Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Latest version works in pinned version of MicroMamba v0.1.12 in M1 but breaks in v0.1.13 #93

Open
ppalmes opened this issue May 30, 2023 · 6 comments
Open

Latest version works in pinned version of MicroMamba v0.1.12 in M1 but breaks in v0.1.13 #93

ppalmes opened this issue May 30, 2023 · 6 comments

Comments

@ppalmes
Copy link

ppalmes commented May 30, 2023

I need to pin the micromamba version to v0.1.12. Using the latest micromamba breaks condapkg:

Stacktrace:
  [1] pipeline_error
    @ ./process.jl:565 [inlined]
  [2] run(::Cmd; wait::Bool)
    @ Base ./process.jl:480
  [3] run(::Cmd)
    @ Base ./process.jl:477
  [4] _run(io::IO, cmd::Cmd, args::Any; flags::Any)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:370
  [5] _resolve_conda_install(io::Any, conda_env::Any, specs::Any, channels::Any; create::Any)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:271
  [6] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:526
  [7] resolve()
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:384
  [8] add(pkgs::AbstractVector; resolve::Any, file::Any, kw::Base.Pairs{Symbol, V, Tuple{Vararg{Symbol, N}}, NamedTuple{names, T}} where {V, N, names, T<:Tuple{Vararg{Any, N}}})
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/deps.jl:222
  [9] add(pkgs::AbstractVector)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/deps.jl:215
 [10] add(args::Vector{String})
    @ CondaPkg.PkgREPL ~/.julia/packages/CondaPkg/osUdN/src/PkgREPL.jl:125
 [11] do_cmd!(command::Pkg.REPLMode.Command, repl::LineEditREPL)
    @ Pkg.REPLMode /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:412
 [12] do_cmd(repl::LineEditREPL, input::String; do_rethrow::Bool)
    @ Pkg.REPLMode /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:390
 [13] do_cmd
    @ /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:380 [inlined]
 [14] (::Pkg.REPLMode.var"#24#27"{LineEditREPL, REPL.LineEdit.Prompt})(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool)
    @ Pkg.REPLMode /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:557
 [15] #invokelatest#2
    @ ./essentials.jl:816 [inlined]
 [16] invokelatest
    @ ./essentials.jl:813 [inlined]
 [17] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/REPL/src/LineEdit.jl:2647
 [18] run_frontend(repl::LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/REPL/src/REPL.jl:1300
 [19] (::REPL.var"#62#68"{LineEditREPL, REPL.REPLBackendRef})()
    @ REPL ./task.jl:514
@cjdoris
Copy link
Collaborator

cjdoris commented Jun 2, 2023

Can you give a full MWE with all output please?

@ppalmes
Copy link
Author

ppalmes commented Jun 2, 2023

in mac silicon, using latest Julia 1.9.0

julia>
] activate --temp
] add PythonCall
] add CondaPkg
julia> using CondaPkg
] conda add pandas

(jl_XK11xL) pkg> conda add pandas
    CondaPkg Found dependencies: /var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/CondaPkg.toml
    CondaPkg Found dependencies: /Users/ppalmes/.julia/packages/PythonCall/1f5yE/CondaPkg.toml
    CondaPkg Found dependencies: /Users/ppalmes/.julia/packages/PythonCall/1f5yE/CondaPkg.toml
    CondaPkg Found dependencies: /Users/ppalmes/.julia/packages/AutoMLPipeline/iy1ee/CondaPkg.toml
    CondaPkg Resolving changes
             + pandas
             + python
             + scikit-learn
    CondaPkg Creating environment
             │ /Users/ppalmes/.julia/artifacts/7cfea9db5b54ceb7d9109c8728914c9459303a75/bin/micromamba
             │ -r /Users/ppalmes/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
             │ create
             │ -y
             │ -p /var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/.CondaPkg/env
             │ --override-channels
             │ --no-channel-priority
             │ pandas[version='*']
             │ python[version='*']
             │ python[version='>=3.7,<4',channel='conda-forge',build='*cpython*']
             │ scikit-learn[version='*']
             │ -c conda-forge
             │ -c mkl
             └ -c scikit-learn

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

scikit-learn/osx-arm64                                        No change
mkl/osx-arm64                                                 No change
mkl/noarch                                                    No change
scikit-learn/noarch                                           No change
conda-forge/osx-arm64                              @   3.0MB/s  2.3s
conda-forge/noarch                                 @   3.5MB/s  3.8s
ERROR: failed process: Process(`/Users/ppalmes/.julia/artifacts/7cfea9db5b54ceb7d9109c8728914c9459303a75/bin/micromamba -r /Users/ppalmes/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root create -y -p /var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/.CondaPkg/env --override-channels --no-channel-priority "pandas[version='*']" "python[version='*']" "python[version='>=3.7,<4',channel='conda-forge',build='*cpython*']" "scikit-learn[version='*']" -c conda-forge -c mkl -c scikit-learn`, ProcessSignaled(11)) [0]

