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Errors occurred when installing #3

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xieduo7 opened this issue Aug 9, 2022 · 6 comments
Open

Errors occurred when installing #3

xieduo7 opened this issue Aug 9, 2022 · 6 comments

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@xieduo7
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xieduo7 commented Aug 9, 2022

I posted the commands and logs below:

/data/xieduo/software/J-Space.jl
$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.7.3 (2022-05-06)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> activate .
ERROR: syntax: space before "." not allowed in "activate ." at REPL[1]:1
Stacktrace:
 [1] top-level scope
   @ none:1

(@v1.7) pkg> activate .
  Activating project at `/data/xieduo/software/J-Space.jl`

(J_Space) pkg> instantiate
┌ Warning: The active manifest file is an older format with no julia version entry. Dependencies may have been resolved with a different julia version.
└ @ /data/xieduo/software/J-Space.jl/Manifest.toml:0
   Installed ImageIO ────────────── v0.5.9
   Installed BioGenerics ────────── v0.1.1
   Installed PNGFiles ───────────── v0.3.16
   Installed TiffImages ─────────── v0.5.5
   Installed MutableArithmetics ─── v1.0.2
   Installed OffsetArrays ───────── v1.11.0
   Installed GraphMakie ─────────── v0.3.0
   Installed PDMats ─────────────── v0.11.10
   Installed OpenEXR ────────────── v0.3.2
   Installed ModernGL ───────────── v1.1.4
   Installed NetworkLayout ──────── v0.4.3
   Installed GLMakie ────────────── v0.4.7
   Installed StaticArrays ───────── v1.4.4
   Installed CEnum ──────────────── v0.4.2
   Installed GLM ────────────────── v1.7.0
   Installed MetaGraphs ─────────── v0.7.1
   Installed Netpbm ─────────────── v1.0.2
   Installed BioSequences ───────── v2.0.5
   Installed SignedDistanceFields ─ v0.4.0
   Installed Static ─────────────── v0.6.4
   Installed EllipsisNotation ───── v1.5.1
   Installed JLD2 ───────────────── v0.4.22
   Installed FileIO ─────────────── v1.14.0
   Installed DataFrames ─────────── v1.3.0
   Installed ScanByte ───────────── v0.3.0
   Installed SIMD ───────────────── v3.4.1
   Installed ArnoldiMethod ──────── v0.2.0
   Installed NLopt ──────────────── v0.6.5
   Installed BenchmarkTools ─────── v1.3.1
   Installed PolygonOps ─────────── v0.1.2
   Installed CodecBzip2 ─────────── v0.7.2
   Installed MathOptInterface ───── v1.2.0
   Installed SpecialFunctions ───── v1.8.4
   Installed IfElse ─────────────── v0.1.1
   Installed PkgVersion ─────────── v0.1.1
   Installed isoband_jll ────────── v0.2.3+0
   Installed BioSymbols ─────────── v4.0.4
   Installed MathProgBase ───────── v0.7.8
   Installed Graphs ─────────────── v1.4.1
   Installed Graphics ───────────── v1.1.1
   Installed MappedArrays ───────── v0.4.1
   Installed FreeType ───────────── v4.0.0
   Installed IndexableBitVectors ── v1.0.0
   Installed PaddedViews ────────── v0.5.11
   Installed StatsAPI ───────────── v1.3.0
   Installed GridLayoutBase ─────── v0.6.5
   Installed MosaicViews ────────── v0.3.3
   Installed Automa ─────────────── v0.8.2
   Installed StatsBase ──────────── v0.33.14
   Installed Match ──────────────── v1.2.0
   Installed ColorTypes ─────────── v0.11.2
   Installed Twiddle ────────────── v1.1.2
   Installed TensorCore ─────────── v0.1.1
   Installed Plots ──────────────── v1.27.6
   Installed Isoband ────────────── v0.1.1
   Installed ImageCore ──────────── v0.9.3
   Installed FreeTypeAbstraction ── v0.9.9
   Installed Inflate ────────────── v0.1.2
   Installed Imath_jll ──────────── v3.1.2+0
   Installed PooledArrays ───────── v1.4.2
   Installed Packing ────────────── v0.4.2
   Installed ColorVectorSpace ───── v0.9.8
   Installed AbstractTrees ──────── v0.3.4
   Installed ArrayInterface ─────── v5.0.8
   Installed StackViews ─────────── v0.1.1
   Installed StringDistances ────── v0.11.2
   Installed InverseFunctions ───── v0.1.4
   Installed SimpleTraits ───────── v0.9.4
   Installed ColorBrewer ────────── v0.4.0
   Installed MeshIO ─────────────── v0.4.10
   Installed OpenEXR_jll ────────── v3.1.1+0
   Installed FASTX ──────────────── v1.2.0
   Installed NLopt_jll ──────────── v2.7.1+0
   Installed MathTeXEngine ──────── v0.2.1
   Installed StableRNGs ─────────── v0.1.2
   Installed IntervalSets ───────── v0.5.4
   Installed Latexify ───────────── v0.15.15
   Installed GLFW ───────────────── v3.4.1
   Installed MakieCore ──────────── v0.1.3
   Installed Tables ─────────────── v1.6.1
   Installed IndirectArrays ─────── v1.0.0
   Installed ShaderAbstractions ─── v0.2.9
   Installed StructArrays ───────── v0.6.7
   Installed FillArrays ─────────── v0.12.8
   Installed Animations ─────────── v0.4.1
   Installed Distributions ──────── v0.25.35
   Installed ColorSchemes ───────── v3.18.0
   Installed PhyloNetworks ──────── v0.14.2
   Installed CSV ────────────────── v0.9.11
   Installed Makie ──────────────── v0.15.3
  Downloaded artifact: isoband
  Downloaded artifact: Imath
  Downloaded artifact: OpenEXR
  Downloaded artifact: NLopt
    Building ModernGL → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/344f8896e55541e30d5ccffcbf747c98ad57ca47/build.log`
Precompiling project...
  ✗ GLMakie
  ✗ J_Space
  150 dependencies successfully precompiled in 123 seconds (87 already precompiled)
  2 dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages

(J_Space) pkg> instantiate
Precompiling project...
  ✗ J_Space
  0 dependencies successfully precompiled in 26 seconds (237 already precompiled, 1 skipped during auto due to previous errors)
  1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package

(J_Space) pkg> instantiate
Precompiling project...
  ✗ J_Space
  0 dependencies successfully precompiled in 28 seconds (237 already precompiled, 1 skipped during auto due to previous errors)
  1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package

(J_Space) pkg> using J_Space
ERROR: `using` is not a recognized command. Type ? for help with available commands

julia> using J_Space
[ Info: Precompiling J_Space [fd1b0027-9d6f-49b5-97ba-2af5672b046a]
┌ Warning:     OpenGL/GLFW wasn't loaded correctly or couldn't be initialized.
│     This likely means, you're on a headless server without having OpenGL support setup correctly.
│     Have a look at the troubleshooting section in the readme:
│     https://github.com/JuliaPlots/Makie.jl/tree/master/GLMakie#troubleshooting-opengl.
└ @ GLMakie ~/.julia/packages/GLMakie/pFGSp/src/gl_backend.jl:4
ERROR: LoadError: InitError: Exception[GLFW.GLFWError(GLFW.PLATFORM_ERROR, "X11: The DISPLAY environment variable is missing"), ErrorException("glfwInit failed")]
Stacktrace:
  [1] __init__()
    @ GLFW ~/.julia/packages/GLFW/BWxfF/src/GLFW.jl:35
  [2] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base ./loading.jl:768
  [3] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base ./loading.jl:854
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1097
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] top-level scope
    @ ~/.julia/packages/GLMakie/pFGSp/src/gl_backend.jl:2
  [8] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [9] include(x::String)
    @ GLMakie ~/.julia/packages/GLMakie/pFGSp/src/GLMakie.jl:1
 [10] top-level scope
    @ ~/.julia/packages/GLMakie/pFGSp/src/GLMakie.jl:36
 [11] include
    @ ./Base.jl:418 [inlined]
 [12] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
    @ Base ./loading.jl:1318
 [13] top-level scope
    @ none:1
 [14] eval
    @ ./boot.jl:373 [inlined]
 [15] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [16] top-level scope
    @ none:1
during initialization of module GLFW
in expression starting at /home/xieduo/.julia/packages/GLMakie/pFGSp/src/gl_backend.jl:1
in expression starting at /home/xieduo/.julia/packages/GLMakie/pFGSp/src/GLMakie.jl:1
ERROR: LoadError: Failed to precompile GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a] to /home/xieduo/.julia/compiled/v1.7/GLMakie/jl_bEogKC.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include
    @ ./Base.jl:418 [inlined]
  [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1318
  [9] top-level scope
    @ none:1
 [10] eval
    @ ./boot.jl:373 [inlined]
 [11] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [12] top-level scope
    @ none:1
in expression starting at /data/xieduo/software/J-Space.jl/src/J_Space.jl:5
ERROR: Failed to precompile J_Space [fd1b0027-9d6f-49b5-97ba-2af5672b046a] to /home/xieduo/.julia/compiled/v1.7/J_Space/jl_H9VpCw.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1466
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1410
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1120
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1013
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:997

