Precompile error of SymbolicRegression

[krosenfeld-IDM]

I ran into some strange errors during the docker build stage of the benchmark/official_competitors/pysr/Dockerfile after building the srbench-core benchmark/official_competitors/Dockerfile. The error (copied below) was reproduced in mamba environments on multiple machines when installing pysr v0.11.0 using the conda-forge channel. In those environments there was no issue in installing SymbolicRegression wthin julia (e.g., julia -e 'using Pkg; pkg"activate --temp"; pkg"add SymbolicRegression PyCall"; pkg"build PyCall"; pkg"precompile"')

I was ultimately able to run pysr.install() in my mamba environments as well as build the Dockerfile by requiring pysr==0.14.3 (and running conda clean).

I saw that there were some issues with the conda-forge installation (e.g., https://github.com/MilesCranmer/PySR/issues/347). I am not sure that this was related but am documenting for your reference.

#0 building with "default" instance using docker driver

#1 [internal] load .dockerignore
#1 transferring context: 2B done
#1 DONE 0.0s

#2 [internal] load build definition from Dockerfile
#2 transferring dockerfile: 318B done
#2 DONE 0.0s

#3 [internal] load metadata for docker.io/library/srbench-core:latest
#3 DONE 0.0s

#4 [internal] load build context
#4 DONE 0.0s

#5 [stage-0 1/5] FROM docker.io/library/srbench-core:latest
#5 DONE 0.0s

#4 [internal] load build context
#4 transferring context: 718B done
#4 DONE 0.0s

#5 [stage-0 1/5] FROM docker.io/library/srbench-core:latest
#5 CACHED

#6 [stage-0 2/5] COPY . /tmp/pysr
#6 DONE 0.1s

#7 [stage-0 3/5] WORKDIR /tmp/pysr
#7 DONE 0.0s

#8 [stage-0 4/5] RUN --mount=type=cache,target=/opt/conda/pkgs mamba env create -n method -f environment.yml
#8 63.75 
#8 63.75                   __    __    __    __
#8 63.75                  /  \  /  \  /  \  /  \
#8 63.75                 /    \/    \/    \/    \
#8 63.75 ███████████████/  /██/  /██/  /██/  /████████████████████████
#8 63.75               /  / \   / \   / \   / \  \____
#8 63.75              /  /   \_/   \_/   \_/   \    o \__,
#8 63.75             / _/                       \_____/  `
#8 63.75             |/
#8 63.75         ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
#8 63.75         ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
#8 63.75         ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
#8 63.75         ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
#8 63.75         ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
#8 63.75         ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝
#8 63.75 
#8 63.75         mamba (0.21.0) supported by @QuantStack
#8 63.75 
#8 63.75         GitHub:  https://github.com/mamba-org/mamba
#8 63.75         Twitter: https://twitter.com/QuantStack
#8 63.75 
#8 63.75 █████████████████████████████████████████████████████████████
#8 63.75 
#8 63.75 Transaction
#8 63.75 
#8 63.75   Prefix: /opt/conda/envs/method
#8 63.75 
#8 63.75   Updating specs:
#8 63.75 
#8 63.75    - pysr==0.11.0
#8 63.75 
#8 63.75 
#8 63.75   Package                    Version  Build                Channel                   Size
#8 63.75 ───────────────────────────────────────────────────────────────────────────────────────────
#8 63.75   Install:
#8 63.75 ───────────────────────────────────────────────────────────────────────────────────────────
#8 63.75 
#8 63.75   + _libgcc_mutex                0.1  conda_forge          conda-forge/linux-64       3kB
#8 63.75   + _openmp_mutex                4.5  2_gnu                conda-forge/linux-64      24kB
#8 63.75   + arpack                     3.7.0  hdefa2d7_2           conda-forge/linux-64     220kB
#8 63.75   + brotli-python              1.0.9  py310hd8f1fbe_9      conda-forge/linux-64     326kB
#8 63.75   + bzip2                      1.0.8  h7f98852_4           conda-forge/linux-64     496kB
#8 63.75   + c-ares                    1.19.1  hd590300_0           conda-forge/linux-64     113kB
#8 63.75   + ca-certificates        2023.7.22  hbcca054_0           conda-forge/linux-64     150kB
#8 63.75   + certifi                2023.7.22  pyhd8ed1ab_0         conda-forge/noarch       154kB
#8 63.75   + charset-normalizer         3.2.0  pyhd8ed1ab_0         conda-forge/noarch        46kB
#8 63.75   + curl                       8.2.0  hca28451_0           conda-forge/linux-64      91kB
#8 63.75   + gettext                   0.21.1  h27087fc_0           conda-forge/linux-64       4MB