Stacktrace:
  [1] pipeline_error
    @ ./process.jl:565 [inlined]
  [2] run(::Cmd; wait::Bool)
    @ Base ./process.jl:480
  [3] run(::Cmd)
    @ Base ./process.jl:477
  [4] _run(io::IO, cmd::Cmd, args::Any; flags::Any)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:370
  [5] _resolve_conda_install(io::Any, conda_env::Any, specs::Any, channels::Any; create::Any)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:271
  [6] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:526
  [7] resolve()
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/resolve.jl:384
  [8] add(pkgs::AbstractVector; resolve::Any, file::Any, kw::Base.Pairs{Symbol, V, Tuple{Vararg{Symbol, N}}, NamedTuple{names, T}} where {V, N, names, T<:Tuple{Vararg{Any, N}}})
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/deps.jl:222
  [9] add(pkgs::AbstractVector)
    @ CondaPkg ~/.julia/packages/CondaPkg/osUdN/src/deps.jl:215
 [10] add(args::Vector{String})
    @ CondaPkg.PkgREPL ~/.julia/packages/CondaPkg/osUdN/src/PkgREPL.jl:125
 [11] do_cmd!(command::Pkg.REPLMode.Command, repl::LineEditREPL)
    @ Pkg.REPLMode /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:412
 [12] do_cmd(repl::LineEditREPL, input::String; do_rethrow::Bool)
    @ Pkg.REPLMode /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:390
 [13] do_cmd
    @ /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:380 [inlined]
 [14] (::Pkg.REPLMode.var"#24#27"{LineEditREPL, REPL.LineEdit.Prompt})(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool)
    @ Pkg.REPLMode /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/REPLMode/REPLMode.jl:557
 [15] #invokelatest#2
    @ ./essentials.jl:816 [inlined]
 [16] invokelatest
    @ ./essentials.jl:813 [inlined]
 [17] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/REPL/src/LineEdit.jl:2647
 [18] run_frontend(repl::LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL /Applications/Julia-1.9.app/Contents/Resources/julia/share/julia/stdlib/v1.9/REPL/src/REPL.jl:1300
 [19] (::REPL.var"#62#68"{LineEditREPL, REPL.REPLBackendRef})()
    @ REPL ./task.jl:514

(jl_XK11xL) pkg>

@ppalmes
Copy link
Author

ppalmes commented Jun 2, 2023

it is basically the micromamba_jll v1.4.4+0 installed by MicroMamba v0.1.13.

If i pin Micromamba to v0.1.12, the problem is resolved.

@ppalmes
Copy link
Author

ppalmes commented Jun 2, 2023

the artifacts pulled by micromamba v1.4.4 is the one causing it.

@ppalmes
Copy link
Author

ppalmes commented Jun 2, 2023 •
edited 

(jl_XK11xL) pkg> add MicroMamba#v0.1.12
   Resolving package versions...
    Updating `/private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/Project.toml`
  [0b3b1443] + MicroMamba v0.1.12 `https://github.com/cjdoris/MicroMamba.jl.git#v0.1.12`
    Updating `/private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/Manifest.toml`
  [0b3b1443] ~ MicroMamba v0.1.13 ⇒ v0.1.12 `https://github.com/cjdoris/MicroMamba.jl.git#v0.1.12`

(jl_XK11xL) pkg> update
    Updating registry at `~/.julia/registries/General.toml`
  No Changes to `/private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/Project.toml`
    Updating `/private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_XK11xL/Manifest.toml`
  [0f8b85d8] ↑ JSON3 v1.12.0 ⇒ v1.13.0
  [aea7be01] ↑ PrecompileTools v1.1.1 ⇒ v1.1.2
  [66db9d55] - SnoopPrecompile v1.0.3
  [f8abcde7] ↑ micromamba_jll v1.4.1+0 ⇒ v1.4.3+0
  
  (jl_XK11xL) pkg> conda add pandas
    CondaPkg Found dependencies: /var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_6OwvA5/CondaPkg.toml
    CondaPkg Found dependencies: /Users/ppalmes/.julia/packages/PythonCall/1f5yE/CondaPkg.toml
    CondaPkg Found dependencies: /Users/ppalmes/.julia/packages/PythonCall/1f5yE/CondaPkg.toml
    CondaPkg Found dependencies: /Users/ppalmes/.julia/packages/AutoMLPipeline/iy1ee/CondaPkg.toml
    CondaPkg Resolving changes
             + pandas
             + python
             + scikit-learn
    CondaPkg Creating environment
             │ /Users/ppalmes/.julia/artifacts/7f0773ec03c61dc0b4217f99234c20426df480dd/bin/micromamba
             │ -r /Users/ppalmes/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
             │ create
             │ -y
             │ -p /var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_6OwvA5/.CondaPkg/env
             │ --override-channels
             │ --no-channel-priority
             │ pandas[version='*']
             │ python[version='*']
             │ python[version='>=3.7,<4',channel='conda-forge',build='*cpython*']
             │ scikit-learn[version='*']
             │ -c conda-forge
             │ -c mkl
             └ -c scikit-learn

