Package evaluation to test Cclib on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T16:48:55.077 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.76s ################################################################################ # Installation # Installing Cclib... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [6bf0c929] + Cclib v0.4.0 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [a963bdd2] + AtomsBase v0.3.5 [6bf0c929] + Cclib v0.4.0 [992eb4ea] + CondaPkg v0.2.33 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [0f8b85d8] + JSON3 v1.14.3 [1914dd2f] + MacroTools v0.5.16 [0b3b1443] + MicroMamba v0.1.14 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [7b2266bf] + PeriodicTable v1.2.1 [fa939f87] + Pidfile v1.3.0 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [6099a3de] + PythonCall v0.9.28 [ae029012] + Requires v1.3.1 [6c6a2e73] + Scratch v1.3.0 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [1986cc42] + Unitful v1.25.1 [a7773ee8] + UnitfulAtomic v1.0.0 [e17b2a0c] + UnsafePointers v1.0.0 ⌅ [f8abcde7] + micromamba_jll v1.5.12+0 [4d7b5844] + pixi_jll v0.41.3+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 v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+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 4.36s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4500.3 ms ✓ AtomsBase 4646.5 ms ✓ MicroMamba 7012.2 ms ✓ CondaPkg 25256.2 ms ✓ PythonCall 68370.2 ms ✓ Cclib 5 dependencies successfully precompiled in 110 seconds. 58 already precompiled. 1 dependency had output during precompilation: ┌ Cclib │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/Cclib/k8BWz/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/mkWc2/CondaPkg.toml │ CondaPkg Resolving changes │ + cclib (pip) │ + openssl │ + python │ + uv │ CondaPkg Initialising pixi │ │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ │ init │ │ --format pixi │ └ /home/pkgeval/.julia/environments/v1.14/.CondaPkg │ ✔ Created /home/pkgeval/.julia/environments/v1.14/.CondaPkg/pixi.toml │ CondaPkg Wrote /home/pkgeval/.julia/environments/v1.14/.CondaPkg/pixi.toml │ │ [dependencies] │ │ openssl = ">=3, <3.6" │ │ uv = ">=0.4" │ │ │ │ [dependencies.python] │ │ version = ">=3.9,<4" │ │ build = "*cp*" │ │ channel = "conda-forge" │ │ │ │ [pypi-dependencies] │ │ cclib = "*" │ │ │ │ [project] │ │ name = ".CondaPkg" │ │ description = "automatically generated by CondaPkg.jl" │ │ platforms = ["linux-64"] │ │ channel-priority = "strict" │ └ channels = ["conda-forge"] │ CondaPkg Installing packages │ │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ │ install │ └ --manifest-path /home/pkgeval/.julia/environments/v1.14/.CondaPkg/pixi.toml │ ✔ The default environment has been installed. └ Precompilation completed after 104.29s ################################################################################ # Testing # Testing Cclib Status `/tmp/jl_XY4meN/Project.toml` ⌅ [a963bdd2] AtomsBase v0.3.5 [6bf0c929] Cclib v0.4.0 [992eb4ea] CondaPkg v0.2.33 [8bb1440f] DelimitedFiles v1.9.1 [6099a3de] PythonCall v0.9.28 [1986cc42] Unitful v1.25.1 [a7773ee8] UnitfulAtomic v1.0.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XY4meN/Manifest.toml` ⌅ [a963bdd2] AtomsBase v0.3.5 [6bf0c929] Cclib v0.4.0 [992eb4ea] CondaPkg v0.2.33 [9a962f9c] DataAPI v1.16.0 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [0f8b85d8] JSON3 v1.14.3 [1914dd2f] MacroTools v0.5.16 [0b3b1443] MicroMamba v0.1.14 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [7b2266bf] PeriodicTable v1.2.1 [fa939f87] Pidfile v1.3.0 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [6099a3de] PythonCall v0.9.28 [ae029012] Requires v1.3.1 [6c6a2e73] Scratch v1.3.0 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [1986cc42] Unitful v1.25.1 [a7773ee8] UnitfulAtomic v1.0.0 [e17b2a0c] UnsafePointers