JuliaPy / JuliaPy/PyCall.jl

PyCall broken with 1.7.3?

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Beschreibung

I am hoping my environment is messed up somehow

I just start Julia, 'using PyCall' and y to 'add PyCall'

I get 'ERROR: LoadError: PyCall not properly installed. Please run Pkg.build("PyCall")'

See below for the requested and failed Pkg.build("PyCall")

The log files are here
https://drive.google.com/file/d/1pXBCoMkFoQu9bOEhGvu51ntcgbAHs0-v/view?usp=sharing
https://drive.google.com/file/d/10uqQc-4ih_1A-uSvZPT4l404pJJdjq_e/view?usp=sharing

`
(base) C02GC228MD6T:~ peter.wolf$ julia
...Version 1.7.3 (2022-05-06)
...

julia> using PyCall
│ Package PyCall not found, but a package named PyCall is available from a
│ registry.
│ Install package?
│ (@v1.7) pkg> add PyCall
└ (y/n) [y]: y
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Updating `~/.julia/environments/v1.7/Project.toml`
[438e738f] + PyCall v1.93.1
Updating `~/.julia/environments/v1.7/Manifest.toml`
[8f4d0f93] + Conda v1.7.0
[682c06a0] + JSON v0.21.3
[1914dd2f] + MacroTools v0.5.9
[69de0a69] + Parsers v2.3.2
[438e738f] + PyCall v1.93.1
[81def892] + VersionParsing v1.3.0
[37e2e46d] + LinearAlgebra
[a63ad114] + Mmap
[e66e0078] + CompilerSupportLibraries_jll
[4536629a] + OpenBLAS_jll
[8e850b90] + libblastrampoline_jll
[ Info: Precompiling PyCall [438e738f-606a-5dbb-bf0a-cddfbfd45ab0]
ERROR: LoadError: PyCall not properly installed. Please run Pkg.build("PyCall")
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] top-level scope
@ ~/.julia/packages/PyCall/7a7w0/src/startup.jl:44
[3] include(mod::Module, _path::String)
@ Base ./Base.jl:418
[4] include(x::String)
@ PyCall ~/.julia/packages/PyCall/7a7w0/src/PyCall.jl:1
[5] top-level scope
@ ~/.julia/packages/PyCall/7a7w0/src/PyCall.jl:38
[6] include
@ ./Base.jl:418 [inlined]
[7] 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
[8] top-level scope
@ none:1
[9] eval
@ ./boot.jl:373 [inlined]
[10] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[11] top-level scope
@ none:1
in expression starting at /Users/peter.wolf/.julia/packages/PyCall/7a7w0/src/startup.jl:41
in expression starting at /Users/peter.wolf/.julia/packages/PyCall/7a7w0/src/PyCall.jl:1
ERROR: Failed to precompile PyCall [438e738f-606a-5dbb-bf0a-cddfbfd45ab0] to /Users/peter.wolf/.julia/compiled/v1.7/PyCall/jl_ypJJQ7.
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
`

`
julia> using Pkg

julia> Pkg.build("PyCall")
Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/6e47d11ea2776bc5627421d59cdcc1296c058071/build.log`
Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/1fc929f47d7c151c839c5fc1375929766fb8edcc/build.log`
ERROR: Error building `PyCall`, showing the last 100 of log:
transformers -> huggingface-hub[version='<1.0,>=0.1.0']
huggingface-hub

Package responses conflicts for:
datasets -> responses[version='<0.19']
responses

Package importlib-metadata conflicts for:
transformers -> importlib_metadata -> importlib-metadata[version='>=1.1.3,<1.1.4.0a0|>=1.6.0,<1.6.1.0a0|>=1.6.1,<1.6.2.0a0|>=1.7.0,<1.7.1.0a0|>=2.0.0,<2.0.1.0a0|>=3.10.0,<3.10.1.0a0|>=4.11.3,<4.11.4.0a0|>=4.8.2,<4.8.3.0a0|>=4.8.1,<4.8.2.0a0|>=4.6.4,<4.6.5.0a0|>=3.7.3,<3.7.4.0a0']
sacremoses -> click -> importlib-metadata
datasets -> importlib_metadata -> importlib-metadata[version='>=1.1.3,<1.1.4.0a0|>=1.6.0,<1.6.1.0a0|>=1.6.1,<1.6.2.0a0|>=1.7.0,<1.7.1.0a0|>=2.0.0,<2.0.1.0a0|>=3.10.0,<3.10.1.0a0|>=4.11.3,<4.11.4.0a0|>=4.8.2,<4.8.3.0a0|>=4.8.1,<4.8.2.0a0|>=4.6.4,<4.6.5.0a0|>=3.7.3,<3.7.4.0a0']
click -> importlib-metadata