#8 63.75   + git                       2.41.0  pl5321h86e50cf_0     conda-forge/linux-64      10MB
#8 63.75   + gmp                        6.2.1  h58526e2_0           conda-forge/linux-64     826kB
#8 63.75   + gmpy2                      2.1.2  py310h3ec546c_1      conda-forge/linux-64     220kB
#8 63.75   + icu                         72.1  hcb278e6_0           conda-forge/linux-64      12MB
#8 63.75   + idna                         3.4  pyhd8ed1ab_0         conda-forge/noarch        57kB
#8 63.75   + joblib                     1.3.0  pyhd8ed1ab_1         conda-forge/noarch       221kB
#8 63.75   + julia                      1.9.2  hb81c242_0           conda-forge/linux-64      93MB
#8 63.75   + keyutils                   1.6.1  h166bdaf_0           conda-forge/linux-64     118kB
#8 63.75   + krb5                      1.21.1  h659d440_0           conda-forge/linux-64       1MB
#8 63.75   + ld_impl_linux-64            2.40  h41732ed_0           conda-forge/linux-64     705kB
#8 63.75   + libblas                    3.9.0  17_linux64_openblas  conda-forge/linux-64      14kB
#8 63.75   + libcblas                   3.9.0  17_linux64_openblas  conda-forge/linux-64      14kB
#8 63.75   + libcurl                    8.2.0  hca28451_0           conda-forge/linux-64     372kB
#8 63.75   + libedit             3.1.20191231  he28a2e2_2           conda-forge/linux-64     124kB
#8 63.75   + libev                       4.33  h516909a_1           conda-forge/linux-64     106kB
#8 63.75   + libexpat                   2.5.0  hcb278e6_1           conda-forge/linux-64      78kB
#8 63.75   + libffi                     3.4.2  h7f98852_5           conda-forge/linux-64      58kB
#8 63.75   + libgcc-ng                 13.1.0  he5830b7_0           conda-forge/linux-64     776kB
#8 63.75   + libgfortran-ng            13.1.0  h69a702a_0           conda-forge/linux-64      23kB
#8 63.75   + libgfortran5              13.1.0  h15d22d2_0           conda-forge/linux-64       1MB
#8 63.75   + libgit2                    1.6.4  h747ad27_0           conda-forge/linux-64     845kB
#8 63.75   + libgomp                   13.1.0  he5830b7_0           conda-forge/linux-64     419kB
#8 63.75   + libhwloc                   2.9.1  nocuda_h7313eea_6    conda-forge/linux-64       3MB
#8 63.75   + libiconv                    1.17  h166bdaf_0           conda-forge/linux-64       1MB
#8 63.75   + liblapack                  3.9.0  17_linux64_openblas  conda-forge/linux-64      14kB
#8 63.75   + libnghttp2                1.52.0  h61bc06f_0           conda-forge/linux-64     622kB
#8 63.75   + libnsl                     2.0.0  h7f98852_0           conda-forge/linux-64      31kB
#8 63.75   + libopenblas               0.3.23  pthreads_h80387f5_0  conda-forge/linux-64       5MB
#8 63.75   + libopenblas-ilp64         0.3.23  pthreads_h5c82d6a_0  conda-forge/linux-64       5MB
#8 63.75   + libsqlite                 3.42.0  h2797004_0           conda-forge/linux-64     829kB
#8 63.75   + libssh2                   1.11.0  h0841786_0           conda-forge/linux-64     271kB
#8 63.75   + libstdcxx-ng              13.1.0  hfd8a6a1_0           conda-forge/linux-64       4MB
#8 63.75   + libunwind                  1.6.2  h9c3ff4c_0           conda-forge/linux-64      75kB
#8 63.75   + libutf8proc                2.8.0  h166bdaf_0           conda-forge/linux-64     101kB
#8 63.75   + libuuid                   2.38.1  h0b41bf4_0           conda-forge/linux-64      34kB
#8 63.75   + libxml2                   2.11.4  h0d562d8_0           conda-forge/linux-64     704kB
#8 63.75   + libzlib                   1.2.13  hd590300_5           conda-forge/linux-64      62kB
#8 63.75   + mbedtls                    3.3.0  hcb278e6_0           conda-forge/linux-64     996kB
#8 63.75   + metis                      5.1.1  h59595ed_0           conda-forge/linux-64       4MB
#8 63.75   + mpc                        1.3.1  hfe3b2da_0           conda-forge/linux-64     116kB
#8 63.75   + mpfr                       4.2.0  hb012696_0           conda-forge/linux-64     631kB
#8 63.75   + mpmath                     1.3.0  pyhd8ed1ab_0         conda-forge/noarch       438kB
#8 63.75   + ncurses                      6.4  hcb278e6_0           conda-forge/linux-64     881kB
#8 63.75   + numpy                     1.25.1  py310ha4c1d20_0      conda-forge/linux-64       7MB
#8 63.75   + openblas-ilp64            0.3.23  pthreads_h3d04fff_0  conda-forge/linux-64       5MB