Do you have any suggestions?

Best,
Duo
@Alessandro-Guidi
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Collaborator

Hello, we are already working to solve your problem.
We will get back to you with more details in the next few days.

Alessandro

@Alessandro-Guidi
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Where are you running it? Your problem is the same as the one mentioned in our README under the "POSSIBLE PROBLEMS" section.
Because the GLMakie library, which uses the GPU, may give this error when using a virtual machine with Ubuntu.
I await your feedback.

Alessandro

@Alessandro-Guidi
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Collaborator

Hi @xieduo7 ,
I have changed the backend to plot file, now J-Space uses CairoMakie and your problem should be fixed.
I hope you will try again J-Space to give me feedback.

Alessandro

@xieduo7
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xieduo7 commented Sep 22, 2022 •
edited
Loading

Hi @Alessandro-Guidi ,

Thank you for your work. But I have come across another issue when running the example code. I will open another issue.

However, for the installation of J_Space, can I install it using Pkg.add? I have tried it but failed (by the way, I used this package under julia Version 1.7.3 and Linux version 3.10.0-1160.41.1.el7.x86_64 ([email protected]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Tue Aug 31 14:52:47 UTC 2021 instead of a virtual machine):

julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.7.3 (2022-05-06)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using J_Space
ERROR: ArgumentError: Package J_Space not found in current path:
- Run `import Pkg; Pkg.add("J_Space")` to install the J_Space package.

Stacktrace:
 [1] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:967

julia> import Pkg; Pkg.add("/data/xieduo/software/J-Space.jl")
ERROR: `/data/xieduo/software/J-Space.jl` is not a valid package name. Perhaps you meant `/data/xieduo/software/J-Space`
The argument appears to be a URL or path, perhaps you meant `Pkg.add(url="...")` or `Pkg.add(path="...")`.
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68
  [2] check_package_name
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:128 [inlined]
  [3] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:225
  [4] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
  [5] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
  [6] #add#27
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
  [7] add
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
  [8] #add#26
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
  [9] add(pkg::String)
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:141
 [10] top-level scope
    @ REPL[2]:1