Package cffi conflicts for:
pytorch -> cffi
transformers -> pytorch -> cffi
conda-content-trust -> cryptography -> cffi[version='!=1.11.3,>=1.8|>=1.12|>=1.8|>=1.7']
brotlipy -> cffi[version='>=1.0.0']
soundfile -> cffi[version='>=1.0']
cryptography -> cffi[version='!=1.11.3,>=1.8|>=1.12|>=1.8|>=1.7']
cffi
pyopenssl -> cryptography[version='>=35.0'] -> cffi[version='!=1.11.3,>=1.8|>=1.12|>=1.8|>=1.7']
urllib3 -> brotlipy[version='>=0.6.0'] -> cffi[version='!=1.11.3,>=1.8|>=1.0.0|>=1.12|>=1.8|>=1.7']

Package multiprocess conflicts for:
datasets -> multiprocess
multiprocess

Package ninja-base conflicts for:
pytorch -> ninja -> ninja-base==1.10.2=haf03e11_5
ninja-base
ninja -> ninja-base==1.10.2=haf03e11_5

Package sacremoses conflicts for:
transformers -> sacremoses
sacremoses

Package async-timeout conflicts for:
aiohttp -> async-timeout[version='<4.0,>=3.0|>=3.0,<4.0|>=4.0.0a3,<5.0|>=1.2,<3.0|>=1.2.0|<5.0,>=4.0.0a3']
datasets -> aiohttp -> async-timeout[version='<4.0,>=3.0|>=3.0,<4.0|>=4.0.0a3,<5.0|>=1.2,<3.0|>=1.2.0|<5.0,>=4.0.0a3']
async-timeout

Package zstd conflicts for:
pyarrow -> arrow-cpp[version='>=4.0.1,<4.0.2.0a0'] -> zstd[version='>=1.3.3,<1.3.4.0a0|>=1.3.7,<1.3.8.0a0|>=1.4.5,<1.5.0a0|>=1.4.9,<1.5.0a0']
conda-package-handling -> libarchive[version='>=3.3.3'] -> zstd[version='>=1.3.3,<1.3.4.0a0|>=1.3.7,<1.3.8.0a0|>=1.4.4,<1.5.0a0|>=1.5.0,<1.6.0a0|>=1.5.2,<1.6.0a0']

Package futures conflicts for:
pyarrow -> futures
conda[version='>=4.12.0'] -> conda-package-handling[version='>=1.3.0'] -> futures
conda-package-handling -> futures

Package joblib conflicts for:
joblib
transformers -> sacremoses -> joblib
sacremoses -> joblib

Package pyarrow conflicts for:
pyarrow
datasets -> pyarrow[version='>=0.17.1|>=5.0.0']

Package pandas conflicts for:
pyarrow -> pandas
datasets -> pandas
pandas

Package pyparsing conflicts for:
packaging -> pyparsing[version='!=3.0.5,>=2.0.2|>=2.0.2|>=2.0.2,!=3.0.5']
pyparsing
huggingface-hub -> packaging[version='>=20.9'] -> pyparsing[version='!=3.0.5,>=2.0.2|>=2.0.2|>=2.0.2,!=3.0.5']
datasets -> packaging -> pyparsing[version='!=3.0.5,>=2.0.2|>=2.0.2|>=2.0.2,!=3.0.5']
transformers -> packaging[version='>=20.0'] -> pyparsing[version='!=3.0.5,>=2.0.2|>=2.0.2|>=2.0.2,!=3.0.5']

Package zope.interface conflicts for:
attrs -> zope.interface
aiohttp -> attrs[version='>=17.3.0'] -> zope.interface