#8 63.75   + openlibm                   0.8.1  h7f98852_0           conda-forge/linux-64     212kB
#8 63.75   + openspecfun                0.5.5  hb600da9_1           conda-forge/linux-64     156kB
#8 63.75   + openssl                    3.1.1  hd590300_1           conda-forge/linux-64       3MB
#8 63.75   + p7zip                      16.02  h9c3ff4c_1001        conda-forge/linux-64       2MB
#8 63.75   + packaging                   23.1  pyhd8ed1ab_0         conda-forge/noarch        46kB
#8 63.75   + pandas                     2.0.3  py310h7cbd5c2_1      conda-forge/linux-64      12MB
#8 63.75   + pcre2                      10.40  hc3806b6_0           conda-forge/linux-64       2MB
#8 63.75   + perl                      5.32.1  4_hd590300_perl5     conda-forge/linux-64      13MB
#8 63.75   + pip                       23.2.1  pyhd8ed1ab_0         conda-forge/noarch         1MB
#8 63.75   + platformdirs               3.9.1  pyhd8ed1ab_0         conda-forge/noarch        20kB
#8 63.75   + pooch                      1.7.0  pyha770c72_3         conda-forge/noarch        51kB
#8 63.75   + pyjulia                    0.6.1  pyhd8ed1ab_0         conda-forge/noarch        56kB
#8 63.75   + pysocks                    1.7.1  pyha2e5f31_6         conda-forge/noarch        19kB
#8 63.75   + pysr                      0.11.0  py310hff52083_2      conda-forge/linux-64       6MB
#8 63.75   + python                   3.10.12  hd12c33a_0_cpython   conda-forge/linux-64      26MB
#8 63.75   + python-dateutil            2.8.2  pyhd8ed1ab_0         conda-forge/noarch       246kB
#8 63.75   + python-tzdata             2023.3  pyhd8ed1ab_0         conda-forge/noarch       143kB
#8 63.75   + python_abi                  3.10  3_cp310              conda-forge/linux-64       6kB
#8 63.75   + pytz                      2023.3  pyhd8ed1ab_0         conda-forge/noarch       187kB
#8 63.75   + readline                     8.2  h8228510_1           conda-forge/linux-64     281kB
#8 63.75   + requests                  2.31.0  pyhd8ed1ab_0         conda-forge/noarch        57kB
#8 63.75   + scikit-learn               1.3.0  py310hf7d194e_0      conda-forge/linux-64       8MB
#8 63.75   + scipy                     1.11.1  py310ha4c1d20_0      conda-forge/linux-64      15MB
#8 63.75   + setuptools                68.0.0  pyhd8ed1ab_0         conda-forge/noarch       464kB
#8 63.75   + six                       1.16.0  pyh6c4a22f_0         conda-forge/noarch        14kB
#8 63.75   + suitesparse               5.10.1  h9e50725_1           conda-forge/linux-64       3MB
#8 63.75   + sympy                       1.12  pypyh9d50eac_103     conda-forge/noarch         4MB
#8 63.75   + tbb                     2021.9.0  hf52228f_0           conda-forge/linux-64       2MB
#8 63.75   + threadpoolctl              3.2.0  pyha21a80b_0         conda-forge/noarch        21kB
#8 63.75   + tk                        8.6.12  h27826a3_0           conda-forge/linux-64       3MB
#8 63.75   + typing-extensions          4.7.1  hd8ed1ab_0           conda-forge/noarch        10kB
#8 63.75   + typing_extensions          4.7.1  pyha770c72_0         conda-forge/noarch        36kB
#8 63.75   + tzdata                     2023c  h71feb2d_0           conda-forge/noarch       118kB
#8 63.75   + urllib3                    2.0.4  pyhd8ed1ab_0         conda-forge/noarch        98kB
#8 63.75   + wheel                     0.41.0  pyhd8ed1ab_0         conda-forge/noarch        57kB
#8 63.75   + xz                         5.2.6  h166bdaf_0           conda-forge/linux-64     418kB
#8 63.75   + zlib                      1.2.13  hd590300_5           conda-forge/linux-64      93kB
#8 63.75   + zstd                       1.5.2  hfc55251_7           conda-forge/linux-64     431kB
#8 63.75 
#8 63.75   Summary:
#8 63.75 
#8 63.75   Install: 94 packages
#8 63.75 
#8 63.75   Total download: 273MB
#8 63.75 
#8 63.75 ───────────────────────────────────────────────────────────────────────────────────────────
#8 63.75 
#8 63.75 
#8 63.75 
#8 63.75 Looking for: ['pysr==0.11.0']
#8 63.75 
#8 63.75 
#8 63.75 Preparing transaction: ...working... done
#8 63.75 Verifying transaction: ...working... done
#8 63.75 Executing transaction: ...working... done
#8 63.75 #
#8 63.75 # To activate this environment, use
#8 63.75 #
#8 63.75 #     $ conda activate method
#8 63.75 #
#8 63.75 # To deactivate an active environment, use
#8 63.75 #
#8 63.75 #     $ conda deactivate
#8 63.75 
#8 63.76 
#8 DONE 64.6s