v1.0.0 ⌅ [f8abcde7] micromamba_jll v1.5.12+0 [4d7b5844] pixi_jll v0.41.3+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 v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+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/Cclib/k8BWz/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/mkWc2/CondaPkg.toml CondaPkg Resolving changes + cclib (pip) + openssl + python + uv CondaPkg Initialising pixi │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ init │ --format pixi └ /tmp/jl_XY4meN/.CondaPkg ✔ Created /tmp/jl_XY4meN/.CondaPkg/pixi.toml CondaPkg Wrote /tmp/jl_XY4meN/.CondaPkg/pixi.toml │ [dependencies] │ openssl = ">=3, <3.6" │ uv = ">=0.4" │ │ [dependencies.python] │ version = ">=3.9,<4" │ build = "*cp*" │ channel = "conda-forge" │ │ [pypi-dependencies] │ cclib = "*" │ │ [project] │ name = ".CondaPkg" │ description = "automatically generated by CondaPkg.jl" │ platforms = ["linux-64"] │ channel-priority = "strict" └ channels = ["conda-forge"] CondaPkg Installing packages │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ install └ --manifest-path /tmp/jl_XY4meN/.CondaPkg/pixi.toml ✔ The default environment has been installed. /tmp/jl_XY4meN/.CondaPkg/.pixi/envs/default/lib/python3.14/site-packages/cclib/method/volume.py:16: SyntaxWarning: "\p" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\p"? A raw string is also an option. \psi (x, y, z) = x^a * y^b * z^c * exp(-\lambda * r^2) Unable to determine the type of logfile ['./data/uracil_two.xyz'], try the fallback mechanism Could not import `openbabel`, fallback mechanism might not work. Cclib.jl: Error During Test at /home/pkgeval/.julia/packages/Cclib/k8BWz/test/runtests.jl:9 Got exception outside of a @test ArgumentError: Unsupported file format Stacktrace: [1] ccread(file::String) @ Cclib ~/.julia/packages/Cclib/k8BWz/src/functions.jl:109 [2] macro expansion @ ~/.julia/packages/Cclib/k8BWz/test/runtests.jl:11 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [4] top-level scope @ ~/.julia/packages/Cclib/k8BWz/test/runtests.jl:10 [5] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [6] top-level scope @ none:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [9] _start() @ Base ./client.jl:577 caused by: Python: AttributeError: 'NoneType' object has no attribute '__dict__' Python stacktrace: none Stacktrace: [1] pythrow() @ PythonCall.Core ~/.julia/packages/PythonCall/mkWc2/src/Core/err.jl:77 [2] errcheck @ ~/.julia/packages/PythonCall/mkWc2/src/Core/err.jl:10 [inlined] [3] pygetattr(x::Py, k::String) @ PythonCall.Core ~/.julia/packages/PythonCall/mkWc2/src/Core/builtins.jl:58 [4] getproperty @ ~/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:250 [inlined] [5] pyccread(file::String) @ Cclib ~/.julia/packages/Cclib/k8BWz/src/functions.jl:9 [6] get_data(file::String) @ Cclib ~/.julia/packages/Cclib/k8BWz/src/functions.jl:15 [7] ccread(file::String) @ Cclib ~/.julia/packages/Cclib/k8BWz/src/functions.jl:105 [8] macro expansion @ ~/.julia/packages/Cclib/k8BWz/test/runtests.jl:11 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [10] top-level scope @ ~/.julia/packages/Cclib/k8BWz/test/runtests.jl:10 [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [12] top-level scope @ none:6 [13] eval(m::Module, e::Any) @ Core ./boot.jl:489 [14] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [15] _start() @ Base ./client.jl:577 Test Summary: | Error Total Time Cclib.jl | 1 1 15.2s RNG of the outermost testset: Random.Xoshiro(0x278b839788fbdbfc, 0x1cf1ed7fba040f26, 0x11f62509569b97ba, 0xaf7cdf4a196b21c9, 0xa49a204c19ffec8f) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Cclib/k8BWz/test/runtests.jl:9 Testing failed after 88.78s ERROR: LoadError: Package Cclib errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 248.77s: package tests unexpectedly errored