┌ Info: Using the Python distribution in the Conda package by default.
└ To use a different Python version, set ENV["PYTHON"]="pythoncommand" and re-run Pkg.build("PyCall").
[ Info: Running `conda install -y numpy` in root environment
ERROR: LoadError: failed process: Process(setenv(`/Users/peter.wolf/miniconda3/envs/phinder/bin/conda install -y numpy`,["XPC_FLAGS=0x0", "_CE_M=", "PATH=/Users/peter.wolf/opt/miniconda3/bin:/Users/peter.wolf/opt/miniconda3/condabin:/Users/peter.wolf/.cargo/bin:/Applications/Julia-1.7.app/Contents/Resources/julia/bin:/Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin", "PWD=/Users/peter.wolf", "XPC_SERVICE_NAME=0", "TERM_PROGRAM=Apple_Terminal", "SHELL=/bin/bash", "MAVEN_OPTS=-Xmx1024m", "__CF_USER_TEXT_ENCODING=0x1F7:0x0:0x0", "OPENBLAS_NUM_THREADS=8" … "_CE_CONDA=", "USER=peter.wolf", "JULIA_EDITOR=emacsclient", "TERM=xterm-256color", "HOME=/Users/peter.wolf", "TERM_PROGRAM_VERSION=440", "JULIA_HOME=/Applications/Julia-1.7.app/Contents/Resources/julia", "JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home", "OPENBLAS_MAIN_FREE=1", "PYTHONIOENCODING=UTF-8"]), ProcessExited(1)) [1]

Stacktrace:
[1] pipeline_error
@ ./process.jl:540 [inlined]
[2] run(::Cmd; wait::Bool)
@ Base ./process.jl:455
[3] run
@ ./process.jl:453 [inlined]
[4] runconda(args::Cmd, env::String)
@ Conda ~/.julia/packages/Conda/x2UxR/src/Conda.jl:128
[5] add(pkg::String, env::String; channel::String)
@ Conda ~/.julia/packages/Conda/x2UxR/src/Conda.jl:222
[6] add (repeats 2 times)
@ ~/.julia/packages/Conda/x2UxR/src/Conda.jl:221 [inlined]
[7] top-level scope
@ ~/.julia/packages/PyCall/7a7w0/deps/build.jl:79
[8] include(fname::String)
@ Base.MainInclude ./client.jl:451
[9] top-level scope
@ none:5
in expression starting at /Users/peter.wolf/.julia/packages/PyCall/7a7w0/deps/build.jl:43

Full log at /Users/peter.wolf/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/1fc929f47d7c151c839c5fc1375929766fb8edcc/build.log
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68
[2] (::Pkg.Operations.var"#62#67"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec})()
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:962
[3] withenv(::Pkg.Operations.var"#62#67"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, ::Pair{String, String}, ::Vararg{Pair{String}})
@ Base ./env.jl:172
[4] (::Pkg.Operations.var"#99#103"{String, Bool, Bool, Bool, Pkg.Operations.var"#62#67"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec})()
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1506
[5] with_temp_env(fn::Pkg.Operations.var"#99#103"{String, Bool, Bool, Bool, Pkg.Operations.var"#62#67"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec}, temp_env::String)
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1390
[6] (::Pkg.Operations.var"#98#102"{Bool, Bool, Bool, Pkg.Operations.var"#62#67"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String)
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1469
[7] mktempdir(fn::Pkg.Operations.var"#98#102"{Bool, Bool, Bool, Pkg.Operations.var"#62#67"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String)
@ Base.Filesystem ./file.jl:750
[8] mktempdir(fn::Function, parent::String) (repeats 2 times)
@ Base.Filesystem ./file.jl:748
[9] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project; force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1435
[10] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project)
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1432
[11] build_versions(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}; verbose::Bool)
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:943
[12] build(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}, verbose::Bool)
@ Pkg.Operations /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:822
[13] build(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; verbose::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
@ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:992
[14] build(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
[15] build(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
[16] #build#99
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
[17] build
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
[18] #build#98
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
[19] build(pkg::String)
@ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:141
[20] top-level scope
@ REPL[3]:1
`

Beitragsleitfaden

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Rechercherichtung

Start with deps/build.jl and Conda.jl at the failing Pkg.build("PyCall") path, then inspect the referenced build log and the startup.jl error. Reproduce on Julia 1.7.3 with the shown environment and determine whether PyCall can build and `using PyCall` can load successfully without the reported dependency-resolution failure.

Vom Indexierungsmodell aus dem Issue-Text verfasst.

Bewertung

Tech-Stack
julia, python
Bereich
backend
Issue-Typ
Bug
Schwierigkeit
4/5
Geschätzter Aufwand
3-5 Tage
Aktivitätsstatus
Veraltet
Klarheit
Muss geklärt werden
Anfängerfreundlichkeit
25/100

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