#9 [stage-0 5/5] RUN mamba run -n method /bin/bash install.sh
#9 285.4 ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['/bin/bash', '-c', 'mamba run -n method /bin/bash install.sh']' command failed.  (See above for error)
#9 285.4 ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['/bin/bash', 'install.sh']' command failed.  (See above for error)
#9 285.4 [ Info: Julia version info
#9 285.4 [ Info: Julia executable: /opt/conda/envs/method/bin/julia
#9 285.4 [ Info: Trying to import PyCall...
#9 285.4 WARNING: method definition for dpeekbyte at /opt/conda/envs/method/share/pysr/depot/packages/Parsers/34hDN/src/utils.jl:199 declares type variable T but does not use it.
#9 285.4 ┌ Info: PyCall is already installed and compatible with Python executable.
#9 285.4 │ 
#9 285.4 │ PyCall:
#9 285.4 │     python: /opt/conda/envs/method/bin/python
#9 285.4 │     libpython: /opt/conda/envs/method/lib/libpython3.10.so.1.0
#9 285.4 │ Python:
#9 285.4 │     python: /opt/conda/envs/method/bin/python
#9 285.4 └     libpython: 
#9 285.4 WARNING: method definition for dpeekbyte at /opt/conda/envs/method/share/pysr/depot/packages/Parsers/34hDN/src/utils.jl:199 declares type variable T but does not use it.
#9 285.4   Activating project at `/opt/conda/envs/method/share/pysr/depot/environments/pysr-0.11.0`
#9 285.4   Installing known registries into `/opt/conda/envs/method/share/julia`
#9 285.4      Cloning git-repo `https://github.com/MilesCranmer/SymbolicRegression.jl`
#9 285.4      Cloning git-repo `https://github.com/JuliaParallel/ClusterManagers.jl`
#9 285.4     Updating registry at `/opt/conda/envs/method/share/julia/registries/General.toml`
#9 285.4    Resolving package versions...
#9 285.4   No Changes to `/opt/conda/envs/method/share/pysr/depot/environments/pysr-0.11.0/Project.toml`
#9 285.4     Updating `/opt/conda/envs/method/share/pysr/depot/environments/pysr-0.11.0/Manifest.toml`
#9 285.4   [44cfe95a] ↑ Pkg v1.8.0 ⇒ v1.9.2
#9 285.4   [10745b16] ~ Statistics ⇒ v1.9.0
#9 285.4   [fa267f1f] ↑ TOML v1.0.0 ⇒ v1.0.3
#9 285.4   [e66e0078] ↑ CompilerSupportLibraries_jll v0.5.2+0 ⇒ v1.0.5+0
#9 285.4   [c8ffd9c3] ↑ MbedTLS_jll v2.28.0+0 ⇒ v2.28.2+0
#9 285.4   [14a3606d] ↑ MozillaCACerts_jll v2022.2.1 ⇒ v2022.10.11
#9 285.4   [4536629a] ↑ OpenBLAS_jll v0.3.20+0 ⇒ v0.3.21+4
#9 285.4   [bea87d4a] + SuiteSparse_jll v5.10.1+6
#9 285.4   [83775a58] ↑ Zlib_jll v1.2.12+3 ⇒ v1.2.13+0
#9 285.4   [8e850b90] ↑ libblastrampoline_jll v5.1.1+0 ⇒ v5.8.0+0
#9 285.4 Precompiling project...
#9 285.4 �[32m  ✓ �[39m�[90mDefineSingletons�[39m
#9 285.4 �[32m  ✓ �[39m�[90mCompat�[39m
#9 285.4 �[32m  ✓ �[39m�[90mCombinatorics�[39m
#9 285.4 �[32m  ✓ �[39m�[90mAutoHashEquals�[39m
#9 285.4 �[32m  ✓ �[39m�[90mOrderedCollections�[39m
#9 285.4 �[32m  ✓ �[39m�[90mRequires�[39m
#9 285.4 �[32m  ✓ �[39mClusterManagers
#9 285.4 �[32m  ✓ �[39m�[90mUnPack�[39m
#9 285.4 �[32m  ✓ �[39m�[90mStructTypes�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDataValueInterfaces�[39m
#9 285.4 �[32m  ✓ �[39m�[90mRealDot�[39m
#9 285.4 �[32m  ✓ �[39m�[90mPositiveFactorizations�[39m
#9 285.4 �[32m  ✓ �[39m�[90mReexport�[39m
#9 285.4 �[32m  ✓ �[39m�[90mInverseFunctions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mExprTools�[39m
#9 285.4 �[32m  ✓ �[39m�[90mAbstractTrees�[39m
#9 285.4 �[32m  ✓ �[39m�[90mIfElse�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDocStringExtensions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mConstructionBase�[39m
#9 285.4 �[32m  ✓ �[39m�[90mRecipesBase�[39m
#9 285.4 �[32m  ✓ �[39m�[90mAdapt�[39m
#9 285.4 �[32m  ✓ �[39m�[90mIrrationalConstants�[39m
#9 285.4 �[32m  ✓ �[39m�[90mIteratorInterfaceExtensions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDataAPI�[39m
#9 285.4 �[32m  ✓ �[39m�[90mStatsAPI�[39m
#9 285.4 �[32m  ✓ �[39m�[90mArgCheck�[39m
#9 285.4 �[32m  ✓ �[39m�[90mCompilerSupportLibraries_jll�[39m
#9 285.4 �[32m  ✓ �[39m�[90mCompositionsBase�[39m
#9 285.4 �[32m  ✓ �[39m�[90mArrayInterfaceCore�[39m
#9 285.4 �[32m  ✓ �[39m�[90mCEnum�[39m
#9 285.4 �[32m  ✓ �[39m�[90mInitialValues�[39m
#9 285.4 �[32m  ✓ �[39m�[90mTermInterface�[39m
#9 285.4 �[32m  ✓ �[39m�[90mStaticArraysCore�[39m
#9 285.4 �[32m  ✓ �[39m�[90mBijections�[39m
#9 285.4 �[32m  ✓ �[39m�[90mPreferences�[39m
#9 285.4 �[32m  ✓ �[39m�[90mBaselet�[39m
#9 285.4 �[32m  ✓ �[39m�[90mNaNMath�[39m
#9 285.4 �[32m  ✓ �[39m�[90mIRTools�[39m
#9 285.4 �[32m  ✓ �[39m�[90mFillArrays�[39m
#9 285.4 �[32m  ✓ �[39m�[90mMutableArithmetics�[39m
#9 285.4 �[32m  ✓ �[39m�[90mZygoteRules�[39m
#9 285.4 �[32m  ✓ �[39m�[90mCommonSubexpressions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mChainRulesCore�[39m
