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Julia 1.8 update #11

Merged
merged 1 commit into from
May 29, 2024
Merged

Julia 1.8 update #11

merged 1 commit into from
May 29, 2024

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fonsp
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@fonsp fonsp commented Apr 17, 2023

Hello! 👋

This binder currently fails to build, I think this is happening because it is using Julia 1.8 during the build, but this environment was generated using Julia 1.6, and one of the pinned dependencies (RDatasets.jl) used internal Julia API (ccall) in a way that was not future-proof.

What I did to generate the files in this PR:

  • Run julia --project inside the repo with Julia 1.8
  • import Pkg
  • Pkg.upgrade_manifest() (not strictly necessary, but Julia 1.7 started using a new format for Manifest.toml. You see a warning otherwise.)
  • Pkg.update() (update all packages to latest and update Manifest.toml

You can test my branch with:

https://mybinder.org/v2/gh/fonsp/demo-julia/julia-18-update it works!

Logs from failing binder build on current `main` 
Waiting for build to start...
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�[0m�[91m   Installed Parsers ───────── v2.5.8
�[0m�[91m   Installed IJulia ────────── v1.24.0
�[0m�[91m   Installed JLLWrappers ───── v1.4.1
�[0m�[91m   Installed ZeroMQ_jll ────── v4.3.4+0
�[0m�[91m   Installed libsodium_jll ─── v1.0.20+0
�[0m�[91m   Installed SnoopPrecompile ─ v1.0.3
�[0m�[91m   Installed MbedTLS ───────── v1.1.7
   Installed SoftGlobalScope ─ v1.1.0
�[0m�[91m    Updating `/srv/julia/pkg/environments/v1.8/Project.toml`
  [7073ff75] + IJulia v1.24.0
�[0m�[91m    Updating `/srv/julia/pkg/environments/v1.8/Manifest.toml`
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�[0m�[91m    Building Conda ─→ `/srv/julia/pkg/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/e32a90da027ca45d84678b826fffd3110bb3fc90/build.log`
�[0m�[91m    Building IJulia → `/srv/julia/pkg/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/59e19713542dd9dd02f31d59edbada69530d6a14/build.log`
�[0m�[91mPrecompiling�[0m�[91m �[0m�[91mproject...�[0m�[91m
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�[0m�[91m  10 dependencies successfully precompiled in 15 seconds. 6 already precompiled.
�[0m�[91m[ Info: Installing Julia kernelspec in /srv/conda/envs/notebook/share/jupyter/kernels/julia-1.8
�[0m�[91m┌ Warning: The active manifest file is an older format with no julia version entry. Dependencies may have been resolved with a different julia version.
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�[0m�[91m�[32m  ✓ �[39m�[90mDistributions�[39m�[0m�[91m
�[0m�[91m�[32m  ✓ �[39m�[90mKernelDensity�[39m�[0m�[91m
�[0m�[91m�[32m  ✓ �[39mGadfly
�[0m�[91m�[32m  ✓ �[39m�[90mDataFrames�[39m�[0m�[91m
�[0m�[91m�[32m  ✓ �[39m�[90mRData�[39m�[0m�[91m
�[0m�[91m�[91m  ✗ �[39mRDatasets
�[0m�[91m  75 dependencies successfully precompiled in 198 seconds. 7 already precompiled.
  �[91m3�[39m dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages�[0m�[91m
�[0m�[91m   Installed MKL_jll ─ v2021.1.1+2
�[0m�[91m┌ Warning: The active manifest file at `/home/jovyan/Manifest.toml` has an old format that is being maintained.
│ To update to the new format, which is supported by Julia versions ≥ 1.6.2, run `Pkg.upgrade_manifest()` which will upgrade the format without re-resolving.
│ To then record the julia version re-resolve with `Pkg.resolve()` and if there are resolve conflicts consider `Pkg.update()`.
â”” @ Pkg.Types /cache/build/default-amdci4-2/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/manifest.jl:287
�[0m�[91m  No Changes�[0m�[91m to `~/Project.toml`
�[0m�[91m    Updating `~/Manifest.toml`
�[0m�[91m  [8f4d0f93] - Conda v1.5.2
  [7073ff75] - IJulia v1.23.2
 �[0m�[91m [739be429] - MbedTLS v1.0.3
�[0m�[91m  [b85f4697] - SoftGlobalScope v1.1.0
  [81def892] �[0m�[91m- VersionParsing v1.2.0
 �[0m�[91m [c2297ded] �[0m�[91m- ZMQ v1.2.1
�[0m�[91m⌅�[0m�[91m [856f044c] �[0m�[91m↑ MKL_jll v2021.1.1+1 ⇒ v2021.1.1+2
  [8f1865be] - ZeroMQ_jll v4.3.4+0
  [a9144af2] - libsodium_jll v1.0.20+0
  [0dad84c5] �[0m�[91m~ ArgTools ⇒ v1.1.1
  [f43a241f] �[0m�[91m~ Downloads ⇒ v1.6.0
�[0m�[91m  [b27032c2] ~ LibCURL ⇒ v0.6.3
  [ca575930] ~ NetworkOptions ⇒ v1.2.0
  [44cfe95a] ~ Pkg ⇒ v1.8.0
  [ea8e919c] ~ SHA ⇒ v0.7.0
  [fa267f1f] ~ TOML ⇒ v1.0.0
  [a4e569a6] ~ Tar ⇒ v1.10.1
�[0m�[91m  [e66e0078] ~ CompilerSupportLibraries_jll ⇒ v1.0.1+0
  [deac9b47] ~ LibCURL_jll ⇒ v7.84.0+0
  [29816b5a] ~ LibSSH2_jll ⇒ v1.10.2+0
  [c8ffd9c3] ~ MbedTLS_jll ⇒ v2.28.0+0
  [14a3606d] �[0m�[91m~ MozillaCACerts_jll ⇒ v2022.2.1
  [4536629a] �[0m�[91m+ OpenBLAS_jll v0.3.20+0
 �[0m�[91m [83775a58] ~ Zlib_jll ⇒ v1.2.12+3
  [8e850b90] + libblastrampoline_jll v5.1.1+0
  [8e850ede] ~ nghttp2_jll ⇒ v1.48.0+0
  [3f19e933] ~ p7zip_jll ⇒ v17.4.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
�[0m�[91m┌ Warning: The Pkg REPL mode is intended for interactive use only, and should not be used from scripts. It is recommended to use the functional API instead.
â”” @ Pkg.REPLMode /cache/build/default-amdci4-2/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/REPLMode/REPLMode.jl:379
�[0m�[91mPrecompiling�[0m�[91m �[0m�[91mproject...�[0m�[91m
�[0m�[91m�[32m  ✓ �[39m�[90mOpenBLAS_jll�[39m�[0m�[91m
�[0m�[91m�[32m  ✓ �[39m�[90mMKL_jll�[39m�[0m�[91m
�[0m�[91m�[32m  ✓ �[39m�[90mlibblastrampoline_jll�[39m
�[0m�[91m�[91m  ✗ �[39m�[90mSentinelArrays�[39m
�[0m�[91m�[91m  ✗ �[39m�[90mCSV�[39m
�[0m�[91m�[32m  ✓ �[39m�[90mFFTW�[39m
�[0m�[91m�[32m  ✓ �[39m�[90mKernelDensity�[39m
�[0m�[91m�[91m  ✗ �[39mRDatasets
�[0m�[91m�[32m  ✓ �[39mGadfly
�[0m�[91m  6 dependencies successfully precompiled in 44 seconds. 78 already precompiled.
�[0m�[91m
�[0m�[91mERROR: �[0m�[91mThe following 1 direct dependency failed to precompile:

RDatasets [ce6b1742-4840-55fa-b093-852dadbb1d8b]

Failed to precompile RDatasets [ce6b1742-4840-55fa-b093-852dadbb1d8b] to /srv/julia/pkg/compiled/v1.8/RDatasets/jl_2O94e1.
ERROR: LoadError: ccall method definition: argument 1 type doesn't correspond to a C type
Stacktrace:
 [1] top-level scope
   @ /srv/julia/pkg/packages/SentinelArrays/VbnBp/src/SentinelArrays.jl:209
 [2] include
   @ ./Base.jl:419 [inlined]
 [3] 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:1554
 [4] top-level scope
   @ stdin:1
in expression starting at /srv/julia/pkg/packages/SentinelArrays/VbnBp/src/SentinelArrays.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile SentinelArrays [91c51154-3ec4-41a3-a24f-3f23e20d615c] to /srv/julia/pkg/compiled/v1.8/SentinelArrays/jl_5HnZZo.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /srv/julia/pkg/packages/CSV/Zl2ww/src/CSV.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /srv/julia/pkg/compiled/v1.8/CSV/jl_htt4Dv.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /srv/julia/pkg/packages/RDatasets/eRbZP/src/RDatasets.jl:1
in expression starting at stdin:1�[0m�[91m
Stacktrace:�[0m�[91m
�[0m�[91m [1] pkgerror(msg::�[0m�[91mString)
   @ Pkg.Types �[0m�[91m/srv/julia/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67�[0m�[91m
�[0m�[91m [2] �[0m�[91mprecompile(ctx::�[0m�[91mPkg.Types.Context, pkgs�[0m�[91m::�[0m�[91mVector{String}; internal_call::�[0m�[91mBool, strict�[0m�[91m::Bool, warn_loaded::�[0m�[91mBool, already_instantiated::�[0m�[91mBool, kwargs::�[0m�[91mBase.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1435
 [3] precompile
   @ /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1072 [inlined]
 [4] #precompile#225
   @ /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1071 [inlined]
 [5] precompile (repeats 2 times)
   @ /srv/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1071 [inlined]
 [6] do_cmd!(command::Pkg.REPLMode.Command, repl::Pkg.REPLMode.MiniREPL)
   @ Pkg.REPLMode �[0m�[91m/srv/julia/share/julia/stdlib/v1.8/Pkg/src/REPLMode/REPLMode.jl:406
 [7] do_cmd(repl::Pkg.REPLMode.MiniREPL, input::String; do_rethrow::Bool)
   @ Pkg.REPLMode /srv/julia/share/julia/stdlib/v1.8/Pkg/src/REPLMode/REPLMode.jl:387
 [8] top-level scope
   @ none:1
�[0mRemoving intermediate container 2fac049b0a26
The command '/bin/sh -c JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); Pkg.resolve(); pkg"precompile"'' returned a non-zero code: 1

@minrk minrk merged commit 950270c into binder-examples:main May 29, 2024
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fonsp commented May 30, 2024

@minrk I could update to Julia 1.10 if you like?

@fonsp fonsp deleted the julia-18-update branch May 30, 2024 07:12
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minrk commented May 30, 2024

That would be great, thanks! Sorry for forgetting about this one

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