
 - ModernGL                      0.0.7
 - Mustache                      0.0.14
 - Mux                           0.2.0
 - NLopt                         0.3.1
 - NaNMath                       0.2.1
 - Nettle                        0.2.2
 - Optim                         0.4.4
 - PDMats                        0.4.1
 - Polynomials                   0.0.5
 - PyCall                        1.4.0
 - PyPlot                        2.1.1
 - Quaternions                   0.1.0
 - RasterIO                      0.0.0-             master (unregistered)
 - Reactive                      0.3.0
 - Reexport                      0.0.3
 - Requests                      0.3.6
 - Requires                      0.2.2
 - SHA                           0.1.2
 - SIUnits                       0.0.6
 - Showoff                       0.0.6
 - SortingAlgorithms             0.0.6
 - StatsBase                     0.8.0
 - StatsFuns                     0.2.0
 - Switch                        0.0.1
 - TexExtensions                 0.0.3
 - Tk                            0.3.7
 - URIParser                     0.1.3
 - WebSockets                    0.1.2
 - Winston                       0.11.13
 - WoodburyMatrices              0.1.5
 - ZMQ                           0.3.1
 - ZipFile                       0.2.6
 - Zlib                          0.1.12
pfitzseb commented 8 years ago

Yeah, you should probably try calling Pkg.free("JuliaParser") to get onto the latest tagged version.

mkborregaard commented 8 years ago

Thanks, that worked! Should I close the issue?

sglyon commented 8 years ago

Yep, let's close it.

Glad it works now.