#9 285.4 �[32m  ✓ �[39m�[90mParameters�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDataStructures�[39m
#9 285.4 �[32m  ✓ �[39m�[90mStatic�[39m
#9 285.4 �[32m  ✓ �[39m�[90mTimerOutputs�[39m
#9 285.4 �[32m  ✓ �[39m�[90mJSON3�[39m
#9 285.4 �[32m  ✓ �[39m�[90mLossFunctions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mReferenceables�[39m
#9 285.4 �[32m  ✓ �[39m�[90mGPUArraysCore�[39m
#9 285.4 �[32m  ✓ �[39m�[90mTableTraits�[39m
#9 285.4 �[32m  ✓ �[39m�[90mSetfield�[39m
#9 285.4 �[32m  ✓ �[39m�[90mMissings�[39m
#9 285.4 �[32m  ✓ �[39m�[90mJLLWrappers�[39m
#9 285.4 �[32m  ✓ �[39m�[90mArrayInterfaceStaticArraysCore�[39m
#9 285.4 �[32m  ✓ �[39m�[90mAbstractFFTs�[39m
#9 285.4 �[32m  ✓ �[39m�[90mChangesOfVariables�[39m
#9 285.4 �[91m  ✗ �[39m�[90mSortingAlgorithms�[39m
#9 285.4 �[32m  ✓ �[39m�[90mArrayInterface�[39m
#9 285.4 �[32m  ✓ �[39m�[90mStaticArrays�[39m
#9 285.4 �[32m  ✓ �[39m�[90mTables�[39m
#9 285.4 �[32m  ✓ �[39m�[90mLLVMExtra_jll�[39m
#9 285.4 �[32m  ✓ �[39m�[90mOpenSpecFun_jll�[39m
#9 285.4 �[32m  ✓ �[39m�[90mSplittablesBase�[39m
#9 285.4 �[32m  ✓ �[39m�[90mMultivariatePolynomials�[39m
#9 285.4 �[32m  ✓ �[39m�[90mLogExpFunctions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDiffResults�[39m
#9 285.4 �[32m  ✓ �[39m�[90mArrayInterfaceStaticArrays�[39m
#9 285.4 �[32m  ✓ �[39m�[90mStructArrays�[39m
#9 285.4 �[32m  ✓ �[39m�[90mFiniteDiff�[39m
#9 285.4 �[32m  ✓ �[39m�[90mBangBang�[39m
#9 285.4 �[32m  ✓ �[39m�[90mLLVM�[39m
#9 285.4 �[32m  ✓ �[39m�[90mRecursiveArrayTools�[39m
#9 285.4 �[91m  ✗ �[39m�[90mStatsBase�[39m
#9 285.4 �[32m  ✓ �[39m�[90mSpecialFunctions�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDynamicPolynomials�[39m
#9 285.4 �[32m  ✓ �[39m�[90mChainRules�[39m
#9 285.4 �[32m  ✓ �[39m�[90mDiffRules�[39m
#9 285.4 �[32m  ✓ �[39m�[90mMicroCollections�[39m
#9 285.4 �[32m  ✓ �[39m�[90mGPUArrays�[39m
#9 285.4 �[32m  ✓ �[39m�[90mTransducers�[39m
#9 285.4 �[32m  ✓ �[39m�[90mForwardDiff�[39m
#9 285.4 �[32m  ✓ �[39m�[90mThreadsX�[39m
#9 285.4 �[32m  ✓ �[39m�[90mPreallocationTools�[39m
#9 285.4 �[32m  ✓ �[39m�[90mNLSolversBase�[39m
#9 285.4 �[32m  ✓ �[39m�[90mZygote�[39m
#9 285.4 �[32m  ✓ �[39m�[90mMetatheory�[39m
#9 285.4 �[32m  ✓ �[39m�[90mLabelledArrays�[39m
#9 285.4 �[32m  ✓ �[39m�[90mLineSearches�[39m
#9 285.4 �[91m  ✗ �[39m�[90mOptim�[39m
#9 285.4 �[32m  ✓ �[39m�[90mSymbolicUtils�[39m
#9 285.4 �[91m  ✗ �[39mSymbolicRegression
#9 285.4   89 dependencies successfully precompiled in 229 seconds. 13 already precompiled.
#9 285.4   �[33m9�[39m dependencies had warnings during precompilation:�[33m
#9 285.4 ┌ �[39mSymbolicUtils [d1185830-fcd6-423d-90d6-eec64667417b]�[33m
#9 285.4 │  �[39mWARNING: method definition for OneHotArray at /opt/conda/envs/method/share/pysr/depot/packages/MicroCollections/Qsg6U/src/onehot.jl:79 declares type variable N but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for adapt_structure at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/partitionby.jl:50 declares type variable inbounds but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for _foldl_array at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/processes.jl:222 declares type variable T but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for multiplyexistingvar at /opt/conda/envs/method/share/pysr/depot/packages/DynamicPolynomials/juS7t/src/mult.jl:1 declares type variable C but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for multiplyexistingvar at /opt/conda/envs/method/share/pysr/depot/packages/DynamicPolynomials/juS7t/src/mult.jl:6 declares type variable C but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mDynamicPolynomials [7c1d4256-1411-5781-91ec-d7bc3513ac07]�[33m
#9 285.4 │  �[39mWARNING: method definition for multiplyexistingvar at /opt/conda/envs/method/share/pysr/depot/packages/DynamicPolynomials/juS7t/src/mult.jl:1 declares type variable C but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for multiplyexistingvar at /opt/conda/envs/method/share/pysr/depot/packages/DynamicPolynomials/juS7t/src/mult.jl:6 declares type variable C but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mJSON3 [0f8b85d8-7281-11e9-16c2-39a750bddbf1]�[33m
#9 285.4 │  �[39mWARNING: method definition for dpeekbyte at /opt/conda/envs/method/share/pysr/depot/packages/Parsers/34hDN/src/utils.jl:199 declares type variable T but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mLineSearches [d3d80556-e9d4-5f37-9878-2ab0fcc64255]�[33m
