search

korbinian90 / CLEARSWI.jl

improved susceptibility weighted imaging using multi-echo aquisitions
https://korbinian90.github.io/CLEARSWI.jl/dev
MIT License
27 stars 11 forks source link

mriresearch tools doesn't install with clearswi #6

Closed stebo85 closed 2 years ago

stebo85 commented 2 years ago

Dear Korbinian,

I am trying to install clearswi in Neurodesk, but I get a dependency error with MriResearchTools:

I am running in Ubuntu 20.04 with base julia:

using Pkg
Pkg.add(PackageSpec(url="https://github.com/korbinian90/CLEARSWI.jl"))
Pkg.add(PackageSpec(url="https://github.com/korbinian90/MriResearchTools.jl"))

and I get:

 Cloning git-repo `https://github.com/korbinian90/CLEARSWI.jl`
   Updating git-repo `https://github.com/korbinian90/CLEARSWI.jl`
  Resolving package versions...
    Cloning default registries into `~/.julia`
    Cloning registry from "https://github.com/JuliaRegistries/General.git"
      Added registry `General` to `~/.julia/registries/General`
  Installed AxisAlgorithms ───── v1.0.1
  Installed Ratios ───────────── v0.4.2
  Installed Compat ───────────── v3.39.0
  Installed FFTW_jll ─────────── v3.3.9+8
  Installed FFTW ─────────────── v1.3.2
  Installed MriResearchTools ─── v0.5.1
  Installed TranscodingStreams ─ v0.9.6
  Installed IntelOpenMP_jll ──── v2018.0.3+2
  Installed FixedPointNumbers ── v0.8.4
  Installed Adapt ────────────── v3.3.1
  Installed CodecZlib ────────── v0.7.0
  Installed OffsetArrays ─────── v1.10.7
  Installed ROMEO ────────────── v0.1.5
  Installed LazyArtifacts ────── v1.3.0
  Installed WoodburyMatrices ─── v0.5.4
  Installed ChainRulesCore ───── v1.8.0
  Installed JLLWrappers ──────── v1.3.0
  Installed DataStructures ───── v0.18.10
  Installed StaticArrays ─────── v1.2.13
  Installed Artifacts ────────── v1.3.0
  Installed Zlib_jll ─────────── v1.2.11+18
  Installed Reexport ─────────── v1.2.2
  Installed TOML ─────────────── v1.0.3
  Installed MappedArrays ─────── v0.3.0
  Installed MKL_jll ──────────── v2021.1.1+2
  Installed Preferences ──────── v1.2.2
  Installed AbstractFFTs ─────── v1.0.1
  Installed Requires ─────────── v1.1.3
  Installed OrderedCollections ─ v1.4.1
  Installed Interpolations ───── v0.13.4
  Installed NIfTI ────────────── v0.5.6
######################################################################## 100.0%##O=#  #                                                        ######################################################################## 100.0%
######################################################################## 100.0%##O#- #                                                         ######################################################################## 100.0%
######################################################################## 100.0%##O#- #                                                         ######################################################################## 100.0%
   Updating `~/.julia/environments/v1.4/Project.toml`
  [06ae4d9b] + CLEARSWI v0.2.4 #master (https://github.com/korbinian90/CLEARSWI.jl)
   Updating `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] + AbstractFFTs v1.0.1
  [79e6a3ab] + Adapt v3.3.1
  [56f22d72] + Artifacts v1.3.0
  [13072b0f] + AxisAlgorithms v1.0.1
  [06ae4d9b] + CLEARSWI v0.2.4 #master (https://github.com/korbinian90/CLEARSWI.jl)
  [d360d2e6] + ChainRulesCore v1.8.0
  [944b1d66] + CodecZlib v0.7.0
  [34da2185] + Compat v3.39.0
  [864edb3b] + DataStructures v0.18.10
  [7a1cc6ca] + FFTW v1.3.2
  [f5851436] + FFTW_jll v3.3.9+8
  [53c48c17] + FixedPointNumbers v0.8.4
  [1d5cc7b8] + IntelOpenMP_jll v2018.0.3+2
  [a98d9a8b] + Interpolations v0.13.4
  [692b3bcd] + JLLWrappers v1.3.0
  [4af54fe1] + LazyArtifacts v1.3.0
  [856f044c] + MKL_jll v2021.1.1+2
  [dbb5928d] + MappedArrays v0.3.0
  [557dad86] + MriResearchTools v0.5.1
  [a3a9e032] + NIfTI v0.5.6
  [6fe1bfb0] + OffsetArrays v1.10.7
  [bac558e1] + OrderedCollections v1.4.1
  [21216c6a] + Preferences v1.2.2
  [1ea8258b] + ROMEO v0.1.5
  [c84ed2f1] + Ratios v0.4.2
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.1.3
  [90137ffa] + StaticArrays v1.2.13
  [fa267f1f] + TOML v1.0.3
  [3bb67fe8] + TranscodingStreams v0.9.6
  [efce3f68] + WoodburyMatrices v0.5.4
  [83775a58] + Zlib_jll v1.2.11+18
  [2a0f44e3] + Base64 
  [ade2ca70] + Dates 
  [8bb1440f] + DelimitedFiles 
  [8ba89e20] + Distributed 
  [b77e0a4c] + InteractiveUtils 
  [76f85450] + LibGit2 
  [8f399da3] + Libdl 
  [37e2e46d] + LinearAlgebra 
  [56ddb016] + Logging 
  [d6f4376e] + Markdown 