julia> import Pkg; Pkg.add(path="/data/xieduo/software/J-Space.jl")
     Cloning git-repo `/data/xieduo/software/J-Space.jl`
    Updating git-repo `/data/xieduo/software/J-Space.jl`
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
ERROR: Unsatisfiable requirements detected for package GraphMakie [1ecd5474]:
 GraphMakie [1ecd5474] log:
 ├─possible versions are: 0.1.0-0.4.1 or uninstalled
 ├─restricted to versions * by J_Space [fd1b0027], leaving only versions 0.1.0-0.4.1
 │ └─J_Space [fd1b0027] log:
 │   ├─possible versions are: 0.1.0 or uninstalled
 │   └─J_Space [fd1b0027] is fixed to version 0.1.0
 ├─restricted by compatibility requirements with AbstractPlotting [537997a7] to versions: 0.2.0-0.4.1 or uninstalled, leaving only versions: 0.2.0-0.4.1
 │ └─AbstractPlotting [537997a7] log:
 │   ├─possible versions are: 0.9.0-0.18.3 or uninstalled
 │   ├─restricted by compatibility requirements with PlotUtils [995b91a9] to versions: 0.9.0-0.10.6 or uninstalled
 │   │ └─PlotUtils [995b91a9] log:
 │   │   ├─possible versions are: 0.5.0-1.3.1 or uninstalled
 │   │   ├─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.5.0-1.3.1
 │   │   │ └─Plots [91a5bcdd] log:
 │   │   │   ├─possible versions are: 0.12.1-1.33.0 or uninstalled
 │   │   │   ├─restricted to versions * by SubClonalSelection [f2909333], leaving only versions 0.12.1-1.33.0
 │   │   │   │ └─SubClonalSelection [f2909333] log:
 │   │   │   │   ├─possible versions are: 0.0.0 or uninstalled
 │   │   │   │   └─SubClonalSelection [f2909333] is fixed to version 0.0.0
 │   │   │   ├─restricted by compatibility requirements with StatsPlots [f3b207a7] to versions: 0.14.0-1.33.0
 │   │   │   │ └─StatsPlots [f3b207a7] log:
 │   │   │   │   ├─possible versions are: 0.10.0-0.15.3 or uninstalled
 │   │   │   │   ├─restricted to versions * by CanEvolve [28e55d1b], leaving only versions 0.10.0-0.15.3
 │   │   │   │   │ └─CanEvolve [28e55d1b] log:
 │   │   │   │   │   ├─possible versions are: 0.1.0 or uninstalled
 │   │   │   │   │   └─CanEvolve [28e55d1b] is fixed to version 0.1.0
 │   │   │   │   └─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.10.0-0.14.33 or uninstalled, leaving only versions: 0.10.0-0.14.33
 │   │   │   │     └─Plots [91a5bcdd] log: see above
 │   │   │   ├─restricted by compatibility requirements with RecipesBase [3cdcf5f2] to versions: 0.12.1-0.29.9 or uninstalled, leaving only versions: 0.14.0-0.29.9
 │   │   │   │ └─RecipesBase [3cdcf5f2] log:
 │   │   │   │   ├─possible versions are: 0.4.0-1.2.1 or uninstalled
 │   │   │   │   ├─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.4.0-1.2.1
 │   │   │   │   │ └─Plots [91a5bcdd] log: see above
 │   │   │   │   ├─restricted by compatibility requirements with StatsPlots [f3b207a7] to versions: 0.5.0-1.2.1
 │   │   │   │   │ └─StatsPlots [f3b207a7] log: see above
 │   │   │   │   └─restricted by compatibility requirements with CancerSeqSim [c7b3ebfe] to versions: 0.4.0-0.8.0, leaving only versions: 0.5.0-0.8.0
 │   │   │   │     └─CancerSeqSim [c7b3ebfe] log:
 │   │   │   │       ├─possible versions are: 0.2.0 or uninstalled
 │   │   │   │       └─restricted to versions * by SubClonalSelection [f2909333], leaving only versions 0.2.0
 │   │   │   │         └─SubClonalSelection [f2909333] log: see above
 │   │   │   └─restricted by compatibility requirements with StaticArrays [90137ffa] to versions: 0.21.0-1.33.0 or uninstalled, leaving only versions: 0.21.0-0.29.9
 │   │   │     └─StaticArrays [90137ffa] log:
 │   │   │       ├─possible versions are: 0.8.0-1.5.7 or uninstalled
 │   │   │       ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.8.3-1.5.7
 │   │   │       │ └─PhyloNetworks [33ad39ac] log:
 │   │   │       │   ├─possible versions are: 0.9.0-0.15.2 or uninstalled
 │   │   │       │   └─restricted to versions * by J_Space [fd1b0027], leaving only versions 0.9.0-0.15.2
 │   │   │       │     └─J_Space [fd1b0027] log: see above
 │   │   │       └─restricted by compatibility requirements with GeometryBasics [5c1252a2] to versions: 0.12.0-1.5.7
 │   │   │         └─GeometryBasics [5c1252a2] log:
 │   │   │           ├─possible versions are: 0.1.0-0.4.4 or uninstalled
 │   │   │           └─restricted by compatibility requirements with NetworkLayout [46757867] to versions: 0.3.0-0.4.4
 │   │   │             └─NetworkLayout [46757867] log:
 │   │   │               ├─possible versions are: 0.2.0-0.4.4 or uninstalled
 │   │   │               ├─restricted to versions * by J_Space [fd1b0027], leaving only versions 0.2.0-0.4.4
 │   │   │               │ └─J_Space [fd1b0027] log: see above
 │   │   │               └─restricted by compatibility requirements with GraphMakie [1ecd5474] to versions: 0.3.0-0.4.4
 │   │   │                 └─GraphMakie [1ecd5474] log: see above
 │   │   └─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.5.0-0.6.5
 │   │     └─Plots [91a5bcdd] log: see above
 │   └─restricted by compatibility requirements with GeometryBasics [5c1252a2] to versions: [0.9.0-0.9.27, 0.12.9-0.18.3] or uninstalled, leaving only versions: 0.9.0-0.9.27 or uninstalled
 │     └─GeometryBasics [5c1252a2] log: see above
 └─restricted by compatibility requirements with Makie [ee78f7c6] to versions: 0.1.0 or uninstalled — no versions left
   └─Makie [ee78f7c6] log:
     ├─possible versions are: 0.9.0-0.17.13 or uninstalled
     ├─restricted by compatibility requirements with PlotUtils [995b91a9] to versions: 0.9.0-0.12.0 or uninstalled
     │ └─PlotUtils [995b91a9] log: see above
     └─restricted by compatibility requirements with AbstractPlotting [537997a7] to versions: [0.9.0-0.9.6, 0.13.0-0.17.13] or uninstalled, leaving only versions: 0.9.0-0.9.6 or uninstalled
       └─AbstractPlotting [537997a7] log: see above
Stacktrace:
  [1] propagate_constraints!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool)
    @ Pkg.Resolve ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1063
  [2] propagate_constraints! (repeats 2 times)
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1000 [inlined]
  [3] simplify_graph!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool)
    @ Pkg.Resolve ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1519
  [4] simplify_graph! (repeats 2 times)
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1519 [inlined]
  [5] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:335
  [6] targeted_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1154
  [7] tiered_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1139
  [8] _resolve(io::Base.TTY, env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1160
  [9] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1176
 [10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:268
 [11] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
 [12] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
 [13] #add#26
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
 [14] add
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
 [15] add(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::String, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:166
 [16] top-level scope
    @ REPL[3]:1