#9 285.4 │  �[39mWARNING: method definition for TwiceDifferentiable at /opt/conda/envs/method/share/pysr/depot/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:96 declares type variable TH but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mThreadsX [ac1d9e8a-700a-412c-b207-f0111f4b6c0d]�[33m
#9 285.4 │  �[39mWARNING: method definition for OneHotArray at /opt/conda/envs/method/share/pysr/depot/packages/MicroCollections/Qsg6U/src/onehot.jl:79 declares type variable N but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for adapt_structure at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/partitionby.jl:50 declares type variable inbounds but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for _foldl_array at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/processes.jl:222 declares type variable T but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mMicroCollections [128add7d-3638-4c79-886c-908ea0c25c34]�[33m
#9 285.4 │  �[39mWARNING: method definition for OneHotArray at /opt/conda/envs/method/share/pysr/depot/packages/MicroCollections/Qsg6U/src/onehot.jl:79 declares type variable N but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mTransducers [28d57a85-8fef-5791-bfe6-a80928e7c999]�[33m
#9 285.4 │  �[39mWARNING: method definition for OneHotArray at /opt/conda/envs/method/share/pysr/depot/packages/MicroCollections/Qsg6U/src/onehot.jl:79 declares type variable N but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for adapt_structure at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/partitionby.jl:50 declares type variable inbounds but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for _foldl_array at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/processes.jl:222 declares type variable T but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mMetatheory [e9d8d322-4543-424a-9be4-0cc815abe26c]�[33m
#9 285.4 │  �[39mWARNING: method definition for OneHotArray at /opt/conda/envs/method/share/pysr/depot/packages/MicroCollections/Qsg6U/src/onehot.jl:79 declares type variable N but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for adapt_structure at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/partitionby.jl:50 declares type variable inbounds but does not use it.�[33m
#9 285.4 │  �[39mWARNING: method definition for _foldl_array at /opt/conda/envs/method/share/pysr/depot/packages/Transducers/HBMTc/src/processes.jl:222 declares type variable T but does not use it.�[33m
#9 285.4 └  �[39m�[33m
#9 285.4 ┌ �[39mNLSolversBase [d41bc354-129a-5804-8e4c-c37616107c6c]�[33m
#9 285.4 │  �[39mWARNING: method definition for TwiceDifferentiable at /opt/conda/envs/method/share/pysr/depot/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:96 declares type variable TH but does not use it.�[33m
#9 285.4 └  �[39m
#9 285.4 
#9 285.4 Traceback (most recent call last):
#9 285.4   File "<string>", line 1, in <module>
#9 285.4   File "/opt/conda/envs/method/lib/python3.10/site-packages/pysr/julia_helpers.py", line 93, in install
#9 285.4     Main.eval(f"Pkg.precompile({io_arg})")
#9 285.4   File "/opt/conda/envs/method/lib/python3.10/site-packages/julia/core.py", line 627, in eval
#9 285.4     ans = self._call(src)
#9 285.4   File "/opt/conda/envs/method/lib/python3.10/site-packages/julia/core.py", line 555, in _call
#9 285.4     self.check_exception(src)
#9 285.4   File "/opt/conda/envs/method/lib/python3.10/site-packages/julia/core.py", line 609, in check_exception
#9 285.4     raise JuliaError(u'Exception \'{}\' occurred while calling julia code:\n{}'
#9 285.4 julia.core.JuliaError: Exception 'The following 1 direct dependency failed to precompile:
#9 285.4 
#9 285.4 SymbolicRegression [8254be44-1295-4e6a-a16d-46603ac705cb]
#9 285.4 
#9 285.4 Failed to precompile SymbolicRegression [8254be44-1295-4e6a-a16d-46603ac705cb] to "/opt/conda/envs/method/share/julia/compiled/v1.9/SymbolicRegression/jl_pZZdbK".
#9 285.4 WARNING: method definition for dpeekbyte at /opt/conda/envs/method/share/pysr/depot/packages/Parsers/34hDN/src/utils.jl:199 declares type variable T but does not use it.
#9 285.4 WARNING: method definition for TwiceDifferentiable at /opt/conda/envs/method/share/pysr/depot/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:96 declares type variable TH but does not use it.
#9 285.4 ERROR: LoadError: UndefVarError: `Float` not defined
#9 285.4 Stacktrace:
#9 285.4   [1] getproperty(x::Module, f::Symbol)
#9 285.4     @ Base ./Base.jl:31
#9 285.4   [2] top-level scope
#9 285.4     @ /opt/conda/envs/method/share/pysr/depot/packages/SortingAlgorithms/PEcBU/src/SortingAlgorithms.jl:125
#9 285.4   [3] include
#9 285.4     @ ./Base.jl:457 [inlined]