  [a63ad114] + Mmap 
  [44cfe95a] + Pkg 
  [de0858da] + Printf 
  [3fa0cd96] + REPL 
  [9a3f8284] + Random 
  [ea8e919c] + SHA 
  [9e88b42a] + Serialization 
  [1a1011a3] + SharedArrays 
  [6462fe0b] + Sockets 
  [2f01184e] + SparseArrays 
  [10745b16] + Statistics 
  [8dfed614] + Test 
  [cf7118a7] + UUIDs 
  [4ec0a83e] + Unicode 
   Building FFTW → `~/.julia/packages/FFTW/G3lSO/deps/build.log`
    Cloning git-repo `https://github.com/korbinian90/MriResearchTools.jl`
   Updating git-repo `https://github.com/korbinian90/MriResearchTools.jl`
  Resolving package versions...
julia version requirement for package `MriResearchTools [557dad86]` not satisfied
julia version requirement for package `MriResearchTools [557dad86]` not satisfied
julia version requirement for package `MriResearchTools [557dad86]` not satisfied
julia version requirement for package `MriResearchTools [557dad86]` not satisfied
ERROR: LoadError: Unsatisfiable requirements detected for package ROMEO [1ea8258b]:
 ROMEO [1ea8258b] log:
 ├─possible versions are: [0.1.0-0.1.5, 0.2.0-0.2.8] or uninstalled
 ├─restricted to versions 0.2.5-0.2 by MriResearchTools [557dad86], leaving only versions 0.2.5-0.2.8
 │ └─MriResearchTools [557dad86] log:
 │   ├─possible versions are: 0.5.2 or uninstalled
 │   └─MriResearchTools [557dad86] is fixed to version 0.5.2
 └─restricted by julia compatibility requirements to versions: 0.1.0-0.1.5 or uninstalled — no versions left
Stacktrace:
 [1] propagate_constraints!(::Pkg.Resolve.Graph, ::Set{Int64}; log_events::Bool) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Resolve/graphtype.jl:1010
 [2] propagate_constraints! at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Resolve/graphtype.jl:951 [inlined] (repeats 2 times)
 [3] simplify_graph!(::Pkg.Resolve.Graph, ::Set{Int64}; clean_graph::Bool) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Resolve/graphtype.jl:1465
 [4] simplify_graph! at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Resolve/graphtype.jl:1465 [inlined] (repeats 2 times)
 [5] resolve_versions!(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:341
 [6] targeted_resolve(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Pkg.Types.PreserveLevel) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:1057
 [7] tiered_resolve(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:1043
 [8] _resolve at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:1063 [inlined]
 [9] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Array{Base.UUID,1}; preserve::Pkg.Types.PreserveLevel, platform::Pkg.BinaryPlatforms.Linux) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:1078
 [10] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; preserve::Pkg.Types.PreserveLevel, platform::Pkg.BinaryPlatforms.Linux, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:159
 [11] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:112
 [12] #add#27 at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:109 [inlined]
 [13] add at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:109 [inlined]
 [14] #add#23 at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:106 [inlined]
 [15] add(::Pkg.Types.PackageSpec) at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:106
 [16] top-level scope at /opt/install_packages.jl:3
 [17] include(::Module, ::String) at ./Base.jl:377
 [18] exec_options(::Base.JLOptions) at ./client.jl:288
 [19] _start() at ./client.jl:484
in expression starting at /opt/install_packages.jl:3
korbinian90 commented 2 years ago

Hi Steffen,

Thanks for reporting this issue! The problem is Pkg.add(PackageSpec(url="https://github.com/korbinian90/MriResearchTools.jl")), which uses the newest version on github of the package (requiring at least julia 1.5). The command Pkg.add(PackageSpec(MriResearchTools") instead solves this problem, as it uses the julia package manager to resolve version conflicts, which works because MriResearchTools is a registered julia package. I replaced the command in the README file as well.

I started to use julia 1.5 features since it has been released over a year ago, so I would recommend updating to a newer julia version to receive the newest version of the packages. (julia 1.6 had a lot of performance improvements for faster package loading/ compilation times and the soon to be released julia 1.7 will probably be the next LTS version)

stebo85 commented 2 years ago

Dear Korbinian,

Perfect. Upgrading julia to 1.6.4 solved the problem :)

Thank you so much Cheers Steffen