Best,
Duo

@Alessandro-Guidi
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Alessandro-Guidi commented Sep 22, 2022 •
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Hi @xieduo7 ,

You can now install J-Space using Pkg.add.
You can use import Pkg; Pkg.add(path="path/your/local/project") as you did or you can use URL from github: import Pkg; Pkg.add(url="https://github.com/BIMIB-DISCo/J-Space.jl.git")

For your problem, I have several suggestions, but first can I see the list of currently installed packages? You need to run Pkg.status()

@xieduo7
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xieduo7 commented Sep 23, 2022 •
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Hi @Alessandro-Guidi ，

The packege status:

julia> Pkg.status()
      Status `~/.julia/environments/v1.7/Project.toml`
  [336ed68f] CSV v0.10.4
  [28e55d1b] CanEvolve v0.1.0 `https://github.com/tomouellette/CanEvolve.jl#main`
  [a93c6f00] DataFrames v0.21.8
  [31c24e10] Distributions v0.23.12
  [38e38edf] GLM v1.8.0
  [7073ff75] IJulia v1.23.3
  [91a5bcdd] Plots v0.29.9
  [2913bbd2] StatsBase v0.33.16
  [f3b207a7] StatsPlots v0.14.33
  [f2909333] SubClonalSelection v0.0.0 `https://github.com/marcjwilliams1/SubClonalSelection.jl#master`
  [9d95f2ec] TypedTables v1.4.0