#9 285.4   [4] _require(pkg::Base.PkgId, env::String)
#9 285.4     @ Base ./loading.jl:1840
#9 285.4   [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
#9 285.4     @ Base ./loading.jl:1660
#9 285.4   [6] macro expansion
#9 285.4     @ ./loading.jl:1648 [inlined]
#9 285.4   [7] macro expansion
#9 285.4     @ ./lock.jl:267 [inlined]
#9 285.4   [8] require(into::Module, mod::Symbol)
#9 285.4     @ Base ./loading.jl:1611
#9 285.4   [9] include
#9 285.4     @ ./Base.jl:457 [inlined]
#9 285.4  [10] _require(pkg::Base.PkgId, env::String)
#9 285.4     @ Base ./loading.jl:1840
#9 285.4  [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
#9 285.4     @ Base ./loading.jl:1660
#9 285.4  [12] macro expansion
#9 285.4     @ ./loading.jl:1648 [inlined]
#9 285.4  [13] macro expansion
#9 285.4     @ ./lock.jl:267 [inlined]
#9 285.4  [14] require(into::Module, mod::Symbol)
#9 285.4     @ Base ./loading.jl:1611
#9 285.4  [15] include
#9 285.4     @ ./Base.jl:457 [inlined]
#9 285.4  [16] _require(pkg::Base.PkgId, env::String)
#9 285.4     @ Base ./loading.jl:1840
#9 285.4  [17] _require_prelocked(uuidkey::Base.PkgId, env::String)
#9 285.4     @ Base ./loading.jl:1660
#9 285.4  [18] macro expansion
#9 285.4     @ ./loading.jl:1648 [inlined]
#9 285.4  [19] macro expansion
#9 285.4     @ ./lock.jl:267 [inlined]
#9 285.4  [20] require(into::Module, mod::Symbol)
#9 285.4     @ Base ./loading.jl:1611
#9 285.4  [21] include(mod::Module, _path::String)
#9 285.4     @ Base ./Base.jl:457
#9 285.4  [22] include(x::String)
#9 285.4     @ SymbolicRegression.CoreModule /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/Core.jl:1
#9 285.4  [23] top-level scope
#9 285.4     @ /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/Core.jl:5
#9 285.4  [24] include(mod::Module, _path::String)
#9 285.4     @ Base ./Base.jl:457
#9 285.4  [25] include(x::String)
#9 285.4     @ SymbolicRegression /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/SymbolicRegression.jl:1
#9 285.4  [26] top-level scope
#9 285.4     @ /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/SymbolicRegression.jl:90
#9 285.4  [27] include
#9 285.4     @ ./Base.jl:457 [inlined]
#9 285.4  [28] 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, UInt128}}, source::Nothing)
#9 285.4     @ Base ./loading.jl:2049
#9 285.4  [29] top-level scope
#9 285.4     @ stdin:3
#9 285.4 in expression starting at /opt/conda/envs/method/share/pysr/depot/packages/SortingAlgorithms/PEcBU/src/SortingAlgorithms.jl:3
#9 285.4 in expression starting at /opt/conda/envs/method/share/pysr/depot/packages/StatsBase/XgjIN/src/StatsBase.jl:1
#9 285.4 in expression starting at /opt/conda/envs/method/share/pysr/depot/packages/Optim/Zq1jM/src/Optim.jl:1
#9 285.4 in expression starting at /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/OptionsStruct.jl:1
#9 285.4 in expression starting at /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/Core.jl:1
#9 285.4 in expression starting at /opt/conda/envs/method/share/pysr/depot/packages/SymbolicRegression/zN8di/src/SymbolicRegression.jl:1
#9 285.4 in expression starting at stdin:3' occurred while calling julia code:
#9 285.4 Pkg.precompile(io=stderr)
#9 285.4 
#9 285.4 
#9 285.5 
#9 285.5                   __    __    __    __
#9 285.5                  /  \  /  \  /  \  /  \
#9 285.5                 /    \/    \/    \/    \
#9 285.5 ███████████████/  /██/  /██/  /██/  /████████████████████████
#9 285.5               /  / \   / \   / \   / \  \____
#9 285.5              /  /   \_/   \_/   \_/   \    o \__,
#9 285.5             / _/                       \_____/  `
#9 285.5             |/
#9 285.5         ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
#9 285.5         ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
#9 285.5         ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
#9 285.5         ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
#9 285.5         ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
#9 285.5         ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝
#9 285.5 
#9 285.5         mamba (0.21.0) supported by @QuantStack
#9 285.5 
#9 285.5         GitHub:  https://github.com/mamba-org/mamba
#9 285.5         Twitter: https://twitter.com/QuantStack
#9 285.5 
#9 285.5 █████████████████████████████████████████████████████████████
#9 285.5 
#9 285.5 
#9 285.5                   __    __    __    __
#9 285.5                  /  \  /  \  /  \  /  \
#9 285.5                 /    \/    \/    \/    \
#9 285.5 ███████████████/  /██/  /██/  /██/  /████████████████████████
#9 285.5               /  / \   / \   / \   / \  \____
