Package evaluation of PyMBAR on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T14:02:31.360 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.53s ################################################################################ # Installation # Installing PyMBAR... Resolving package versions... Installed Conda ── v1.10.2 Installed PyCall ─ v1.96.4 Updating `~/.julia/environments/v1.11/Project.toml` [ea233917] + PyMBAR v0.1.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.16.0 [8f4d0f93] + Conda v1.10.2 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [438e738f] + PyCall v1.96.4 [ea233917] + PyMBAR v0.1.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.4.0 [81def892] + VersionParsing v1.3.0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log` Installation completed after 70.55s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 20.82s ################################################################################ # Testing # Testing PyMBAR Status `/tmp/jl_3zDrbM/Project.toml` [8f4d0f93] Conda v1.10.2 [31c24e10] Distributions v0.25.118 [438e738f] PyCall v1.96.4 [ea233917] PyMBAR v0.1.0 [44cfe95a] Pkg v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_3zDrbM/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.16.0 [8f4d0f93] Conda v1.10.2 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [92d709cd] IrrationalConstants v0.2.4 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.3.0 [438e738f] PyCall v1.96.4 [ea233917] PyMBAR v0.1.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.4.0 [81def892] VersionParsing v1.3.0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log` [ Info: Running `conda install -q -y statsmodels` in root environment Channels: - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64 added / updated specs: - statsmodels The following packages will be downloaded: package | build ---------------------------|----------------- pandas-2.2.3 | py312hf9745cd_1 14.7 MB conda-forge patsy-1.0.1 | pyhd8ed1ab_1 182 KB conda-forge python-dateutil-2.9.0.post0| pyhff2d567_1 217 KB conda-forge python-tzdata-2025.2 | pyhd8ed1ab_0 141 KB conda-forge pytz-2024.1 | pyhd8ed1ab_0 184 KB conda-forge scipy-1.15.2 | py312ha707e6e_0 16.3 MB conda-forge six-1.17.0 | pyhd8ed1ab_0 16 KB conda-forge statsmodels-0.14.4 | py312hc0a28a1_0 11.5 MB conda-forge ------------------------------------------------------------ Total: 43.3 MB The following NEW packages will be INSTALLED: pandas conda-forge/linux-64::pandas-2.2.3-py312hf9745cd_1 patsy conda-forge/noarch::patsy-1.0.1-pyhd8ed1ab_1 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 python-tzdata conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 scipy conda-forge/linux-64::scipy-1.15.2-py312ha707e6e_0 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 statsmodels conda-forge/linux-64::statsmodels-0.14.4-py312hc0a28a1_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Precompiling PyMBAR... 6195.6 ms ✓ PyMBAR 1 dependency successfully precompiled in 9 seconds. 70 already precompiled. [ Info: Installing pymbar via the Conda pymbar package... [ Info: Running `conda config --add channels conda-forge --file /home/pkgeval/.julia/conda/3/x86_64/condarc-julia.yml --force` in root environment /home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic( [ Info: Running `conda install -q -y pymbar` in root environment Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64 added / updated specs: - pymbar The following packages will be downloaded: package | build ---------------------------|----------------- importlib-metadata-8.6.1 | pyha770c72_0 28 KB conda-forge jax-0.5.2 | pyhd8ed1ab_0 1.5 MB conda-forge jaxlib-0.5.2 |cpu_py312h860c521_1 66.1 MB conda-forge libabseil-20250127.1 | cxx17_hbbce691_0 1.3 MB conda-forge libgrpc-1.71.0 | he753a82_0 7.8 MB conda-forge libprotobuf-5.29.3 | h501fc15_0 3.2 MB conda-forge libre2-11-2024.07.02 | hba17884_3 205 KB conda-forge ml_dtypes-0.5.1 | py312hf9745cd_0 284 KB conda-forge nomkl-1.0 | h5ca1d4c_0 4 KB conda-forge numexpr-2.10.2 |py312h6a710ac_100 191 KB conda-forge opt_einsum-3.4.0 | pyhd8ed1ab_1 61 KB conda-forge pymbar-4.0.3 | h7900ff3_3 7 KB conda-forge pymbar-core-4.0.3 | py312hc0a28a1_3 184 KB conda-forge re2-2024.07.02 | h9925aae_3 26 KB conda-forge zipp-3.21.0 | pyhd8ed1ab_1 21 KB conda-forge ------------------------------------------------------------ Total: 80.9 MB The following NEW packages will be INSTALLED: importlib-metadata conda-forge/noarch::importlib-metadata-8.6.1-pyha770c72_0 jax conda-forge/noarch::jax-0.5.2-pyhd8ed1ab_0 jaxlib conda-forge/linux-64::jaxlib-0.5.2-cpu_py312h860c521_1 libabseil conda-forge/linux-64::libabseil-20250127.1-cxx17_hbbce691_0 libgrpc conda-forge/linux-64::libgrpc-1.71.0-he753a82_0 libprotobuf conda-forge/linux-64::libprotobuf-5.29.3-h501fc15_0 libre2-11 conda-forge/linux-64::libre2-11-2024.07.02-hba17884_3 ml_dtypes conda-forge/linux-64::ml_dtypes-0.5.1-py312hf9745cd_0 nomkl conda-forge/noarch::nomkl-1.0-h5ca1d4c_0 numexpr conda-forge/linux-64::numexpr-2.10.2-py312h6a710ac_100 opt_einsum conda-forge/noarch::opt_einsum-3.4.0-pyhd8ed1ab_1 pymbar conda-forge/linux-64::pymbar-4.0.3-h7900ff3_3 pymbar-core conda-forge/linux-64::pymbar-core-4.0.3-py312hc0a28a1_3 re2 conda-forge/linux-64::re2-2024.07.02-h9925aae_3 zipp conda-forge/noarch::zipp-3.21.0-pyhd8ed1ab_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data. ****** PyMBAR will use 64-bit JAX! ******* * JAX is currently set to 32-bit bitsize * * which is its default. * * * * PyMBAR requires 64-bit mode and WILL * * enable JAX's 64-bit mode when called. * * * * This MAY cause problems with other * * Uses of JAX in the same code. * ****************************************** Test Summary: | Pass Total Time initialize PyMBAR.jl | 1 1 0.3s Test Summary: | Pass Total Time test statistical inefficiency | 3 3 9.2s Testing PyMBAR tests passed Testing completed after 103.05s PkgEval succeeded after 223.1s