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
scikit-learn/osx-arm64                                        No change
scikit-learn/noarch                                           No change
mkl/noarch                                                    No change
mkl/osx-arm64                                                 No change

Transaction

  Prefix: /private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_6OwvA5/.CondaPkg/env

  Updating specs:

   - pandas=*
   - python=*
   - conda-forge::python[version='>=3.7,<4',build=*cpython*]
   - scikit-learn=*


  Package                Version  Build                 Channel           Size
────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────

  + brotli                 1.0.9  h1a8c8d9_8            conda-forge     Cached
  + brotli-bin             1.0.9  h1a8c8d9_8            conda-forge     Cached
  + bzip2                  1.0.8  h3422bc3_4            conda-forge     Cached
  + ca-certificates     2023.5.7  hf0a4a13_0            conda-forge     Cached
  + certifi             2023.5.7  pyhd8ed1ab_0          conda-forge     Cached
  + charset-normalizer     3.1.0  pyhd8ed1ab_0          conda-forge     Cached
  + idna                     3.4  pyhd8ed1ab_0          conda-forge     Cached
  + joblib                 1.2.0  pyhd8ed1ab_0          conda-forge     Cached
  + libblas                3.9.0  16_osxarm64_openblas  conda-forge     Cached
  + libbrotlicommon        1.0.9  h1a8c8d9_8            conda-forge     Cached
  + libbrotlidec           1.0.9  h1a8c8d9_8            conda-forge     Cached
  + libbrotlienc           1.0.9  h1a8c8d9_8            conda-forge     Cached
  + libcblas               3.9.0  16_osxarm64_openblas  conda-forge     Cached
  + libcxx                16.0.4  h4653b0c_0            conda-forge     Cached
  + libexpat               2.5.0  hb7217d7_1            conda-forge     Cached
  + libffi                 3.4.2  h3422bc3_5            conda-forge     Cached
  + libgfortran            5.0.0  12_2_0_hd922786_31    conda-forge     Cached
  + libgfortran5          12.2.0  h0eea778_31           conda-forge     Cached
  + liblapack              3.9.0  16_osxarm64_openblas  conda-forge     Cached
  + libopenblas           0.3.21  openmp_hc731615_3     conda-forge     Cached
  + libsqlite             3.42.0  hb31c410_0            conda-forge     Cached
  + libzlib               1.2.13  h03a7124_4            conda-forge     Cached
  + llvm-openmp           16.0.4  h1c12783_0            conda-forge     Cached
  + ncurses                  6.3  h07bb92c_1            conda-forge     Cached
  + numpy                 1.24.3  py311hb8f3215_0       conda-forge     Cached
  + openssl                3.1.1  h53f4e23_1            conda-forge     Cached
  + packaging               23.1  pyhd8ed1ab_0          conda-forge     Cached
  + pandas                 2.0.2  py311h9e438b8_0       conda-forge     Cached
  + pip                   23.1.2  pyhd8ed1ab_0          conda-forge     Cached
  + platformdirs           3.5.1  pyhd8ed1ab_0          conda-forge     Cached
  + pooch                  1.7.0  pyha770c72_3          conda-forge     Cached
  + pysocks                1.7.1  pyha2e5f31_6          conda-forge     Cached
  + python                3.11.3  h1456518_0_cpython    conda-forge     Cached
  + python-dateutil        2.8.2  pyhd8ed1ab_0          conda-forge     Cached
  + python-tzdata         2023.3  pyhd8ed1ab_0          conda-forge     Cached
  + python_abi              3.11  3_cp311               conda-forge     Cached
  + pytz                  2023.3  pyhd8ed1ab_0          conda-forge     Cached
  + readline                 8.2  h92ec313_1            conda-forge     Cached
  + requests              2.31.0  pyhd8ed1ab_0          conda-forge     Cached
  + scikit-learn           1.2.2  py311hf0b18b8_2       conda-forge     Cached
  + scipy                 1.10.1  py311h93d07a4_3       conda-forge     Cached
  + setuptools            67.7.2  pyhd8ed1ab_0          conda-forge     Cached
  + six                   1.16.0  pyh6c4a22f_0          conda-forge     Cached
  + threadpoolctl          3.1.0  pyh8a188c0_0          conda-forge     Cached
  + tk                    8.6.12  he1e0b03_0            conda-forge     Cached
  + typing-extensions      4.6.3  hd8ed1ab_0            conda-forge       10kB
  + typing_extensions      4.6.3  pyha770c72_0          conda-forge       35kB
  + tzdata                 2023c  h71feb2d_0            conda-forge     Cached
  + urllib3                2.0.2  pyhd8ed1ab_0          conda-forge     Cached
  + wheel                 0.40.0  pyhd8ed1ab_0          conda-forge     Cached
  + xz                     5.2.6  h57fd34a_0            conda-forge     Cached