For the installation, I still can't succeed (see code posted below). What is the Julia version you used to develop this package? Unlike python, julia is very unstable among different versions and I always came across problems when I use a different version of julia with the package developed. Maybe you can create a conda environment yml file as gatk did so that we can install this package by creating a new conda environment and install the required dependencies automatically to ensure in the same environment as yours.

julia> import Pkg; Pkg.add(path="/data/xieduo/software/J-Space.jl")
    Updating git-repo `/data/xieduo/software/J-Space.jl`
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
ERROR: Unsatisfiable requirements detected for package GraphMakie [1ecd5474]:
 GraphMakie [1ecd5474] log:
 ├─possible versions are: 0.1.0-0.4.1 or uninstalled
 ├─restricted to versions * by J_Space [fd1b0027], leaving only versions 0.1.0-0.4.1
 │ └─J_Space [fd1b0027] log:
 │   ├─possible versions are: 0.1.0 or uninstalled
 │   └─J_Space [fd1b0027] is fixed to version 0.1.0
 ├─restricted by compatibility requirements with AbstractPlotting [537997a7] to versions: 0.2.0-0.4.1 or uninstalled, leaving only versions: 0.2.0-0.4.1
 │ └─AbstractPlotting [537997a7] log:
 │   ├─possible versions are: 0.9.0-0.18.3 or uninstalled
 │   ├─restricted by compatibility requirements with PlotUtils [995b91a9] to versions: 0.9.0-0.10.6 or uninstalled
 │   │ └─PlotUtils [995b91a9] log:
 │   │   ├─possible versions are: 0.5.0-1.3.1 or uninstalled
 │   │   ├─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.5.0-1.3.1
 │   │   │ └─Plots [91a5bcdd] log:
 │   │   │   ├─possible versions are: 0.12.1-1.33.0 or uninstalled
 │   │   │   ├─restricted to versions * by SubClonalSelection [f2909333], leaving only versions 0.12.1-1.33.0
 │   │   │   │ └─SubClonalSelection [f2909333] log:
 │   │   │   │   ├─possible versions are: 0.0.0 or uninstalled
 │   │   │   │   └─SubClonalSelection [f2909333] is fixed to version 0.0.0
 │   │   │   ├─restricted by compatibility requirements with StatsPlots [f3b207a7] to versions: 0.14.0-1.33.0
 │   │   │   │ └─StatsPlots [f3b207a7] log:
 │   │   │   │   ├─possible versions are: 0.10.0-0.15.3 or uninstalled
 │   │   │   │   ├─restricted to versions * by CanEvolve [28e55d1b], leaving only versions 0.10.0-0.15.3
 │   │   │   │   │ └─CanEvolve [28e55d1b] log:
 │   │   │   │   │   ├─possible versions are: 0.1.0 or uninstalled
 │   │   │   │   │   └─CanEvolve [28e55d1b] is fixed to version 0.1.0
 │   │   │   │   └─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.10.0-0.14.33 or uninstalled, leaving only versions: 0.10.0-0.14.33
 │   │   │   │     └─Plots [91a5bcdd] log: see above
 │   │   │   ├─restricted by compatibility requirements with RecipesBase [3cdcf5f2] to versions: 0.12.1-0.29.9 or uninstalled, leaving only versions: 0.14.0-0.29.9
 │   │   │   │ └─RecipesBase [3cdcf5f2] log:
 │   │   │   │   ├─possible versions are: 0.4.0-1.2.1 or uninstalled
 │   │   │   │   ├─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.4.0-1.2.1
 │   │   │   │   │ └─Plots [91a5bcdd] log: see above
 │   │   │   │   ├─restricted by compatibility requirements with StatsPlots [f3b207a7] to versions: 0.5.0-1.2.1
 │   │   │   │   │ └─StatsPlots [f3b207a7] log: see above
 │   │   │   │   └─restricted by compatibility requirements with CancerSeqSim [c7b3ebfe] to versions: 0.4.0-0.8.0, leaving only versions: 0.5.0-0.8.0
 │   │   │   │     └─CancerSeqSim [c7b3ebfe] log:
 │   │   │   │       ├─possible versions are: 0.2.0 or uninstalled
 │   │   │   │       └─restricted to versions * by SubClonalSelection [f2909333], leaving only versions 0.2.0
 │   │   │   │         └─SubClonalSelection [f2909333] log: see above
 │   │   │   └─restricted by compatibility requirements with StaticArrays [90137ffa] to versions: 0.21.0-1.33.0 or uninstalled, leaving only versions: 0.21.0-0.29.9
