Package evaluation to test AllenSDK on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T14:49:13.146 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 6.68s ################################################################################ # Installation # Installing AllenSDK... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [9d22b198] + AllenSDK v0.4.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [9d22b198] + AllenSDK v0.4.0 [992eb4ea] + CondaPkg v0.2.36 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.6.1 [1914dd2f] + MacroTools v0.5.16 [0b3b1443] + MicroMamba v0.1.15 ⌅ [bac558e1] + OrderedCollections v1.8.2 [69de0a69] + Parsers v2.8.6 [fa939f87] + Pidfile v1.3.0 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [6099a3de] + PythonCall v0.9.35 [6c6a2e73] + Scratch v1.3.0 [ec057cc2] + StructUtils v2.8.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [e17b2a0c] + UnsafePointers v1.0.0 [f8abcde7] + micromamba_jll v2.3.1+0 [4d7b5844] + pixi_jll v0.63.2+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [f489334b] + StyledStrings v1.11.0 [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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [458c3c95] + OpenSSL_jll v3.5.6+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.11s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 116039.9 ms ✓ AllenSDK 1 dependency successfully precompiled in 116 seconds. 52 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 18 dependents of these packages may trigger further precompilation to work with the unexpected versions. 1 dependency had output during precompilation: ┌ AllenSDK │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/5WGSP/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/lKlVY/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/AllenSDK/mNsl5/CondaPkg.toml │ CondaPkg Resolving changes │ + allensdk (pip) │ + argschema (pip) │ + h5py (pip) │ + hdf5 │ + hdmf (pip) │ + libstdcxx │ + libstdcxx-ng │ + numpy │ + openssl │ + pandas │ + pynwb (pip) │ + python │ + scipy │ + setuptools │ + urllib3 │ + uv │ + xarray │ CondaPkg Initialising pixi │ │ /home/pkgeval/.julia/artifacts/4ae17cee0bd922f66b2c72bf2f01c22481a5ec19/bin/pixi │ │ init │ │ --format pixi │ └ /tmp/jl_C79FCv/.CondaPkg │ ✔ Created /tmp/jl_C79FCv/.CondaPkg/pixi.toml │ CondaPkg Wrote /tmp/jl_C79FCv/.CondaPkg/pixi.toml │ │ [dependencies] │ │ openssl = ">=3, <3.6" │ │ urllib3 = "<2" │ │ libstdcxx-ng = ">=3.4,<15.0" │ │ pandas = "==1.5.3" │ │ xarray = "<2023.2.0" │ │ setuptools = "<81" │ │ libstdcxx = ">=3.4,<15.0" │ │ uv = ">=0.4" │ │ hdf5 = "=1.14.6" │ │ numpy = "<1.24" │ │ scipy = "<1.11" │ │ │ │ [dependencies.python] │ │ channel = "conda-forge" │ │ build = "*cp*" │ │ version = ">=3.10,!=3.14.0,!=3.14.1,<4, >=3.9,<3.13" │ │ │ │ [workspace] │ │ name = ".CondaPkg" │ │ platforms = ["linux-64"] │ │ channels = ["conda-forge"] │ │ channel-priority = "strict" │ │ description = "automatically generated by CondaPkg.jl" │ │ │ │ [pypi-dependencies] │ │ h5py = "!=3.12.0" │ │ pynwb = "<3" │ │ allensdk = "==2.16.2" │ │ hdmf = ">3.8,<4" │ └ argschema = ">=3.0.1" │ CondaPkg Installing packages │ │ /home/pkgeval/.julia/artifacts/4ae17cee0bd922f66b2c72bf2f01c22481a5ec19/bin/pixi │ │ install │ └ --manifest-path /tmp/jl_C79FCv/.CondaPkg/pixi.toml │ ✔ The default environment has been installed. └ Precompilation completed after 95.21s ################################################################################ # Testing # Testing AllenSDK Status `/tmp/jl_UPn9g8/Project.toml` [9d22b198] AllenSDK v0.4.0 [6099a3de] PythonCall v0.9.35 [6c6a2e73] Scratch v1.3.