#9 285.5              /  /   \_/   \_/   \_/   \    o \__,
#9 285.5             / _/                       \_____/  `
#9 285.5             |/
#9 285.5         ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
#9 285.5         ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
#9 285.5         ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
#9 285.5         ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
#9 285.5         ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
#9 285.5         ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝
#9 285.5 
#9 285.5         mamba (0.21.0) supported by @QuantStack
#9 285.5 
#9 285.5         GitHub:  https://github.com/mamba-org/mamba
#9 285.5         Twitter: https://twitter.com/QuantStack
#9 285.5 
#9 285.5 █████████████████████████████████████████████████████████████
#9 285.5 
#9 285.5 Julia Version 1.9.2
#9 285.5 Commit e4ee485e90 (2023-07-05 09:39 UTC)
#9 285.5 Platform Info:
#9 285.5   OS: Linux (x86_64-conda-linux-gnu)
#9 285.5   uname: Linux 5.15.0-78-generic #85-Ubuntu SMP Fri Jul 7 15:25:09 UTC 2023 x86_64 x86_64
#9 285.5   CPU: Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz: 
#9 285.5               speed         user         nice          sys         idle          irq
#9 285.5        #1  2593 MHz       4082 s         16 s        874 s     735124 s          0 s
#9 285.5        #2  2593 MHz       4647 s         22 s        886 s     734766 s          0 s
#9 285.5   Memory: 1.9176979064941406 GB (1140.3671875 MB free)
#9 285.5   Uptime: 74160.19 sec
#9 285.5   Load Avg:  0.87  0.56  0.51
#9 285.5   WORD_SIZE: 64
#9 285.5   LIBM: libopenlibm
#9 285.5   LLVM: libLLVM-14.0.6 (ORCJIT, icelake-server)
#9 285.5   Threads: 1 on 2 virtual cores
#9 285.5 Environment:
#9 285.5   JULIA_CONDAPKG_BACKEND_BACKUP = 
#9 285.5   JULIA_CONDAPKG_BACKEND = System
#9 285.5   JULIA_LOAD_PATH = @:@method:@stdlib
#9 285.5   JULIA_LOAD_PATH_BACKUP = 
#9 285.5   JULIA_DEPOT_PATH_BACKUP = 
#9 285.5   JULIA_DEPOT_PATH_PYSR_BACKUP = /opt/conda/envs/method/share/julia:
#9 285.5   JULIA_PROJECT_BACKUP = 
#9 285.5   JULIA_CONDAPKG_EXE = /opt/conda/bin/conda
#9 285.5   JULIA_SSL_CA_ROOTS_PATH = /opt/conda/envs/method/ssl/cacert.pem
#9 285.5   JULIA_DEPOT_PATH = /opt/conda/envs/method/share/julia:/opt/conda/envs/method/share/pysr/depot:
#9 285.5   LD_LIBRARY_PATH = /usr/local/nvidia/lib:/usr/local/nvidia/lib64:
#9 285.5   JULIA_PROJECT = @pysr-0.11.0
#9 285.5   JULIA_SSL_CA_ROOTS_PATH_BACKUP = 
#9 285.5   JULIA_CONDAPKG_EXE_BACKUP = 
#9 285.5   HOME = /root
#9 285.5   CONDA_JL_HOME = /opt/conda/envs/method
#9 285.5   CONDA_JL_HOME_BACKUP = 
#9 285.5   PATH = /opt/conda/envs/method/bin:/opt/conda/condabin:/usr/local/nvidia/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
#9 285.5 
#9 285.5 
#9 ERROR: process "mamba run -n srcomp /bin/bash -c mamba run -n method /bin/bash install.sh" did not complete successfully: exit code: 1
------
 > [stage-0 5/5] RUN mamba run -n method /bin/bash install.sh:
285.5   LD_LIBRARY_PATH = /usr/local/nvidia/lib:/usr/local/nvidia/lib64:
285.5   JULIA_PROJECT = @pysr-0.11.0
285.5   JULIA_SSL_CA_ROOTS_PATH_BACKUP = 
285.5   JULIA_CONDAPKG_EXE_BACKUP = 
285.5   HOME = /root
285.5   CONDA_JL_HOME = /opt/conda/envs/method
285.5   CONDA_JL_HOME_BACKUP = 
285.5   PATH = /opt/conda/envs/method/bin:/opt/conda/condabin:/usr/local/nvidia/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
285.5 
285.5 
------
Dockerfile:8
--------------------
   6 |     WORKDIR /tmp/pysr
   7 |     RUN --mount=type=cache,target=/opt/conda/pkgs mamba env create -n method -f environment.yml
   8 | >>> RUN mamba run -n method /bin/bash install.sh
   9 |     
  10 |     
--------------------
ERROR: failed to solve: process "mamba run -n srcomp /bin/bash -c mamba run -n method /bin/bash install.sh" did not complete successfully: exit code: 1

[MilesCranmer]

The specific error about Float is super weird. Almost seems like some patch file got applied incorrectly.

I wonder if the issue is because the Julia version was not fixed in the Conda environment… could you try fixing it to 1.8? The loaded one you have is 1.9.2 which was not yet released when the experiments were ran.

In retrospect I should have fixed the entire environment rather than just the dependencies. In the meantime when I get a chance I will try to find the exact conda env.

[krosenfeld-IDM]

Fixing julia to v1.8 with pysr v0.11.0 built just fine both for Docker and my local mamba environment.

[MilesCranmer]

Awesome. Thanks for checking! I'll make a PR that fixes this