 │   │   │     └─StaticArrays [90137ffa] log:
 │   │   │       ├─possible versions are: 0.8.0-1.5.7 or uninstalled
 │   │   │       ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.8.3-1.5.7
 │   │   │       │ └─PhyloNetworks [33ad39ac] log:
 │   │   │       │   ├─possible versions are: 0.9.0-0.15.2 or uninstalled
 │   │   │       │   └─restricted to versions * by J_Space [fd1b0027], leaving only versions 0.9.0-0.15.2
 │   │   │       │     └─J_Space [fd1b0027] log: see above
 │   │   │       └─restricted by compatibility requirements with GeometryBasics [5c1252a2] to versions: 0.12.0-1.5.7
 │   │   │         └─GeometryBasics [5c1252a2] log:
 │   │   │           ├─possible versions are: 0.1.0-0.4.4 or uninstalled
 │   │   │           └─restricted by compatibility requirements with NetworkLayout [46757867] to versions: 0.3.0-0.4.4
 │   │   │             └─NetworkLayout [46757867] log:
 │   │   │               ├─possible versions are: 0.2.0-0.4.4 or uninstalled
 │   │   │               ├─restricted to versions * by J_Space [fd1b0027], leaving only versions 0.2.0-0.4.4
 │   │   │               │ └─J_Space [fd1b0027] log: see above
 │   │   │               └─restricted by compatibility requirements with GraphMakie [1ecd5474] to versions: 0.3.0-0.4.4
 │   │   │                 └─GraphMakie [1ecd5474] log: see above
 │   │   └─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.5.0-0.6.5
 │   │     └─Plots [91a5bcdd] log: see above
 │   └─restricted by compatibility requirements with GeometryBasics [5c1252a2] to versions: [0.9.0-0.9.27, 0.12.9-0.18.3] or uninstalled, leaving only versions: 0.9.0-0.9.27 or uninstalled
 │     └─GeometryBasics [5c1252a2] log: see above
 └─restricted by compatibility requirements with Makie [ee78f7c6] to versions: 0.1.0 or uninstalled — no versions left
   └─Makie [ee78f7c6] log:
     ├─possible versions are: 0.9.0-0.17.13 or uninstalled
     ├─restricted by compatibility requirements with PlotUtils [995b91a9] to versions: 0.9.0-0.12.0 or uninstalled
     │ └─PlotUtils [995b91a9] log: see above
     └─restricted by compatibility requirements with AbstractPlotting [537997a7] to versions: [0.9.0-0.9.6, 0.13.0-0.17.13] or uninstalled, leaving only versions: 0.9.0-0.9.6 or uninstalled
       └─AbstractPlotting [537997a7] log: see above
Stacktrace:
  [1] propagate_constraints!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool)
    @ Pkg.Resolve ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1063
  [2] propagate_constraints! (repeats 2 times)
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1000 [inlined]
  [3] simplify_graph!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool)
    @ Pkg.Resolve ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1519
  [4] simplify_graph! (repeats 2 times)
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Resolve/graphtype.jl:1519 [inlined]
  [5] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:335
  [6] targeted_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1154
  [7] tiered_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1139
  [8] _resolve(io::Base.TTY, env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1160
  [9] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1176
 [10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:268
 [11] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
 [12] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
 [13] #add#26
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
 [14] add
    @ ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
 [15] add(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::String, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/software/julia-1.7.3/share/julia/stdlib/v1.7/Pkg/src/API.jl:166
 [16] top-level scope
    @ REPL[2]:1

Best,
Duo

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