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_UPn9g8/Manifest.toml` [9d22b198] AllenSDK v0.4.0 [992eb4ea] CondaPkg v0.2.36 [9a962f9c] DataAPI v1.16.0 [e2d170a0] DataValueInterfaces v1.0.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [1914dd2f] MacroTools v0.5.16 [0b3b1443] MicroMamba v0.1.15 ⌅ [bac558e1] OrderedCollections v1.8.2 [69de0a69] Parsers v2.8.6 [fa939f87] Pidfile v1.3.0 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [6099a3de] PythonCall v0.9.35 [6c6a2e73] Scratch v1.3.0 [ec057cc2] StructUtils v2.8.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [e17b2a0c] UnsafePointers v1.0.0 [f8abcde7] micromamba_jll v2.3.1+0 [4d7b5844] pixi_jll v0.63.2+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings v1.11.0 [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 v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [458c3c95] OpenSSL_jll v3.5.6+0 [83775a58] Zlib_jll v1.3.1+2 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/5WGSP/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/lKlVY/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/AllenSDK/mNsl5/CondaPkg.toml CondaPkg Resolving changes + allensdk (pip) + argschema (pip) + h5py (pip) + hdf5 + hdmf (pip) + libstdcxx + libstdcxx-ng + numpy + openssl + pandas + pynwb (pip) + python + scipy + setuptools + urllib3 + uv + xarray CondaPkg Initialising pixi │ /home/pkgeval/.julia/artifacts/4ae17cee0bd922f66b2c72bf2f01c22481a5ec19/bin/pixi │ init │ --format pixi └ /tmp/jl_UPn9g8/.CondaPkg ✔ Created /tmp/jl_UPn9g8/.CondaPkg/pixi.toml CondaPkg Wrote /tmp/jl_UPn9g8/.CondaPkg/pixi.toml │ [dependencies] │ openssl = ">=3, <3.6" │ urllib3 = "<2" │ libstdcxx-ng = ">=3.4,<15.0" │ pandas = "==1.5.3" │ xarray = "<2023.2.0" │ setuptools = "<81" │ libstdcxx = ">=3.4,<15.0" │ uv = ">=0.4" │ hdf5 = "=1.14.6" │ numpy = "<1.24" │ scipy = "<1.11" │ │ [dependencies.python] │ channel = "conda-forge" │ build = "*cp*" │ version = ">=3.10,!=3.14.0,!=3.14.1,<4, >=3.9,<3.13" │ │ [workspace] │ name = ".CondaPkg" │ platforms = ["linux-64"] │ channels = ["conda-forge"] │ channel-priority = "strict" │ description = "automatically generated by CondaPkg.jl" │ │ [pypi-dependencies] │ h5py = "!=3.12.0" │ pynwb = "<3" │ allensdk = "==2.16.2" │ hdmf = ">3.8,<4" └ argschema = ">=3.0.1" CondaPkg Installing packages │ /home/pkgeval/.julia/artifacts/4ae17cee0bd922f66b2c72bf2f01c22481a5ec19/bin/pixi │ install └ --manifest-path /tmp/jl_UPn9g8/.CondaPkg/pixi.toml ✔ The default environment has been installed. HDF5 version: Test Failed at /home/pkgeval/.julia/packages/AllenSDK/mNsl5/test/runtests.jl:7 Expression: string(AllenSDK.h5py.h5.get_libversion()) == "(1, 14, 6)" Evaluated: "(2, 0, 0)" == "(1, 14, 6)" Stacktrace: [1] top-level scope @ ~/.julia/packages/AllenSDK/mNsl5/test/runtests.jl:7 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1777 [inlined] [3] macro expansion @ ~/.julia/packages/AllenSDK/mNsl5/test/runtests.jl:7 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:680 [inlined] Test Summary: | Fail Total Time HDF5 version | 1 1 7.4s RNG of the outermost testset: Random.Xoshiro(0x1f92b7bf7d434274, 0xb4927d180b083384, 0x958af7fadefa435c, 0xf203ae52a7fe17f2, 0xc71acb309131d56a) ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/AllenSDK/mNsl5/test/runtests.jl:6 Testing failed after 143.76s ERROR: LoadError: Package AllenSDK errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:552 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 435.63s: package has test failures