  Summary:

  Install: 51 packages

  Total download: 45kB

────────────────────────────────────────────────────────────────────────────────



Transaction starting
typing_extensions                                   34.9kB @ 309.3kB/s  0.1s
typing-extensions                                   10.0kB @  63.2kB/s  0.2s
Linking libzlib-1.2.13-h03a7124_4
Linking xz-5.2.6-h57fd34a_0
Linking libexpat-2.5.0-hb7217d7_1
Linking python_abi-3.11-3_cp311
Linking libcxx-16.0.4-h4653b0c_0
Linking llvm-openmp-16.0.4-h1c12783_0
Linking ncurses-6.3-h07bb92c_1
Linking libffi-3.4.2-h3422bc3_5
Linking ca-certificates-2023.5.7-hf0a4a13_0
Linking libbrotlicommon-1.0.9-h1a8c8d9_8
Linking bzip2-1.0.8-h3422bc3_4
Linking libsqlite-3.42.0-hb31c410_0
Linking tk-8.6.12-he1e0b03_0
Linking libgfortran5-12.2.0-h0eea778_31
Linking readline-8.2-h92ec313_1
Linking openssl-3.1.1-h53f4e23_1
Linking libbrotlienc-1.0.9-h1a8c8d9_8
Linking libbrotlidec-1.0.9-h1a8c8d9_8
Linking libgfortran-5.0.0-12_2_0_hd922786_31
Linking brotli-bin-1.0.9-h1a8c8d9_8
Linking libopenblas-0.3.21-openmp_hc731615_3
Linking brotli-1.0.9-h1a8c8d9_8
Linking libblas-3.9.0-16_osxarm64_openblas
Linking libcblas-3.9.0-16_osxarm64_openblas
Linking liblapack-3.9.0-16_osxarm64_openblas
Linking tzdata-2023c-h71feb2d_0
Linking python-3.11.3-h1456518_0_cpython
Linking wheel-0.40.0-pyhd8ed1ab_0
Linking setuptools-67.7.2-pyhd8ed1ab_0
Linking pip-23.1.2-pyhd8ed1ab_0
Linking pysocks-1.7.1-pyha2e5f31_6
Linking idna-3.4-pyhd8ed1ab_0
Linking charset-normalizer-3.1.0-pyhd8ed1ab_0
Linking certifi-2023.5.7-pyhd8ed1ab_0
Linking typing_extensions-4.6.3-pyha770c72_0
Linking packaging-23.1-pyhd8ed1ab_0
Linking six-1.16.0-pyh6c4a22f_0
Linking pytz-2023.3-pyhd8ed1ab_0
Linking python-tzdata-2023.3-pyhd8ed1ab_0
Linking threadpoolctl-3.1.0-pyh8a188c0_0
Linking joblib-1.2.0-pyhd8ed1ab_0
Linking urllib3-2.0.2-pyhd8ed1ab_0
Linking typing-extensions-4.6.3-hd8ed1ab_0
Linking python-dateutil-2.8.2-pyhd8ed1ab_0
Linking requests-2.31.0-pyhd8ed1ab_0
Linking platformdirs-3.5.1-pyhd8ed1ab_0
Linking pooch-1.7.0-pyha770c72_3
Linking numpy-1.24.3-py311hb8f3215_0
Linking scipy-1.10.1-py311h93d07a4_3
Linking pandas-2.0.2-py311h9e438b8_0
Linking scikit-learn-1.2.2-py311hf0b18b8_2

Transaction finished

To activate this environment, use:

    micromamba activate /private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_6OwvA5/.CondaPkg/env

Or to execute a single command in this environment, use:

    micromamba run -p /private/var/folders/9p/_7pkfc6j0871mx05hy51v6lh0000gn/T/jl_6OwvA5/.CondaPkg/env mycommand

@ppalmes
Copy link
Author

ppalmes commented Jun 2, 2023 •
edited

it seems that the latest MicroMamba blocks updating to the latest PrecompileTools?

@cjdoris cjdoris mentioned this issue Jun 5, 2023
Merged
@ppalmes ppalmes mentioned this issue Jun 6, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ppalmes @cjdoris